[English] 日本語
Yorodumi
- EMDB-8596: 70S ribosome complex with dnaX mRNA stemloop and E-site tRNA ("in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-8596
Title70S ribosome complex with dnaX mRNA stemloop and E-site tRNA ("in" conformation)
Map data70S ribosome complex with dnaX mRNA stemloop and E-site tRNA ("in" conformation)
Sample
  • Complex: 70S-dnaX complex
    • RNA: x 6 types
    • Protein or peptide: x 50 types
  • Ligand: x 2 types
Keywords70S ribosome / dnaX / stem-loop / structured mRNA / -1 programmed frameshifting / E site / RIBOSOME
Function / homology
Function and homology information


regulation of translation / large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding ...regulation of translation / large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / small ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
30S ribosomal protein Thx / 30S ribosomal protein Thx / Ribosomal protein L1, bacterial-type / 30S ribosomal protein / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal protein S14, type Z ...30S ribosomal protein Thx / 30S ribosomal protein Thx / Ribosomal protein L1, bacterial-type / 30S ribosomal protein / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal protein S14, type Z / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / : / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / : / Ribosomal protein L5, bacterial-type / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein S14/S29 / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein L16 / Ribosomal protein L28/L24 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L30, bacterial-type / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / : / L28p-like / Ribosomal protein S15, bacterial-type
Similarity search - Domain/homology
Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein bL19 ...Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL34 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL29 / 30S ribosomal protein S17 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / 30S ribosomal protein S14 type Z / 30S ribosomal protein S8 / 50S ribosomal protein L6 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL25 / Small ribosomal subunit protein bTHX / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL31 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein uL1 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL17
Similarity search - Component
Biological speciesThermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) / Escherichia coli K-12 (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsZhang Y / Hong S
CitationJournal: Structure / Year: 2018
Title: Alternative Mode of E-Site tRNA Binding in the Presence of a Downstream mRNA Stem Loop at the Entrance Channel.
Authors: Yan Zhang / Samuel Hong / Ajchareeya Ruangprasert / Georgios Skiniotis / Christine M Dunham /
Abstract: Structured mRNAs positioned downstream of the ribosomal decoding center alter gene expression by slowing protein synthesis. Here, we solved the cryo-EM structure of the bacterial ribosome bound to an ...Structured mRNAs positioned downstream of the ribosomal decoding center alter gene expression by slowing protein synthesis. Here, we solved the cryo-EM structure of the bacterial ribosome bound to an mRNA containing a 3' stem loop that regulates translation. Unexpectedly, the E-site tRNA adopts two distinct orientations. In the first structure, normal interactions with the 50S and 30S E site are observed. However, in the second structure, although the E-site tRNA makes normal interactions with the 50S E site, its anticodon stem loop moves ∼54 Å away from the 30S E site to interact with the 30S head domain and 50S uL5. This position of the E-site tRNA causes the uL1 stalk to adopt a more open conformation that likely represents an intermediate state during E-site tRNA dissociation. These results suggest that structured mRNAs at the entrance channel restrict 30S subunit movement required during translation to slow E-site tRNA dissociation.
History
DepositionFeb 7, 2017-
Header (metadata) releaseMar 7, 2018-
Map releaseMar 7, 2018-
UpdateMar 19, 2025-
Current statusMar 19, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5uq7
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8596.png

Downloads & links

-
Map

FileDownload / File: emd_8596.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation70S ribosome complex with dnaX mRNA stemloop and E-site tRNA ("in" conformation)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 384 pix.
= 384. Å		1 Å/pix.
x 384 pix.
= 384. Å		1 Å/pix.
x 384 pix.
= 384. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.02
Minimum - Maximum-0.04318631 - 0.11155656
Average (Standard dev.)-0.000111771544 (±0.005646717)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 384.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z384.000384.000384.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-200-200-200
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0430.112-0.000

-
Supplemental data

-
Sample components

+
Entire : 70S-dnaX complex

EntireName: 70S-dnaX complex
Components
  • Complex: 70S-dnaX complex
    • RNA: 23S rRNA
    • RNA: 5S rRNA
    • Protein or peptide: 50S ribosomal protein L2
    • Protein or peptide: 50S ribosomal protein L3
    • Protein or peptide: 50S ribosomal protein L4
    • Protein or peptide: 50S ribosomal protein L5
    • Protein or peptide: 50S ribosomal protein L6
    • Protein or peptide: 50S ribosomal protein L9
    • Protein or peptide: 50S ribosomal protein L13
    • Protein or peptide: 50S ribosomal protein L14
    • Protein or peptide: 50S ribosomal protein L15
    • Protein or peptide: 50S ribosomal protein L16
    • Protein or peptide: 50S ribosomal protein L17
    • Protein or peptide: 50S ribosomal protein L18
    • Protein or peptide: 50S ribosomal protein L19
    • Protein or peptide: 50S ribosomal protein L20
    • Protein or peptide: 50S ribosomal protein L21
    • Protein or peptide: 50S ribosomal protein L22
    • Protein or peptide: 50S ribosomal protein L23
    • Protein or peptide: 50S ribosomal protein L24
    • Protein or peptide: 50S ribosomal protein L25
    • Protein or peptide: 50S ribosomal protein L27
    • Protein or peptide: 50S ribosomal protein L28
    • Protein or peptide: 50S ribosomal protein L29
    • Protein or peptide: 50S ribosomal protein L30
    • Protein or peptide: 50S ribosomal protein L31
    • Protein or peptide: 50S ribosomal protein L32
    • Protein or peptide: 50S ribosomal protein L33
    • Protein or peptide: 50S ribosomal protein L34
    • Protein or peptide: 50S ribosomal protein L35
    • Protein or peptide: 50S ribosomal protein L36
    • RNA: 16S rRNA
    • Protein or peptide: 30S ribosomal protein S2
    • Protein or peptide: 30S ribosomal protein S3
    • Protein or peptide: 30S ribosomal protein S4
    • Protein or peptide: 30S ribosomal protein S5
    • Protein or peptide: 30S ribosomal protein S6
    • Protein or peptide: 30S ribosomal protein S7
    • Protein or peptide: 30S ribosomal protein S8
    • Protein or peptide: 30S ribosomal protein S9
    • Protein or peptide: 30S ribosomal protein S10
    • Protein or peptide: 30S ribosomal protein S11
    • Protein or peptide: 30S ribosomal protein S12
    • Protein or peptide: 30S ribosomal protein S13
    • Protein or peptide: 30S ribosomal protein S14 type Z
    • Protein or peptide: 30S ribosomal protein S15
    • Protein or peptide: 30S ribosomal protein S16
    • Protein or peptide: 30S ribosomal protein S17
    • Protein or peptide: 30S ribosomal protein S18
    • Protein or peptide: 30S ribosomal protein S19
    • Protein or peptide: 30S ribosomal protein S20
    • Protein or peptide: 30S ribosomal protein Thx
    • RNA: P-site tRNA fMet
    • Protein or peptide: 50S ribosomal protein L1
    • RNA: E-site tRNA Phe
    • RNA: messenger RNA
  • Ligand: ZINC ION
  • Ligand: IRON/SULFUR CLUSTER

+
Supramolecule #1: 70S-dnaX complex

SupramoleculeName: 70S-dnaX complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#56
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

+
Macromolecule #1: 23S rRNA

MacromoleculeName: 23S rRNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 948.035625 KDa
SequenceString: GUCAAGAUGG UAAGGGCCCA CGGUGGAUGC CUCGGCACCC GAGCCGAUGA AGGACGUGGC UACCUGCGAU AAGCCAGGGG GAGCCGGUA GCGGGCGUGG AUCCCUGGAU GUCCGAAUGG GGGAACCCGG CCGGCGGGAA CGCCGGUCAC CGCGCUUUUG C GCGGGGGG ...String:
GUCAAGAUGG UAAGGGCCCA CGGUGGAUGC CUCGGCACCC GAGCCGAUGA AGGACGUGGC UACCUGCGAU AAGCCAGGGG GAGCCGGUA GCGGGCGUGG AUCCCUGGAU GUCCGAAUGG GGGAACCCGG CCGGCGGGAA CGCCGGUCAC CGCGCUUUUG C GCGGGGGG AACCUGGGGA ACUGAAACAU CUCAGUACCC AGAGGAGAGG AAAGAGAAAU CGACUCCCUG AGUAGCGGCG AG CGAAAGG GGACCAGCCU AAACCGUCCG GCUUGUCCGG GCGGGGUCGU GGGGCCCUCG GACACCGAAU CCCCAGCCUA GCC GAAGCU GUUGGGAAGC AGCGCCAGAG AGGGUGAAAG CCCCGUAGGC GAAAGGUGGG GGGAUAGGUG AGGGUACCCG AGUA CCCCG UGGUUCGUGG AGCCAUGGGG GAAUCUGGGC GGACCACCGC CUAAGGCUAA GUACUCCGGG UGACCGAUAG CGCAC CAGU ACCGUGAGGG AAAGGUGAAA AGAACCCCGG GAGGGGAGUG AAAUAGAGCC UGAAACCGUG GGCUUACAAG CAGUCA CGG CCCCGCAAGG GGUUGUGGCG UGCCUAUUGA AGCAUGAGCC GGCGACUCAC GGUCGUGGGC GAGCUUAAGC CGUUGAG GC GGAGGCGUAG GGAAACCGAG UCCGAACAGG GCGCAAGCGG GCCGCACGCG GCCCGCAAAG UCCGCGGCCG UGGACCCG A AACCGGGCGA GCUAGCCCUG GCCAGGGUGA AGCUGGGGUG AGACCCAGUG GAGGCCCGAA CCGGUGGGGG AUGCAAACC CCUCGGAUGA GCUGGGGCUA GGAGUGAAAA GCUAACCGAG CCCGGAGAUA GCUGGUUCUC CCCGAAAUGA CUUUAGGGUC AGCCUCAGG CGCUGACUGG GGCCUGUAGA GCACUGAUAG GGCUAGGGGG CCCACCAGCC UACCAAACCC UGUCAAACUC C GAAGGGUC CCAGGUGGAG CCUGGGAGUG AGGGCGCGAG CGAUAACGUC CGCGUCCGAG CGCGGGAACA ACCGAGACCG CC AGCUAAG GCCCCCAAGU CUGGGCUAAG UGGUAAAGGA UGUGGCGCCG CGAAGACAGC CAGGAGGUUG GCUUAGAAGC AGC CAUCCU UUAAAGAGUG CGUAAUAGCU CACUGGUCGA GUGGCGCCGC GCCGAAAAUG AUCGGGGCUU AAGCCCAGCG CCGA AGCUG CGGGUCUGGG GGAUGACCCC AGGCGGUAGG GGAGCGUUCC CGAUGCCGAU GAAGGCCGAC CCGCGAGGGC GGCUG GAGG UAAGGGAAGU GCGAAUGCCG GCAUGAGUAA CGAUAAAGAG GGUGAGAAUC CCUCUCGCCG UAAGCCCAAG GGUUCC UAC GCAAUGGUCG UCAGCGUAGG GUUAGGCGGG ACCUAAGGUG AAGCCGAAAG GCGUAGCCGA AGGGCAGCCG GUUAAUA UU CCGGCCCUUC CCGCAGGUGC GAUGGGGGGA CGCUCUAGGC UAGGGGGACC GGAGCCAUGG ACGAGCCCGG CCAGAAGC G CAGGGUGGGA GGUAGGCAAA UCCGCCUCCC AACAAGCUCU GCGUGGUGGG GAAGCCCGUA CGGGUGACAA CCCCCCGAA GCCAGGGAGC CAAGAAAAGC CUCUAAGCAC AACCUGCGGG AACCCGUACC GCAAACCGAC ACAGGUGGGC GGGUGCAAGA GCACUCAGG CGCGCGGGAG AACCCUCGCC AAGGAACUCU GCAAGUUGGC CCCGUAACUU CGGGAGAAGG GGUGCUCCCU G GGGUGAUG AGCCCCGGGG AGCCGCAGUG AACAGGCUCU GGCGACUGUU UACCAAAAAC ACAGCUCUCU GCGAACUCGU AA GAGGAGG UAUAGGGAGC GACGCUUGCC CGGUGCCGGA AGGUCAAGGG GAGGGGUGCA AGCCCCGAAC CGAAGCCCCG GUG AACGGC GGCCG(PSU)AAC(5MU) A(PSU)AA(4OC)GGUCC UAAGGUAGCG AAA(5MU)UC(5MC)UUG UCGGGUAAGU UCCGAC(5MC)UG CACGAAAAGC GUAACGACCG GAGCGCUGUC UCGGCGAGGG ACCCGGUGAA AUUGAACUGG CCGUGAA GA UGCGGCCUAC CCGUGGCAGG ACGAAAAGAC CCCGUGGAGC UUUACUGCAG CCUGGUGUUG GCUCUUGGUC GCGCCUGC G UAGGAUAGGU GGGAGCCUGU GAACCCCCGC CUCCGGGUGG GGGGGAGGCG CCGGUGAAAU ACCACCCUGG CGCGGCUGG GGGCCUAACC CUCGGAUGGG GGGACAGCGC UUGGCGGGCA GUUUGACUG(OMG) GGCGGUCGCC UCCUAAAAGG UAACGG AGG CGCCCAAAGG UCCCCUCAGG CGGGACGGAA AUCCGCCGGA GAGCGCAAGG GUAGAAGGGG GCCUGACUGC GAGGCCU GC AAGCCGAGCA GGGGCGAAAG CCGGGCCUAG UGAACCGGUG GUCCCGUGUG GAAGGGCCAU CGAUCAACGG AUAAAAGU U ACCCCGGGGA UAACAGGCUG AUCUCCCCCG AGCGUCCACA GCGGCGGGGA GGUUUGGCAC CUCG(2MA)UGUCG GCUCG UCGC AUCCUGGGGC UGAAGAAGGU CCCAAGGGUU GGGC(2MU)GUUCG CCCAUUAAAG CGGCACGCGA GCUGGGUUCA GA ACGUCGU GAGACAGU(PSU)C GGUCUCUAUC CGCCACGGGC GCAGGAGGCU UGAGGGGGGC UCUUCCUAGU ACGAGAGGA CCGGAAGGGA CGCACCUCUG GUUUCCCAGC UGUCCCUCCA GGGGCAUAAG CUGGGUAGCC AUGUGCGGAA GGGAUAACCG CUGAAAGCA UCUAAGCGGG AAGCCCGCCC CAAGAUGAGG CCUCCCACGG CGUCAAGCCG GUAAGGACCC GGGAAGACCA C CCGGUGGA UGGGCCGGGG GUGUAAGCGC CGCGAGGCGU UGAGCCGACC GGUCCCAAUC GUCCGAGGUC UUGACCCCUC C

GENBANK: GENBANK: AP008226.1

+
Macromolecule #2: 5S rRNA

MacromoleculeName: 5S rRNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 38.882207 KDa
SequenceString:
UCCCCCGUGC CCAUAGCGGC GUGGAACCAC CCGUUCCCAU UCCGAACACG GAAGUGAAAC GCGCCAGCGC CGAUGGUACU GGGCGGGCG ACCGCCUGGG AGAGUAGGUC GGUGCGGGGG A

GENBANK: GENBANK: AP008226.1

+
Macromolecule #32: 16S rRNA

MacromoleculeName: 16S rRNA / type: rna / ID: 32 / Number of copies: 1
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 493.903656 KDa
SequenceString: UUGUUGGAGA GUUUGAUCCU GGCUCAGGGU GAACGCUGGC GGCGUGCCUA AGACAUGCAA GUCGUGCGGG CCGCGGGGUU UUACUCCGU GGUCAGCGGC GGACGGGUGA GUAACGCGUG GGUGACCUAC CCGGAAGAGG GGGACAACCC GGGGAAACUC G GGCUAAUC ...String:
UUGUUGGAGA GUUUGAUCCU GGCUCAGGGU GAACGCUGGC GGCGUGCCUA AGACAUGCAA GUCGUGCGGG CCGCGGGGUU UUACUCCGU GGUCAGCGGC GGACGGGUGA GUAACGCGUG GGUGACCUAC CCGGAAGAGG GGGACAACCC GGGGAAACUC G GGCUAAUC CCCCAUGUGG ACCCGCCCCU UGGGGUGUGU CCAAAGGGCU UUGCCCGCUU CCGGAUGGGC CCGCGUCCCA UC AGCUAGU UGGUGGGGUA AUGGCCCACC AAGGCGACGA CGGGUAGCCG GUCUGAGAGG AUGGCCGGCC ACAGGGGCAC UGA GACACG GGCCCCACUC CUACGGGAGG CAGCAGUUAG GAAUCUUCCG CAAUGGGCGC AAGCCUGACG GAGCGACGCC GCUU GGAGG AAGAAGCCCU UCGGGGUGUA AACUCCUGAA CCCGGGACGA AACCCCCGAC GAGGGGACUG ACGGUACCGG GGUAA UAGC GCCGGCCAAC UCCG(PSU)GCCAG CAGCC(7MG)CGGU AAUACGGAGG GCGCGAGCGU UACCCGGAUU CACUGGGC G UAAAGGGCGU GUAGGCGGCC UGGGGCGUCC CAUGUGAAAG ACCACGGCUC AACCGUGGGG GAGCGUGGGA UACGCUCAG GCUAGACGGU GGGAGAGGGU GGUGGAAUUC CCGGAGUAGC GGUGAAAUGC GCAGAUACCG GGAGGAACGC CGAUGGCGAA GGCAGCCAC CUGGUCCACC CGUGACGCUG AGGCGCGAAA GCGUGGGGAG CAAACCGGAU UAGAUACCCG GGUAGUCCAC G CCCUAAAC GAUGCGCGCU AGGUCUCUGG GUCUCCUGGG GGCCGAAGCU AACGCGUUAA GCGCGCCGCC UGGGGAGUAC GG CCGCAAG GCUGAAACUC AAAGGAAUUG ACGGGGGCCC GCACAAGCGG UGGAGCAUGU GGUUUAAUUC GAA(M2G)(5MC) AACG CGAAGAACCU UACCAGGCCU UGACAUGCUA GGGAACCCGG GUGAAAGCCU GGGGUGCCCC GCGAGGGGAG CCCUAG CAC AGGUGCUGCA UGGCCGUCGU CAGCUCGUGC CGUGAGGUGU UGGGUUAAGU CCCGCAACGA GCGCAACCCC CGCCGUU AG UUGCCAGCGG UUCGGCCGGG CACUCUAACG GGACUGCCCG CGAAAGCGGG AGGAAGGAGG GGACGACGUC UGGUCAGC A UG(2MG)CCCUUAC GGCCUGGGCG ACACACGUGC UACAAUGCCC ACUACAAAGC GAUGCCACCC GGCAACGGGG AGCUA AUCG CAAAAAGGUG GGCCCAGUUC GGAUUGGGGU CUGCAACCCG ACCCCAUGAA GCCGGAAUCG CUAGUAAUCG CGGAUC AGC CAUGCCGCGG UGAAUACGUU CCCGGGCCUU GUACACAC(5MC)G (4OC)C(5MC)GU(5MC)ACGC CAUGGGAGCG G GCUCUACC CGAAGUCGCC GGGAGCCUAC GGGCAGGCGC CGAGGGUAGG GCCCGUGACU GGGGCGAAGU CG(UR3)AACAA G GUAGCUGUAC CGG(MA6)(MA6)GGUGC GGCUGGAUCA CCUCCUUGCU

GENBANK: GENBANK: AP008226.1

+
Macromolecule #53: P-site tRNA fMet

MacromoleculeName: P-site tRNA fMet / type: rna / ID: 53 / Number of copies: 1
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K-12
Molecular weightTheoretical: 24.801801 KDa
SequenceString:
CGCGGGGUGG AGCAGCCCGG UAGCUCGUCG GGCUCAUAAC CCGAAGGUCG UCGGUUCAAA UCCGGCCCCC GCAACCA

GENBANK: GENBANK: LT615371.1

+
Macromolecule #55: E-site tRNA Phe

MacromoleculeName: E-site tRNA Phe / type: rna / ID: 55 / Number of copies: 1
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K-12
Molecular weightTheoretical: 24.485539 KDa
SequenceString:
GCCCGGAUAG CUCAGUCGGU AGAGCAGGGG AUUGAAAAUC CCCGUGUCCU UGGUUCGAUU CCGAGUCCGG GCACCA

GENBANK: GENBANK: LT615371.1

+
Macromolecule #56: messenger RNA

MacromoleculeName: messenger RNA / type: rna / ID: 56 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 17.773668 KDa
SequenceString:
UAAGGAAAUA AAAAUGUUUA GUGAACCGGC AGCCGCUACC CGCGCGCGGC CGGUA

+
Macromolecule #3: 50S ribosomal protein L2

MacromoleculeName: 50S ribosomal protein L2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 30.401355 KDa
SequenceString: AVKKFKPYTP SRRFMTVADF SEITKTEPEK SLVKPLKKTG GRNNQGRITV RFRGGGHKRL YRIIDFKRWD KVGIPAKVAA IEYDPNRSA RIALLHYVDG EKRYIIAPDG LQVGQQVVAG PDAPIQVGNA LPLRFIPVGT VVHAVELEPK KGAKLARAAG T SAQIQGRE ...String:
AVKKFKPYTP SRRFMTVADF SEITKTEPEK SLVKPLKKTG GRNNQGRITV RFRGGGHKRL YRIIDFKRWD KVGIPAKVAA IEYDPNRSA RIALLHYVDG EKRYIIAPDG LQVGQQVVAG PDAPIQVGNA LPLRFIPVGT VVHAVELEPK KGAKLARAAG T SAQIQGRE GDYVILRLPS GELRKVHGEC YATVGAVGNA DHKNIVLGKA GRSRWLGRRP HVRGAAMNPV DHPHGGGEGR AP RGRPPAS PWGWQTKGLK TRKRRKPSSR FIIARRKK

UniProtKB: Large ribosomal subunit protein uL2

+
Macromolecule #4: 50S ribosomal protein L3

MacromoleculeName: 50S ribosomal protein L3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 22.249953 KDa
SequenceString: MKGILGVKVG MTRIFRDDRA VPVTVILAGP CPVVQRRTPE KDGYTAVQLG FLPQNPKRVN RPLKGHFAKA GVEPVRILRE IRDFNPEGD TVTVEIFKPG ERVDVTGTSK GRGFAGVMKR WNFAGGPDSH GAHKIHRHPG SIGNRKTPGR VYKGKKMAGH Y GAERVTVM ...String:
MKGILGVKVG MTRIFRDDRA VPVTVILAGP CPVVQRRTPE KDGYTAVQLG FLPQNPKRVN RPLKGHFAKA GVEPVRILRE IRDFNPEGD TVTVEIFKPG ERVDVTGTSK GRGFAGVMKR WNFAGGPDSH GAHKIHRHPG SIGNRKTPGR VYKGKKMAGH Y GAERVTVM NLEVVDVIPE ENLLLVKGAV PGPNGGLVIV RETKKA

UniProtKB: Large ribosomal subunit protein uL3

+
Macromolecule #5: 50S ribosomal protein L4

MacromoleculeName: 50S ribosomal protein L4 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 22.512023 KDa
SequenceString: VYQIPVLSPS GRRELAADLP AEINPHLLWE VVRWQLAKRR RGTASTKTRG EVAYSGRKIW PQKHTGRARH GDIGAPIFVG GGVVFGPKP RDYSYTLPKK VRKKGLAMAV ADRAREGKLL LVEAFAGVNG KTKEFLAWAK EAGLDGSESV LLVTGNELVR R AARNLPWV ...String:
VYQIPVLSPS GRRELAADLP AEINPHLLWE VVRWQLAKRR RGTASTKTRG EVAYSGRKIW PQKHTGRARH GDIGAPIFVG GGVVFGPKP RDYSYTLPKK VRKKGLAMAV ADRAREGKLL LVEAFAGVNG KTKEFLAWAK EAGLDGSESV LLVTGNELVR R AARNLPWV VTLAPEGLNV YDIVRTERLV MDLDAWEVFQ NRIGG

UniProtKB: Large ribosomal subunit protein uL4

+
Macromolecule #6: 50S ribosomal protein L5

MacromoleculeName: 50S ribosomal protein L5 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 20.9304 KDa
SequenceString:
PLDVALKRKY YEEVRPELIR RFGYQNVWEV PRLEKVVINQ GLGEAKEDAR ILEKAAQELA LITGQKPAVT RAKKSISNFK LRKGMPIGL RVTLRRDRMW IFLEKLLNVA LPRIRDFRGL NPNSFDGRGN YNLGLREQLI FPEITYDMVD ALRGMDIAVV T TAETDEEA RALLELLGFP FRK

UniProtKB: Large ribosomal subunit protein uL5

+
Macromolecule #7: 50S ribosomal protein L6

MacromoleculeName: 50S ribosomal protein L6 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 18.893082 KDa
SequenceString:
RIGRLPIPVP KGVSVEVAPG RVKVKGPKGE LEVPVSPEMR VVVEEGVVRV ERPSDERRHK SLHGLTRTLI ANAVKGVSEG YSKELLIKG IGYRARLVGR ALELTVGFSH PVVVEPPEGI TFEVPEPTRV RVSGIDKQKV GQVAANIRAI RKPSAYHEKG I YYAGEPVR LKPGK

UniProtKB: 50S ribosomal protein L6

+
Macromolecule #8: 50S ribosomal protein L9

MacromoleculeName: 50S ribosomal protein L9 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 16.164937 KDa
SequenceString:
MKVILLEPLE NLGDVGQVVD VKPGYARNYL LPRGLAVLAT ESNLKALEAR IRAQAKRLAE RKAEAERLKE ILENLTLTIP VRAGETKIY GSVTAKDIAE ALSRQHGVTI DPKRLALEKP IKELGEYVLT YKPHPEVPIQ LKVSVVA

UniProtKB: Large ribosomal subunit protein bL9

+
Macromolecule #9: 50S ribosomal protein L13

MacromoleculeName: 50S ribosomal protein L13 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 15.927903 KDa
SequenceString:
MKTYVPKQVE PRWVLIDAEG KTLGRLATKI ATLLRGKHRP DWTPNVAMGD FVVVVNADKI RVTGKKLEQK IYTRYSGYPG GLKKIPLEK MLATHPERVL EHAVKGMLPK GPLGRRLFKR LKVYAGPDHP HQAQRPEKLE V

UniProtKB: Large ribosomal subunit protein uL13

+
Macromolecule #10: 50S ribosomal protein L14

MacromoleculeName: 50S ribosomal protein L14 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 13.323612 KDa
SequenceString:
MIQPQTYLEV ADNTGARKIM CIRVLKGSNA KYATVGDVIV ASVKEAIPRG AVKEGDVVKA VVVRTKKEIK RPDGSAIRFD DNAAVIINN QLEPRGTRVF GPVARELREK GFMKIVSLAP EVL

UniProtKB: Large ribosomal subunit protein uL14

+
Macromolecule #11: 50S ribosomal protein L15

MacromoleculeName: 50S ribosomal protein L15 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 16.248062 KDa
SequenceString:
MKLSDLRPNP GANKRRKRVG RGPGSGHGKT ATRGHKGQKS RSGGLKDPRR FEGGRSTTLM RLPKRGMQGQ VPGEIKRPRY QGVNLKDLA RFEGEVTPEL LVRAGLLKKG YRLKILGEGE AKPLKVVAHA FSKSALEKLK AAGGEPVLLE

UniProtKB: Large ribosomal subunit protein uL15

+
Macromolecule #12: 50S ribosomal protein L16

MacromoleculeName: 50S ribosomal protein L16 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 15.993909 KDa
SequenceString:
MLMPRRMKYR KQQRGRLKGA TKGGDYVAFG DYGLVALEPA WITAQQIEAA RVAMVRHFRR GGKIFIRIFP DKPYTKKPLE VRMGKGKGN VEGYVAVVKP GRVMFEVAGV TEEQAMEALR IAGHKLPIKT KIVRRDAYDE AQ

UniProtKB: Large ribosomal subunit protein uL16

+
Macromolecule #13: 50S ribosomal protein L17

MacromoleculeName: 50S ribosomal protein L17 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 13.750148 KDa
SequenceString:
MRHLKSGRKL NRHSSHRLAL YRNQAKSLLT HGRITTTVPK AKELRGFVDH LIHLAKRGDL HARRLVLRDL QDVKLVRKLF DEIAPRYRD RQGGYTRVLK LAERRRGDGA PLALVELVE

UniProtKB: Large ribosomal subunit protein bL17

+
Macromolecule #14: 50S ribosomal protein L18

MacromoleculeName: 50S ribosomal protein L18 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 12.43757 KDa
SequenceString:
RLTAYERRKF RVRNRIKRTG RLRLSVFRSL KHIYAQIIDD EKGVTLVSAS SLALKLKGNK TEVARQVGRA LAEKALALGI KQVAFDRGP YKYHGRVKAL AEGAREGGLE F

UniProtKB: Large ribosomal subunit protein uL18

+
Macromolecule #15: 50S ribosomal protein L19

MacromoleculeName: 50S ribosomal protein L19 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 15.503017 KDa
SequenceString:
MNRGALIKLV ESRYVRTDLP EFRPGDTVRV SYKVKEGNRT RIQDFEGIVI RIRRNGFNTT FTVRKVSYGV GVERIFPLHS PLIQKIDIV QRGRARRAKL YFIRNLSDRE IRRKLRADRK RIDQDRAAER AA

UniProtKB: Large ribosomal subunit protein bL19

+
Macromolecule #16: 50S ribosomal protein L20

MacromoleculeName: 50S ribosomal protein L20 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 13.591028 KDa
SequenceString:
PRAKTGVVRR RKHKKILKLA KGYWGLRSKS FRKARETLFA AGNYAYAHRK RRKRDFRRLW IVRINAACRQ HGLNYSTFIH GLKKAGIEV DRKNLADLAV REPQVFAELV ERAKAAQ

UniProtKB: Large ribosomal subunit protein bL20

+
Macromolecule #17: 50S ribosomal protein L21

MacromoleculeName: 50S ribosomal protein L21 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 11.069153 KDa
SequenceString:
MFAIVKTGGK QYRVEPGLKL RVEKLDAEPG ATVELPVLLL GGEKTVVGTP VVEGASVVAE VLGHGRGKKI LVSKFKAKVQ YRRKKGHRQ PYTELLIKEI RG

UniProtKB: Large ribosomal subunit protein bL21

+
Macromolecule #18: 50S ribosomal protein L22

MacromoleculeName: 50S ribosomal protein L22 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 12.678874 KDa
SequenceString:
MEAKAIARYV RISPRKVRLV VDLIRGKSLE EARNILRYTN KRGAYFVAKV LESAAANAVN NHDMLEDRLY VKAAYVDEGP ALKRVLPRA RGRADIIKKR TSHITVILGE KHG

UniProtKB: Large ribosomal subunit protein uL22

+
Macromolecule #19: 50S ribosomal protein L23

MacromoleculeName: 50S ribosomal protein L23 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 10.64665 KDa
SequenceString:
MKTAYDVILA PVLSEKAYAG FAEGKYTFWV HPKATKTEIK NAVETAFKVK VVKVNTLHVR GKKKRLGRYL GKRPDRKKAI VQVAPGQKI EALEGL

UniProtKB: Large ribosomal subunit protein uL23

+
Macromolecule #20: 50S ribosomal protein L24

MacromoleculeName: 50S ribosomal protein L24 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 11.72628 KDa
SequenceString:
MRVKMHVKKG DTVLVASGKY KGRVGKVKEV LPKKYAVIVE GVNIVKKAVR VSPKYPQGGF IEKEAPLHAS KVRPICPACG KPTRVRKKF LENGKKIRVC AKCGGALD

UniProtKB: Large ribosomal subunit protein uL24

+
Macromolecule #21: 50S ribosomal protein L25

MacromoleculeName: 50S ribosomal protein L25 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 21.139299 KDa
SequenceString:
MEYRLKAYYR EGEKPSALRR AGKLPGVMYN RHLNRKVYVD LVEFDKVFRQ ASIHHVIVLE LPDGQSLPTL VRQVNLDKRR RRPEHVDFF VLSDEPVEMY VPLRFVGTPA GVRAGGVLQE IHRDILVKVS PRNIPEFIEV DVSGLEIGDS LHASDLKLPP G VELAVSPE ETIAAVVPPE DVEKLAEEA

UniProtKB: Large ribosomal subunit protein bL25

+
Macromolecule #22: 50S ribosomal protein L27

MacromoleculeName: 50S ribosomal protein L27 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 8.689006 KDa
SequenceString:
GSTRNGRDSQ AKRLGVKRYE GQVVRAGNIL VRQRGTRFKP GKNVGMGRDF TLFALVDGVV EFQDRGRLGR YVHVRPL

UniProtKB: Large ribosomal subunit protein bL27

+
Macromolecule #23: 50S ribosomal protein L28

MacromoleculeName: 50S ribosomal protein L28 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 10.872965 KDa
SequenceString:
SKVCEISGKR PIVANSIQRR GKAKREGGVG KKTTGISKRR QYPNLQKVRV RVAGQEITFR VAASHIPKVY ELVERAKGLK LEGLSPKEI KKELLKLL

UniProtKB: Large ribosomal subunit protein bL28

+
Macromolecule #24: 50S ribosomal protein L29

MacromoleculeName: 50S ribosomal protein L29 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 8.485077 KDa
SequenceString:
MKLSEVRKQL EEARKLSPVE LEKLVREKKR ELMELRFQAS IGQLSQNHKI RDLKRQIARL LTVLNEKRRQ

UniProtKB: Large ribosomal subunit protein uL29

+
Macromolecule #25: 50S ribosomal protein L30

MacromoleculeName: 50S ribosomal protein L30 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 6.667931 KDa
SequenceString:
PRLKVKLVKS PIGYPKDQKA ALKALGLRRL QQERVLEDTP AIRGNVEKVA HLVRVEVVE

UniProtKB: Large ribosomal subunit protein uL30

+
Macromolecule #26: 50S ribosomal protein L31

MacromoleculeName: 50S ribosomal protein L31 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 8.086297 KDa
SequenceString:
MKEGIHPKLV PARIICGCGN VIETYSTKPE IYVEVCSKCH PFYTGQQRFV DTEGRVERFQ RRYGDSYRK

UniProtKB: Large ribosomal subunit protein bL31

+
Macromolecule #27: 50S ribosomal protein L32

MacromoleculeName: 50S ribosomal protein L32 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 6.590854 KDa
SequenceString:
AKHPVPKKKT SKARRDARRS HHALTPPTLV PCPECKAMKP PHTVCPECGY YAGRKVLEV

UniProtKB: Large ribosomal subunit protein bL32

+
Macromolecule #28: 50S ribosomal protein L33

MacromoleculeName: 50S ribosomal protein L33 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 6.5017 KDa
SequenceString:
ASEVRIKLLL ECTECKRRNY ATEKNKRNTP NKLELRKYCP WCRKHTVHRE VKI

UniProtKB: Large ribosomal subunit protein bL33

+
Macromolecule #29: 50S ribosomal protein L34

MacromoleculeName: 50S ribosomal protein L34 / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 5.975255 KDa
SequenceString:
MKRTWQPNRR KRAKTHGFRA RMRTPGGRKV LKRRRQKGRW RLTPAVRK

UniProtKB: Large ribosomal subunit protein bL34

+
Macromolecule #30: 50S ribosomal protein L35

MacromoleculeName: 50S ribosomal protein L35 / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 7.374981 KDa
SequenceString:
PKMKTHKGAK KRVKITASGK VVAMKTGKRH LNWQKSGKEI RQKGRKFVLA KPEAERIKLL LPYE

UniProtKB: Large ribosomal subunit protein bL35

+
Macromolecule #31: 50S ribosomal protein L36

MacromoleculeName: 50S ribosomal protein L36 / type: protein_or_peptide / ID: 31 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 4.435411 KDa
SequenceString:
MKVRASVKRI CDKCKVIRRH GRVYVICENP KHKQRQG

UniProtKB: Large ribosomal subunit protein bL36

+
Macromolecule #33: 30S ribosomal protein S2

MacromoleculeName: 30S ribosomal protein S2 / type: protein_or_peptide / ID: 33 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 26.646852 KDa
SequenceString: VKELLEAGVH FGHERKRWNP KFARYIYAER NGIHIIDLQK TMEELERTFR FIEDLAMRGG TILFVGTKKQ AQDIVRMEAE RAGMPYVNQ RWLGGMLTNF KTISQRVHRL EELEALFASP EIEERPKKEQ VRLKHELERL QKYLSGFRLL KRLPDAIFVV D PTKEAIAV ...String:
VKELLEAGVH FGHERKRWNP KFARYIYAER NGIHIIDLQK TMEELERTFR FIEDLAMRGG TILFVGTKKQ AQDIVRMEAE RAGMPYVNQ RWLGGMLTNF KTISQRVHRL EELEALFASP EIEERPKKEQ VRLKHELERL QKYLSGFRLL KRLPDAIFVV D PTKEAIAV REARKLFIPV IALADTDSDP DLVDYIIPGN DDAIRSIQLI LSRAVDLIIQ ARGGVVEPSP SYA

UniProtKB: Small ribosomal subunit protein uS2

+
Macromolecule #34: 30S ribosomal protein S3

MacromoleculeName: 30S ribosomal protein S3 / type: protein_or_peptide / ID: 34 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 22.86243 KDa
SequenceString: GNKIHPIGFR LGITRDWESR WYAGKKQYRH LLLEDQRIRG LLEKELYSAG LARVDIERAA DNVAVTVHVA KPGVVIGRGG ERIRVLREE LAKLTGKNVA LNVQEVQNPN LSAPLVAQRV AEQIERRFAV RRAIKQAVQR VMESGAKGAK VIVSGRIGGA E QARTEWAA ...String:
GNKIHPIGFR LGITRDWESR WYAGKKQYRH LLLEDQRIRG LLEKELYSAG LARVDIERAA DNVAVTVHVA KPGVVIGRGG ERIRVLREE LAKLTGKNVA LNVQEVQNPN LSAPLVAQRV AEQIERRFAV RRAIKQAVQR VMESGAKGAK VIVSGRIGGA E QARTEWAA QGRVPLHTLR ANIDYGFALA RTTYGVLGVK AYIFLGEV

UniProtKB: Small ribosomal subunit protein uS3

+
Macromolecule #35: 30S ribosomal protein S4

MacromoleculeName: 30S ribosomal protein S4 / type: protein_or_peptide / ID: 35 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 24.242254 KDa
SequenceString: GRYIGPVCRL CRREGVKLYL KGERCYSPKC AMERRPYPPG QHGQKRARRP SDYAVRLREK QKLRRIYGIS ERQFRNLFEE ASKKKGVTG SVFLGLLESR LDNVVYRLGF AVSRRQARQL VRHGHITVNG RRVDLPSYRV RPGDEIAVAE KSRNLELIRQ N LEAMKGRK ...String:
GRYIGPVCRL CRREGVKLYL KGERCYSPKC AMERRPYPPG QHGQKRARRP SDYAVRLREK QKLRRIYGIS ERQFRNLFEE ASKKKGVTG SVFLGLLESR LDNVVYRLGF AVSRRQARQL VRHGHITVNG RRVDLPSYRV RPGDEIAVAE KSRNLELIRQ N LEAMKGRK VGPWLSLDVE GMKGKFLRLP DREDLALPVN EQLVIEFYSR

UniProtKB: Small ribosomal subunit protein uS4

+
Macromolecule #36: 30S ribosomal protein S5

MacromoleculeName: 30S ribosomal protein S5 / type: protein_or_peptide / ID: 36 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 16.144848 KDa
SequenceString:
DFEEKMILIR RTARMQAGGR RFRFGALVVV GDRQGRVGLG FGKAPEVPLA VQKAGYYARR NMVEVPLQNG TIPHEIEVEF GASKIVLKP AAPGTGVIAG AVPRAILELA GVTDILTKEL GSRNPINIAY ATMEALRQLR TKADVERLR

UniProtKB: Small ribosomal subunit protein uS5

+
Macromolecule #37: 30S ribosomal protein S6

MacromoleculeName: 30S ribosomal protein S6 / type: protein_or_peptide / ID: 37 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 11.917675 KDa
SequenceString:
MRRYEVNIVL NPNLDQSQLA LEKEIIQRAL ENYGARVEKV EELGLRRLAY PIAKDPQGYF LWYQVEMPED RVNDLARELR IRDNVRRVM VVKSQEPFLA N

UniProtKB: Small ribosomal subunit protein bS6

+
Macromolecule #38: 30S ribosomal protein S7

MacromoleculeName: 30S ribosomal protein S7 / type: protein_or_peptide / ID: 38 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 17.919775 KDa
SequenceString:
ARRRRAEVRQ LQPDLVYGDV LVTAFINKIM RDGKKNLAAR IFYDACKIIQ EKTGQEPLKV FKQAVENVKP RMEVRSRRVG GANYQVPME VSPRRQQSLA LRWLVQAANQ RPERRAAVRI AHELMDAAEG KGGAVKKKED VERMAEANRA YAHYRW

UniProtKB: Small ribosomal subunit protein uS7

+
Macromolecule #39: 30S ribosomal protein S8

MacromoleculeName: 30S ribosomal protein S8 / type: protein_or_peptide / ID: 39 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 15.737372 KDa
SequenceString:
LTDPIADMLT RIRNATRVYK ESTDVPASRF KEEILRILAR EGFIKGYERV DVDGKPYLRV YLKYGPRRQG PDPRPEQVIH HIRRISKPG RRVYVGVKEI PRVRRGLGIA ILSTSKGVLT DREARKLGVG GELICEVW

UniProtKB: 30S ribosomal protein S8

+
Macromolecule #40: 30S ribosomal protein S9

MacromoleculeName: 30S ribosomal protein S9 / type: protein_or_peptide / ID: 40 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 14.122225 KDa
SequenceString:
EQYYGTGRRK EAVARVFLRP GNGKVTVNGQ DFNEYFQGLV RAVAALEPLR AVDALGHFDA YITVRGGGKS GQIDAIKLGI ARALVQYNP DYRAKLKPLG FLTRDARVVE RKKYGKHKAR RAPQYSK

UniProtKB: Small ribosomal subunit protein uS9

+
Macromolecule #41: 30S ribosomal protein S10

MacromoleculeName: 30S ribosomal protein S10 / type: protein_or_peptide / ID: 41 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 11.056838 KDa
SequenceString:
RIKLRGFDHK TLDASAQKIV EAARRSGAQV SGPIPLPTRV RRFTVIRGPF KHKDSREHFE LRTHNRLVDI INPNRKTIEQ LMTLDLPTG VEIEIKT

UniProtKB: Small ribosomal subunit protein uS10

+
Macromolecule #42: 30S ribosomal protein S11

MacromoleculeName: 30S ribosomal protein S11 / type: protein_or_peptide / ID: 42 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 12.032662 KDa
SequenceString:
QVASGRAYIH ASYNNTIVTI TDPDGNPITW SSGGVIGYKG SRKGTPYAAQ LAALDAAKKA MAYGMQSVDV IVRGTGAGRE QAIRALQAS GLQVKSIVDD TPVPHNGCRP KKKFR

UniProtKB: Small ribosomal subunit protein uS11

+
Macromolecule #43: 30S ribosomal protein S12

MacromoleculeName: 30S ribosomal protein S12 / type: protein_or_peptide / ID: 43 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 13.650211 KDa
SequenceString:
PTINQLVRKG REKVRKKSKV PALKGAPFRR GVCTVVRTVT PKKPNSALRK VAKVRLTSGY EVTAYIPGEG HNLQEHSVVL IRGGRVK(0TD)L PGVRYHIVRG VYDAAGVKDR KKSRSKYGTK KPK

UniProtKB: Small ribosomal subunit protein uS12

+
Macromolecule #44: 30S ribosomal protein S13

MacromoleculeName: 30S ribosomal protein S13 / type: protein_or_peptide / ID: 44 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 13.067221 KDa
SequenceString:
RIAGVEIPRN KRVDVALTYI YGIGKARAKE ALEKTGINPA TRVKDLTEAE VVRLREYVEN TWKLEGELRA EVAANIKRLM DIGCYRGLR HRRGLPVRGQ RTRTNARTRK GPRKT

UniProtKB: Small ribosomal subunit protein uS13

+
Macromolecule #45: 30S ribosomal protein S14 type Z

MacromoleculeName: 30S ribosomal protein S14 type Z / type: protein_or_peptide / ID: 45 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 7.027529 KDa
SequenceString:
ARKALIEKAK RTPKFKVRAY TRCVRCGRAR SVYRFFGLCR ICLRELAHKG QLPGVRKASW

UniProtKB: 30S ribosomal protein S14 type Z

+
Macromolecule #46: 30S ribosomal protein S15

MacromoleculeName: 30S ribosomal protein S15 / type: protein_or_peptide / ID: 46 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 10.447213 KDa
SequenceString:
PITKEEKQKV IQEFARFPGD TGSTEVQVAL LTLRINRLSE HLKVHKKDHH SHRGLLMMVG QRRRLLRYLQ REDPERYRAL IEKLGIRG

UniProtKB: Small ribosomal subunit protein uS15

+
Macromolecule #47: 30S ribosomal protein S16

MacromoleculeName: 30S ribosomal protein S16 / type: protein_or_peptide / ID: 47 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 9.795354 KDa
SequenceString:
MVKIRLARFG SKHNPHYRIV VTDARRKRDG KYIEKIGYYD PRKTTPDWLK VDVERARYWL SVGAQPTDTA RRLLRQAGVF RQ

UniProtKB: Small ribosomal subunit protein bS16

+
Macromolecule #48: 30S ribosomal protein S17

MacromoleculeName: 30S ribosomal protein S17 / type: protein_or_peptide / ID: 48 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 11.722904 KDa
SequenceString:
PKKVLTGVVV SDKMQKTVTV LVERQFPHPL YGKVIKRSKK YLAHDPEEKY KLGDVVEIIE SRPISKRKRF RVLRLVESGR MDLVEKYLI RRQNYESLSK

UniProtKB: 30S ribosomal protein S17

+
Macromolecule #49: 30S ribosomal protein S18

MacromoleculeName: 30S ribosomal protein S18 / type: protein_or_peptide / ID: 49 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 7.897451 KDa
SequenceString:
AKVKATLGEF DLRDYRNVEV LKRFLSETGK ILPRRRTGLS AKEQRILAKT IKRARILGLL PFTEKLVR

UniProtKB: Small ribosomal subunit protein bS18

+
Macromolecule #50: 30S ribosomal protein S19

MacromoleculeName: 30S ribosomal protein S19 / type: protein_or_peptide / ID: 50 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 9.455995 KDa
SequenceString:
PRSLKKGVFV DDHLLEKVLE LNAKGEKRLI KTWSRRSTIV PEMVGHTIAV YNGKQHVPVY ITENMVGHKL GEFAPTRTYR GHG

UniProtKB: Small ribosomal subunit protein uS19

+
Macromolecule #51: 30S ribosomal protein S20

MacromoleculeName: 30S ribosomal protein S20 / type: protein_or_peptide / ID: 51 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 10.876067 KDa
SequenceString:
PKRNLSALKR HRQSLKRRLR NKAKKSAIKT LSKKAIQLAQ EGKAEEALKI MRKAESLIDK AAKGSTLHKN AAARRKSRLM RKVRQLLEA AGAPLIGGG

UniProtKB: Small ribosomal subunit protein bS20

+
Macromolecule #52: 30S ribosomal protein Thx

MacromoleculeName: 30S ribosomal protein Thx / type: protein_or_peptide / ID: 52 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 2.831295 KDa
SequenceString:
GKGDRRTRRG KIWRGTYGKY RPR

UniProtKB: Small ribosomal subunit protein bTHX

+
Macromolecule #54: 50S ribosomal protein L1

MacromoleculeName: 50S ribosomal protein L1 / type: protein_or_peptide / ID: 54 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 24.513211 KDa
SequenceString: KHGKRYRALL EKVDPNKVYT IDEAARLVKE LATAKFDETV EVHAKLGIDP RRSDQNVRGT VSLPHGLGKQ VRVLAIAKGE KIKEAEEAG ADYVGGEEII QKILDGWMDF DAVVATPDVG AVGSKLGRIL GPRGLLPNPK AGTVGFNIGE IIREIKAGRI E FRNDKTGA ...String:
KHGKRYRALL EKVDPNKVYT IDEAARLVKE LATAKFDETV EVHAKLGIDP RRSDQNVRGT VSLPHGLGKQ VRVLAIAKGE KIKEAEEAG ADYVGGEEII QKILDGWMDF DAVVATPDVG AVGSKLGRIL GPRGLLPNPK AGTVGFNIGE IIREIKAGRI E FRNDKTGA IHAPVGKASF PPEKLADNIR AFIRALEAHK PEGAKGTFLR SVYVTTTMGP SVRINPHS

UniProtKB: Large ribosomal subunit protein uL1

+
Macromolecule #57: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 57 / Number of copies: 6 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #58: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 58 / Number of copies: 1 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-5uq7:
70S ribosome complex with dnaX mRNA stemloop and E-site tRNA ("in" conformation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more