[English] 日本語
Yorodumi
- EMDB-13952: Structure of the collided E. coli disome - VemP-stalled 70S ribosome -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-13952
TitleStructure of the collided E. coli disome - VemP-stalled 70S ribosome
Map datadisome map after focused refinement on stalled ribosome
Sample
  • Complex: stalled/leading ribosome of the collided disome structure
    • RNA: x 5 types
    • Protein or peptide: x 52 types
  • Ligand: x 3 types
Function / homology
Function and homology information


negative regulation of cytoplasmic translational initiation / stringent response / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / misfolded RNA binding / transcription antitermination factor activity, RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity ...negative regulation of cytoplasmic translational initiation / stringent response / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / misfolded RNA binding / transcription antitermination factor activity, RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translational termination / DnaA-L2 complex / four-way junction DNA binding / negative regulation of translational initiation / translation repressor activity / translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / ribosome assembly / mRNA regulatory element binding translation repressor activity / response to reactive oxygen species / assembly of large subunit precursor of preribosome / positive regulation of RNA splicing / DNA endonuclease activity / transcription elongation factor complex / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / transcription antitermination / regulation of cell growth / maintenance of translational fidelity / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ribosome binding / large ribosomal subunit / ribosome biogenesis / regulation of translation / cytoplasmic translation / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / tRNA binding / negative regulation of translation / rRNA binding / molecular adaptor activity / ribosome / structural constituent of ribosome / translation / response to antibiotic / mRNA binding / negative regulation of DNA-templated transcription / DNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L1, bacterial-type / Ribosomal protein L1, conserved site / Ribosomal protein L1 / Ribosomal protein L1 signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L25, short-form / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L1p/L10e family ...Ribosomal protein L1, bacterial-type / Ribosomal protein L1, conserved site / Ribosomal protein L1 / Ribosomal protein L1 signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L25, short-form / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L1p/L10e family / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L11, conserved site / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L11 signature. / Ribosomal protein L16 signature 1. / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L11, N-terminal / Ribosomal protein L17 signature. / 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 protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11, RNA binding domain / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L32p, bacterial type / 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 L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L20 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / : / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein L18
Similarity search - Domain/homology
Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL29 ...Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein bL25
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria) / Vibrio alginolyticus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.97 Å
AuthorsKratzat H / Buschauer R / Berninghausen O / Beckmann R
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Nature / Year: 2022
Title: Ribosome collisions induce mRNA cleavage and ribosome rescue in bacteria.
Authors: Kazuki Saito / Hanna Kratzat / Annabelle Campbell / Robert Buschauer / A Maxwell Burroughs / Otto Berninghausen / L Aravind / Rachel Green / Roland Beckmann / Allen R Buskirk /
Abstract: Ribosome rescue pathways recycle stalled ribosomes and target problematic mRNAs and aborted proteins for degradation. In bacteria, it remains unclear how rescue pathways distinguish ribosomes stalled ...Ribosome rescue pathways recycle stalled ribosomes and target problematic mRNAs and aborted proteins for degradation. In bacteria, it remains unclear how rescue pathways distinguish ribosomes stalled in the middle of a transcript from actively translating ribosomes. Here, using a genetic screen in Escherichia coli, we discovered a new rescue factor that has endonuclease activity. SmrB cleaves mRNAs upstream of stalled ribosomes, allowing the ribosome rescue factor tmRNA (which acts on truncated mRNAs) to rescue upstream ribosomes. SmrB is recruited to ribosomes and is activated by collisions. Cryo-electron microscopy structures of collided disomes from E. coli and Bacillus subtilis show distinct and conserved arrangements of individual ribosomes and the composite SmrB-binding site. These findings reveal the underlying mechanisms by which ribosome collisions trigger ribosome rescue in bacteria.
History
DepositionDec 7, 2021-
Header (metadata) releaseMar 16, 2022-
Map releaseMar 16, 2022-
UpdateMar 30, 2022-
Current statusMar 30, 2022Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.45
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.45
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7qg8
  • Surface level: 0.45
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7qg8
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13952.png

Downloads & links

-
Map

FileDownload / File: emd_13952.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationdisome map after focused refinement on stalled ribosome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 600 pix.
= 654. Å		1.09 Å/pix.
x 600 pix.
= 654. Å		1.09 Å/pix.
x 600 pix.
= 654. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45 / Movie #1: 0.45
Minimum - Maximum-0.7361507 - 2.5396688
Average (Standard dev.)-0.007961702 (±0.14811042)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 654.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z654.000654.000654.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS600600600
D min/max/mean-0.7362.540-0.008

-
Supplemental data

-
Additional map: local resolution filtered map

Fileemd_13952_additional_1.map
Annotationlocal resolution filtered map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: disome map

Fileemd_13952_additional_2.map
Annotationdisome map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : stalled/leading ribosome of the collided disome structure

EntireName: stalled/leading ribosome of the collided disome structure
Components
  • Complex: stalled/leading ribosome of the collided disome structure
    • RNA: A-site tRNA
    • Protein or peptide: VemP nascent chain
    • RNA: P-site tRNA
    • RNA: 5S rRNA5S ribosomal RNA
    • 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 L11
    • 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 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: 23S rRNA23S ribosomal RNA
    • Protein or peptide: 50S ribosomal protein L31
    • Protein or peptide: 50S ribosomal protein L1
    • 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, non-modified isoformRibosome
    • 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
    • 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 S21
  • Ligand: MAGNESIUM ION
  • Ligand: POTASSIUM IONPotassium
  • Ligand: water

+
Supramolecule #1: stalled/leading ribosome of the collided disome structure

SupramoleculeName: stalled/leading ribosome of the collided disome structure
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#57

+
Macromolecule #1: A-site tRNA

MacromoleculeName: A-site tRNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 23.545971 KDa
SequenceString:
GCGCGGAUAG CUCAGUCGGU AGAGCAGGGG AUUGAAAAUC CCCGUGUCCU UGGUUCGAUU CCGAGUCCGC GCA

+
Macromolecule #3: P-site tRNA

MacromoleculeName: P-site tRNA / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 24.060287 KDa
SequenceString:
UGGGGUAUCG CCAAGCGGUA AGGCACCGGA UUCUGAUUCC GGCAUUCCGA GGUUCGAAUC CUCGUACCCC AGCCA

+
Macromolecule #4: 5S rRNA

MacromoleculeName: 5S rRNA / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 38.79009 KDa
SequenceString:
UGCCUGGCGG CCGUAGCGCG GUGGUCCCAC CUGACCCCAU GCCGAACUCA GAAGUGAAAC GCCGUAGCGC CGAUGGUAGU GUGGGGUCU CCCCAUGCGA GAGUAGGGAA CUGCCAGGCA U

+
Macromolecule #34: 23S rRNA

MacromoleculeName: 23S rRNA / type: rna / ID: 34 / Number of copies: 1
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 941.306188 KDa
SequenceString: GGUUAAGCGA CUAAGCGUAC ACGGUGGAUG CCCUGGCAGU CAGAGGCGAU GAAGGACGUG CUAAUCUGCG AUAAGCGUCG GUAAGGUGA UAUGAACCGU UAUAACCGGC GAUUUCCGAA UGGGGAAACC CAGUGUGUUU CGACACACUA UCAUUAACUG A AUCCAUAG ...String:
GGUUAAGCGA CUAAGCGUAC ACGGUGGAUG CCCUGGCAGU CAGAGGCGAU GAAGGACGUG CUAAUCUGCG AUAAGCGUCG GUAAGGUGA UAUGAACCGU UAUAACCGGC GAUUUCCGAA UGGGGAAACC CAGUGUGUUU CGACACACUA UCAUUAACUG A AUCCAUAG GUUAAUGAGG CGAACCGGGG GAACUGAAAC AUCUAAGUAC CCCGAGGAAA AGAAAUCAAC CGAGAUUCCC CC AGUAGCG GCGAGCGAAC GGGGAGCAGC CCAGAGCCUG AAUCAGUGUG UGUGUUAGUG GAAGCGUCUG GAAAGGCGCG CGA UACAGG GUGACAGCCC CGUACACAAA AAUGCACAUG CUGUGAGCUC GAUGAGUAGG GCGGGACACG UGGUAUCCUG UCUG AAUAU GGGGGGACCA UCCUCCAAGG CUAAAUACUC CUGACUGACC GAUAGUGAAC CAGUACCGUG AGGGAAAGGC GAAAA GAAC CCCGGCGAGG GGAGUGAAAA AGAACCUGAA ACCGUGUACG UACAAGCAGU GGGAGCACGC UUAGGCGUGU GACUGC GUA CCUUUUGUAU AAUGGGUCAG CGACUUAUAU UCUGUAGCAA GGUUAACCGA AUAGGGGAGC CGAAGGGAAA CCGAGUC UU AACUGGGCGU UAAGUUGCAG GGUAUAGACC CGAAACCCGG UGAUCUAGCC AUGGGCAGGU UGAAGGUUGG GUAACACU A ACUGGAGGAC CGAACCGACU AAUGUUGAAA AAUUAGCGGA UGACUUGUGG CUGGGGGUGA AAGGCCAAUC AAACCGGGA GAUAGCUGGU UCUCCCCGAA AGCUAUUUAG GUAGCGCCUC GUGAAUUCAU CUCCGGGGGU AGAGCACUGU UUCGGCAAGG GGGUCAUCC CGACUUACCA ACCCGAUGCA AACUGCGAAU ACCGGAGAAU GUUAUCACGG GAGACACACG GCGGGUGCUA A CGUCCGUC GUGAAGAGGG AAACAACCCA GACCGCCAGC UAAGGUCCCA AAGUCAUGGU UAAGUGGGAA ACGAUGUGGG AA GGCCCAG ACAGCCAGGA UGUUGGCUUA GAAGCAGCCA UCAUUUAAAG AAAGCGUAAU AGCUCACUGG UCGAGUCGGC CUG CGCGGA AGAUGUAACG GGGCUAAACC AUGCACCGAA GCUGCGGCAG CGACGCUUAU GCGUUGUUGG GUAGGGGAGC GUUC UGUAA GCCUGCGAAG GUGUGCUGUG AGGCAUGCUG GAGGUAUCAG AAGUGCGAAU GCUGACAUAA GUAACGAUAA AGCGG GUGA AAAGCCCGCU CGCCGGAAGA CCAAGGGUUC CUGUCCAACG UUAAUCGGGG CAGGGUGAGU CGACCCCUAA GGCGAG GCC GAAAGGCGUA GUCGAUGGGA AACAGGUUAA UAUUCCUGUA CUUGGUGUUA CUGCGAAGGG GGGACGGAGA AGGCUAU GU UGGCCGGGCG ACGGUUGUCC CGGUUUAAGC GUGUAGGCUG GUUUUCCAGG CAAAUCCGGA AAAUCAAGGC UGAGGCGU G AUGACGAGGC ACUACGGUGC UGAAGCAACA AAUGCCCUGC UUCCAGGAAA AGCCUCUAAG CAUCAGGUAA CAUCAAAUC GUACCCCAAA CCGACACAGG UGGUCAGGUA GAGAAUACCA AGGCGCUUGA GAGAACUCGG GUGAAGGAAC UAGGCAAAAU GGUGCCGUA ACUUCGGGAG AAGGCACGCU GAUAUGUAGG UGAGGUCCCU CGCGGAUGGA GCUGAAAUCA GUCGAAGAUA C CAGCUGGC UGCAACUGUU UAUUAAAAAC ACAGCACUGU GCAAACACGA AAGUGGACGU AUACGGUGUG ACGCCUGCCC GG UGCCGGA AGGUUAAUUG AUGGGGUUAG CGCAAGCGAA GCUCUUGAUC GAAGCCCCGG UAAACGGCGG CCGUAACUAU AAC GGUCCU AAGGUAGCGA AAUUCCUUGU CGGGUAAGUU CCGACCUGCA CGAAUGGCGU AAUGAUGGCC AGGCUGUCUC CACC CGAGA CUCAGUGAAA UUGAACUCGC UGUGAAGAUG CAGUGUACCC GCGGCAAGAC GGAAAGACCC CGUGAACCUU UACUA UAGC UUGACACUGA ACAUUGAGCC UUGAUGUGUA GGAUAGGUGG GAGGCUUUGA AGUGUGGACG CCAGUCUGCA UGGAGC CGA CCUUGAAAUA CCACCCUUUA AUGUUUGAUG UUCUAACGUU GACCCGUAAU CCGGGUUGCG GACAGUGUCU GGUGGGU AG UUUGACUGGG GCGGUCUCCU CCUAAAGAGU AACGGAGGAG CACGAAGGUU GGCUAAUCCU GGUCGGACAU CAGGAGGU U AGUGCAAUGG CAUAAGCCAG CUUGACUGCG AGCGUGACGG CGCGAGCAGG UGCGAAAGCA GGUCAUAGUG AUCCGGUGG UUCUGAAUGG AAGGGCCAUC GCUCAACGGA UAAAAGGUAC UCCGGGGAUA ACAGGCUGAU ACCGCCCAAG AGUUCAUAUC GACGGCGGU GUUUGGCACC UCGAUGUCGG CUCAUCACAU CCUGGGGCUG AAGUAGGUCC CAAGGGUAUG GCUGUUCGCC A UUUAAAGU GGUACGCGAG CUGGGUUUAG AACGUCGUGA GACAGUUCGG UCCCUAUCUG CCGUGGGCGC UGGAGAACUG AG GGGGGCU GCUCCUAGUA CGAGAGGACC GGAGUGGACG CAUCACUGGU GUUCGGGUUG UCAUGCCAAU GGCACUGCCC GGU AGCUAA AUGCGGAAGA GAUAAGUGCU GAAAGCAUCU AAGCACGAAA CUUGCCCCGA GAUGAGUUCU CCCUGACCCU UUAA GGGUC CUGAAGGAAC GUUGAAGACG ACGACGUUGA UAGGCCGGGU GUGUAAGCGC AGCGAUGCGU UGAGCUAACC GGUAC UAAU GAACCGUGAG GCUUAACCU

+
Macromolecule #37: 16S rRNA

MacromoleculeName: 16S rRNA / type: rna / ID: 37 / Number of copies: 1
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 498.725406 KDa
SequenceString: AAUUGAAGAG UUUGAUCAUG GCUCAGAUUG AACGCUGGCG GCAGGCCUAA CACAUGCAAG UCGAACGGUA ACAGGAAGAA GCUUGCUUC UUUGCUGACG AGUGGCGGAC GGGUGAGUAA UGUCUGGGAA ACUGCCUGAU GGAGGGGGAU AACUACUGGA A ACGGUAGC ...String:
AAUUGAAGAG UUUGAUCAUG GCUCAGAUUG AACGCUGGCG GCAGGCCUAA CACAUGCAAG UCGAACGGUA ACAGGAAGAA GCUUGCUUC UUUGCUGACG AGUGGCGGAC GGGUGAGUAA UGUCUGGGAA ACUGCCUGAU GGAGGGGGAU AACUACUGGA A ACGGUAGC UAAUACCGCA UAACGUCGCA AGACCAAAGA GGGGGACCUU CGGGCCUCUU GCCAUCGGAU GUGCCCAGAU GG GAUUAGC UAGUAGGUGG GGUAACGGCU CACCUAGGCG ACGAUCCCUA GCUGGUCUGA GAGGAUGACC AGCCACACUG GAA CUGAGA CACGGUCCAG ACUCCUACGG GAGGCAGCAG UGGGGAAUAU UGCACAAUGG GCGCAAGCCU GAUGCAGCCA UGCC GCGUG UAUGAAGAAG GCCUUCGGGU UGUAAAGUAC UUUCAGCGGG GAGGAAGGGA GUAAAGUUAA UACCUUUGCU CAUUG ACGU UACCCGCAGA AGAAGCACCG GCUAACUCCG UGCCAGCAGC CGCGGUAAUA CGGAGGGUGC AAGCGUUAAU CGGAAU UAC UGGGCGUAAA GCGCACGCAG GCGGUUUGUU AAGUCAGAUG UGAAAUCCCC GGGCUCAACC UGGGAACUGC AUCUGAU AC UGGCAAGCUU GAGUCUCGUA GAGGGGGGUA GAAUUCCAGG UGUAGCGGUG AAAUGCGUAG AGAUCUGGAG GAAUACCG G UGGCGAAGGC GGCCCCCUGG ACGAAGACUG ACGCUCAGGU GCGAAAGCGU GGGGAGCAAA CAGGAUUAGA UACCCUGGU AGUCCACGCC GUAAACGAUG UCGACUUGGA GGUUGUGCCC UUGAGGCGUG GCUUCCGGAG CUAACGCGUU AAGUCGACCG CCUGGGGAG UACGGCCGCA AGGUUAAAAC UCAAAUGAAU UGACGGGGGC CCGCACAAGC GGUGGAGCAU GUGGUUUAAU U CGAUGCAA CGCGAAGAAC CUUACCUGGU CUUGACAUCC ACGGAAGUUU UCAGAGAUGA GAAUGUGCCU UCGGGAACCG UG AGACAGG UGCUGCAUGG CUGUCGUCAG CUCGUGUUGU GAAAUGUUGG GUUAAGUCCC GCAACGAGCG CAACCCUUAU CCU UUGUUG CCAGCGGUCC GGCCGGGAAC UCAAAGGAGA CUGCCAGUGA UAAACUGGAG GAAGGUGGGG AUGACGUCAA GUCA UCAUG GCCCUUACGA CCAGGGCUAC ACACGUGCUA CAAUGGCGCA UACAAAGAGA AGCGACCUCG CGAGAGCAAG CGGAC CUCA UAAAGUGCGU CGUAGUCCGG AUUGGAGUCU GCAACUCGAC UCCAUGAAGU CGGAAUCGCU AGUAAUCGUG GAUCAG AAU GCCACGGUGA AUACGUUCCC GGGCCUUGUA CACACCGCCC GUCACACCAU GGGAGUGGGU UGCAAAAGAA GUAGGUA GC UUAACCUUCG GGAGGGCGCU UACCACUUUG UGAUUCAUGA CUGGGGUGAA GUCGUAACAA GGUAACCGUA GGGGAACC U GCGGUUGGAU CACCUCCU

+
Macromolecule #2: VemP nascent chain

MacromoleculeName: VemP nascent chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria)
Molecular weightTheoretical: 20.531092 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
MHHHHHHHHH HGDYKDDDDK ENLYFQGSAQ IDQKAHVPHF SKLQPFVAVS VSPNSSVDFS EASEESSQSP VSEGHASLDS VALFNSQRW TSYLREGLDD EHVDFVGDLT TPFYADAGYA YSLMDINWRH NQSTFYHFTS DHRISGWKET NAMYVALNSQ F SALEVLFQ GPYPYDVPDY A

+
Macromolecule #5: 50S ribosomal protein L2

MacromoleculeName: 50S ribosomal protein L2 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 29.923619 KDa
SequenceString: MAVVKCKPTS PGRRHVVKVV NPELHKGKPF APLLEKNSKS GGRNNNGRIT TRHIGGGHKQ AYRIVDFKRN KDGIPAVVER LEYDPNRSA NIALVLYKDG ERRYILAPKG LKAGDQIQSG VDAAIKPGNT LPMRNIPVGS TVHNVEMKPG KGGQLARSAG T YVQIVARD ...String:
MAVVKCKPTS PGRRHVVKVV NPELHKGKPF APLLEKNSKS GGRNNNGRIT TRHIGGGHKQ AYRIVDFKRN KDGIPAVVER LEYDPNRSA NIALVLYKDG ERRYILAPKG LKAGDQIQSG VDAAIKPGNT LPMRNIPVGS TVHNVEMKPG KGGQLARSAG T YVQIVARD GAYVTLRLRS GEMRKVEADC RATLGEVGNA EHMLRVLGKA GAARWRGVRP TVRGTAMNPV DHPHGGGEGR NF GKHPVTP WGVQTKGKKT RSNKRTDKFI VRRRSK

+
Macromolecule #6: 50S ribosomal protein L3

MacromoleculeName: 50S ribosomal protein L3 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 22.277535 KDa
SequenceString: MIGLVGKKVG MTRIFTEDGV SIPVTVIEVE ANRVTQVKDL ANDGYRAIQV TTGAKKANRV TKPEAGHFAK AGVEAGRGLW EFRLAEGEE FTVGQSISVE LFADVKKVDV TGTSKGKGFA GTVKRWNFRT QDATHGNSLS HRVPGSIGQN QTPGKVFKGK K MAGQMGNE ...String:
MIGLVGKKVG MTRIFTEDGV SIPVTVIEVE ANRVTQVKDL ANDGYRAIQV TTGAKKANRV TKPEAGHFAK AGVEAGRGLW EFRLAEGEE FTVGQSISVE LFADVKKVDV TGTSKGKGFA GTVKRWNFRT QDATHGNSLS HRVPGSIGQN QTPGKVFKGK K MAGQMGNE RVTVQSLDVV RVDAERNLLL VKGAVPGATG SDLIVKPAVK A

+
Macromolecule #7: 50S ribosomal protein L4

MacromoleculeName: 50S ribosomal protein L4 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 22.121566 KDa
SequenceString: MELVLKDAQS ALTVSETTFG RDFNEALVHQ VVVAYAAGAR QGTRAQKTRA EVTGSGKKPW RQKGTGRARS GSIKSPIWRS GGVTFAARP QDHSQKVNKK MYRGALKSIL SELVRQDRLI VVEKFSVEAP KTKLLAQKLK DMALEDVLII TGELDENLFL A ARNLHKVD ...String:
MELVLKDAQS ALTVSETTFG RDFNEALVHQ VVVAYAAGAR QGTRAQKTRA EVTGSGKKPW RQKGTGRARS GSIKSPIWRS GGVTFAARP QDHSQKVNKK MYRGALKSIL SELVRQDRLI VVEKFSVEAP KTKLLAQKLK DMALEDVLII TGELDENLFL A ARNLHKVD VRDATGIDPV SLIAFDKVVM TADAVKQVEE MLA

+
Macromolecule #8: 50S ribosomal protein L5

MacromoleculeName: 50S ribosomal protein L5 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 20.333611 KDa
SequenceString:
MAKLHDYYKD EVVKKLMTEF NYNSVMQVPR VEKITLNMGV GEAIADKKLL DNAAADLAAI SGQKPLITKA RKSVAGFKIR QGYPIGCKV TLRGERMWEF FERLITIAVP RIRDFRGLSA KSFDGRGNYS MGVREQIIFP EIDYDKVDRV RGLDITITTT A KSDEEGRA LLAAFDFPFR K

+
Macromolecule #9: 50S ribosomal protein L6

MacromoleculeName: 50S ribosomal protein L6 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 18.932791 KDa
SequenceString:
MSRVAKAPVV VPAGVDVKIN GQVITIKGKN GELTRTLNDA VEVKHADNTL TFGPRDGYAD GWAQAGTARA LLNSMVIGVT EGFTKKLQL VGVGYRAAVK GNVINLSLGF SHPVDHQLPA GITAECPTQT EIVLKGADKQ VIGQVAADLR AYRRPEPYKG K GVRYADEV VRTKEAKKK

+
Macromolecule #10: 50S ribosomal protein L9

MacromoleculeName: 50S ribosomal protein L9 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 15.78902 KDa
SequenceString:
MQVILLDKVA NLGSLGDQVN VKAGYARNFL VPQGKAVPAT KKNIEFFEAR RAELEAKLAE VLAAANARAE KINALETVTI ASKAGDEGK LFGSIGTRDI ADAVTAAGVE VAKSEVRLPN GVLRTTGEHE VSFQVHSEVF AKVIVNVVAE

+
Macromolecule #11: 50S ribosomal protein L11

MacromoleculeName: 50S ribosomal protein L11 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 14.894362 KDa
SequenceString:
MAKKVQAYVK LQVAAGMANP SPPVGPALGQ QGVNIMEFCK AFNAKTDSIE KGLPIPVVIT VYADRSFTFV TKTPPAAVLL KKAAGIKSG SGKPNKDKVG KISRAQLQEI AQTKAADMTG ADIEAMTRSI EGTARSMGLV VED

+
Macromolecule #12: 50S ribosomal protein L13

MacromoleculeName: 50S ribosomal protein L13 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 16.050606 KDa
SequenceString:
MKTFTAKPET VKRDWYVVDA TGKTLGRLAT ELARRLRGKH KAEYTPHVDT GDYIIVLNAD KVAVTGNKRT DKVYYHHTGH IGGIKQATF EEMIARRPER VIEIAVKGML PKGPLGRAMF RKLKVYAGNE HNHAAQQPQV LDI

+
Macromolecule #13: 50S ribosomal protein L14

MacromoleculeName: 50S ribosomal protein L14 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 13.565067 KDa
SequenceString:
MIQEQTMLNV ADNSGARRVM CIKVLGGSHR RYAGVGDIIK ITIKEAIPRG KVKKGDVLKA VVVRTKKGVR RPDGSVIRFD GNACVLLNN NSEQPIGTRI FGPVTRELRS EKFMKIISLA PEVL

+
Macromolecule #14: 50S ribosomal protein L15

MacromoleculeName: 50S ribosomal protein L15 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 15.008471 KDa
SequenceString:
MRLNTLSPAE GSKKAGKRLG RGIGSGLGKT GGRGHKGQKS RSGGGVRRGF EGGQMPLYRR LPKFGFTSRK AAITAEIRLS DLAKVEGGV VDLNTLKAAN IIGIQIEFAK VILAGEVTTP VTVRGLRVTK GARAAIEAAG GKIEE

+
Macromolecule #15: 50S ribosomal protein L16

MacromoleculeName: 50S ribosomal protein L16 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 15.312269 KDa
SequenceString:
MLQPKRTKFR KMHKGRNRGL AQGTDVSFGS FGLKAVGRGR LTARQIEAAR RAMTRAVKRQ GKIWIRVFPD KPITEKPLAV RMGKGKGNV EYWVALIQPG KVLYEMDGVP EELAREAFKL AAAKLPIKTT FVTKTVM

+
Macromolecule #16: 50S ribosomal protein L17

MacromoleculeName: 50S ribosomal protein L17 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 14.33562 KDa
SequenceString:
MRHRKSGRQL NRNSSHRQAM FRNMAGSLVR HEIIKTTLPK AKELRRVVEP LITLAKTDSV ANRRLAFART RDNEIVAKLF NELGPRFAS RAGGYTRILK CGFRAGDNAP MAYIELVDRS EKAAAAAE

+
Macromolecule #17: 50S ribosomal protein L18

MacromoleculeName: 50S ribosomal protein L18 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 12.794668 KDa
SequenceString:
MDKKSARIRR ATRARRKLQE LGATRLVVHR TPRHIYAQVI APNGSEVLVA ASTVEKAIAE QLKYTGNKDA AAAVGKAVAE RALEKGIKD VSFDRSGFQY HGRVQALADA AREAGLQF

+
Macromolecule #18: 50S ribosomal protein L19

MacromoleculeName: 50S ribosomal protein L19 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 13.159278 KDa
SequenceString:
MSNIIKQLEQ EQMKQDVPSF RPGDTVEVKV WVVEGSKKRL QAFEGVVIAI RNRGLHSAFT VRKISNGEGV ERVFQTHSPV VDSISVKRR GAVRKAKLYY LRERTGKAAR IKERLN

+
Macromolecule #19: 50S ribosomal protein L20

MacromoleculeName: 50S ribosomal protein L20 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 13.528024 KDa
SequenceString:
MARVKRGVIA RARHKKILKQ AKGYYGARSR VYRVAFQAVI KAGQYAYRDR RQRKRQFRQL WIARINAAAR QNGISYSKFI NGLKKASVE IDRKILADIA VFDKVAFTAL VEKAKAALA

+
Macromolecule #20: 50S ribosomal protein L21

MacromoleculeName: 50S ribosomal protein L21 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 11.586374 KDa
SequenceString:
MYAVFQSGGK QHRVSEGQTV RLEKLDIATG ETVEFAEVLM IANGEEVKIG VPFVDGGVIK AEVVAHGRGE KVKIVKFRRR KHYRKQQGH RQWFTDVKIT GISA

+
Macromolecule #21: 50S ribosomal protein L22

MacromoleculeName: 50S ribosomal protein L22 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 12.253359 KDa
SequenceString:
METIAKHRHA RSSAQKVRLV ADLIRGKKVS QALDILTYTN KKAAVLVKKV LESAIANAEH NDGADIDDLK VTKIFVDEGP SMKRIMPRA KGRADRILKR TSHITVVVSD R

+
Macromolecule #22: 50S ribosomal protein L23

MacromoleculeName: 50S ribosomal protein L23 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 11.252186 KDa
SequenceString:
MIREERLLKV LRAPHVSEKA STAMEKSNTI VLKVAKDATK AEIKAAVQKL FEVEVEVVNT LVVKGKVKRH GQRIGRRSDW KKAYVTLKE GQNLDFVGSA E

+
Macromolecule #23: 50S ribosomal protein L24

MacromoleculeName: 50S ribosomal protein L24 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 11.33925 KDa
SequenceString:
MAAKIRRDDE VIVLTGKDKG KRGKVKNVLS SGKVIVEGIN LVKKHQKPVP ALNQPGGIVE KEAAIQVSNV AIFNAATGKA DRVGFRFED GKKVRFFKSN SETIK

+
Macromolecule #24: 50S ribosomal protein L25

MacromoleculeName: 50S ribosomal protein L25 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 10.713465 KDa
SequenceString:
MFTINAEVRK EQGKGASRRL RAANKFPAII YGGKEAPLAI ELDHDKVMNM QAKAEFYSEV LTIVVDGKEI KVKAQDVQRH PYKPKLQHI DFVRA

+
Macromolecule #25: 50S ribosomal protein L27

MacromoleculeName: 50S ribosomal protein L27 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 9.093498 KDa
SequenceString:
MA(UNK)KKAGGST RNGRDSEAKR LGVKRFGGES VLAGSIIVRQ RGTKFHAGAN VGCGRDHTLF AKADGKVKFE VKGPKN RKF ISIEAE

+
Macromolecule #26: 50S ribosomal protein L28

MacromoleculeName: 50S ribosomal protein L28 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 9.027551 KDa
SequenceString:
MSRVCQVTGK RPVTGNNRSH ALNATKRRFL PNLHSHRFWV ESEKRFVTLR VSAKGMRVID KKGIDTVLAE LRARGEKY

+
Macromolecule #27: 50S ribosomal protein L29

MacromoleculeName: 50S ribosomal protein L29 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 7.286464 KDa
SequenceString:
MKAKELREKS VEELNTELLN LLREQFNLRM QAASGQLQQS HLLKQVRRDV ARVKTLLNEK AGA

+
Macromolecule #28: 50S ribosomal protein L30

MacromoleculeName: 50S ribosomal protein L30 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 6.55482 KDa
SequenceString:
MAKTIKITQT RSAIGRLPKH KATLLGLGLR RIGHTVERED TPAIRGMINA VSFMVKVEE

+
Macromolecule #29: 50S ribosomal protein L32

MacromoleculeName: 50S ribosomal protein L32 / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 6.463445 KDa
SequenceString:
MAVQQNKPTR SKRGMRRSHD ALTAVTSLSV DKTSGEKHLR HHITADGYYR GRKVIAK

+
Macromolecule #30: 50S ribosomal protein L33

MacromoleculeName: 50S ribosomal protein L33 / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 6.388631 KDa
SequenceString:
MAKGIREKIK LVSSAGTGHF YTTTKNKRTK PEKLELKKFD PVVRQHVIYK EAKIK

+
Macromolecule #31: 50S ribosomal protein L34

MacromoleculeName: 50S ribosomal protein L34 / type: protein_or_peptide / ID: 31 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 5.397463 KDa
SequenceString:
MKRTFQPSVL KRNRSHGFRA RMATKNGRQV LARRRAKGRA RLTVSK

+
Macromolecule #32: 50S ribosomal protein L35

MacromoleculeName: 50S ribosomal protein L35 / type: protein_or_peptide / ID: 32 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 7.313032 KDa
SequenceString:
MPKIKTVRGA AKRFKKTGKG GFKHKHANLR HILTKKATKR KRHLRPKAMV SKGDLGLVIA CLPYA

+
Macromolecule #33: 50S ribosomal protein L36

MacromoleculeName: 50S ribosomal protein L36 / type: protein_or_peptide / ID: 33 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 6.315641 KDa
SequenceString:
MKVRASVKKL CRNCKIVKRD GVIRVICSAE PKHKQRQGCI FSSYFSCKVG LSWLD

+
Macromolecule #35: 50S ribosomal protein L31

MacromoleculeName: 50S ribosomal protein L31 / type: protein_or_peptide / ID: 35 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 7.917143 KDa
SequenceString:
MKKDIHPKYE EITASCSCGN VMKIRSTVGH DLNLDVCSKC HPFFTGKQRD VATGGRVDRF NKRFNIPSSK

+
Macromolecule #36: 50S ribosomal protein L1

MacromoleculeName: 50S ribosomal protein L1 / type: protein_or_peptide / ID: 36 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 23.735498 KDa
SequenceString: KLTKRMRVIR EKVDATKQYD INEAIALLKE LATAKFVESV DVAVNLGIDA RKSDQNVRGA TVLPHGTGRS VRVAVFTQGA NAEAAKAAG AELVGMEDLA DQIKKGEMNF DVVIASPDAM RVVGQLGQVL GPRGLMPNPK VGTVTPNVAE AVKNAKAGQV R YRNDKNGI ...String:
KLTKRMRVIR EKVDATKQYD INEAIALLKE LATAKFVESV DVAVNLGIDA RKSDQNVRGA TVLPHGTGRS VRVAVFTQGA NAEAAKAAG AELVGMEDLA DQIKKGEMNF DVVIASPDAM RVVGQLGQVL GPRGLMPNPK VGTVTPNVAE AVKNAKAGQV R YRNDKNGI IHTTIGKVDF DADKLKENLE ALLVALKKAK PTQAKGVYIK KVSISTTMGA GVAVD

+
Macromolecule #38: 30S ribosomal protein S2

MacromoleculeName: 30S ribosomal protein S2 / type: protein_or_peptide / ID: 38 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 26.581479 KDa
SequenceString: MATVSMRDML KAGVHFGHQT RYWNPKMKPF IFGARNKVHI INLEKTVPMF NEALAELNKI ASRKGKILFV GTKRAASEAV KDAALSCDQ FFVNHRWLGG MLTNWKTVRQ SIKRLKDLET QSQDGTFDKL TKKEALMRTR ELEKLENSLG GIKDMGGLPD A LFVIDADH ...String:
MATVSMRDML KAGVHFGHQT RYWNPKMKPF IFGARNKVHI INLEKTVPMF NEALAELNKI ASRKGKILFV GTKRAASEAV KDAALSCDQ FFVNHRWLGG MLTNWKTVRQ SIKRLKDLET QSQDGTFDKL TKKEALMRTR ELEKLENSLG GIKDMGGLPD A LFVIDADH EHIAIKEANN LGIPVFAIVD TNSDPDGVDF VIPGNDDAIR AVTLYLGAVA ATVREGRSQD LASQAEESFV E

+
Macromolecule #39: 30S ribosomal protein S3

MacromoleculeName: 30S ribosomal protein S3 / type: protein_or_peptide / ID: 39 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 24.293199 KDa
SequenceString: MGQKVHPNGI RLGIVKPWNS TWFANTKEFA DNLDSDFKVR QYLTKELAKA SVSRIVIERP AKSIRVTIHT ARPGIVIGKK GEDVEKLRK VVADIAGVPA QINIAEVRKP ELDAKLVADS ITSQLERRVM FRRAMKRAVQ NAMRLGAKGI KVEVSGRLGG A EIARTEWY ...String:
MGQKVHPNGI RLGIVKPWNS TWFANTKEFA DNLDSDFKVR QYLTKELAKA SVSRIVIERP AKSIRVTIHT ARPGIVIGKK GEDVEKLRK VVADIAGVPA QINIAEVRKP ELDAKLVADS ITSQLERRVM FRRAMKRAVQ NAMRLGAKGI KVEVSGRLGG A EIARTEWY REGRVPLHTL RADIDYNTSE AHTTYGVIGV KVWIFKGEIL GGMAAVEQPE

+
Macromolecule #40: 30S ribosomal protein S4

MacromoleculeName: 30S ribosomal protein S4 / type: protein_or_peptide / ID: 40 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 23.514199 KDa
SequenceString: MARYLGPKLK LSRREGTDLF LKSGVRAIDT KCKIEQAPGQ HGARKPRLSD YGVQLREKQK VRRIYGVLER QFRNYYKEAA RLKGNTGEN LLALLEGRLD NVVYRMGFGA TRAEARQLVS HKAIMVNGRV VNIASYQVSP NDVVSIREKA KKQSRVKAAL E LAEQREKP ...String:
MARYLGPKLK LSRREGTDLF LKSGVRAIDT KCKIEQAPGQ HGARKPRLSD YGVQLREKQK VRRIYGVLER QFRNYYKEAA RLKGNTGEN LLALLEGRLD NVVYRMGFGA TRAEARQLVS HKAIMVNGRV VNIASYQVSP NDVVSIREKA KKQSRVKAAL E LAEQREKP TWLEVDAGKM EGTFKRKPER SDLSADINEH LIVELYSK

+
Macromolecule #41: 30S ribosomal protein S5

MacromoleculeName: 30S ribosomal protein S5 / type: protein_or_peptide / ID: 41 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 17.120785 KDa
SequenceString:
MEKQAGELQE KLIAVNRVSK TVKGGRIFSF TALTVVGDGN GRVGFGYGKA REVPAAIQKA MEKARRNMIN VALNNGTLQH PVKGVHTGS RVFMQPASEG TGIIAGGAMR AVLEVAGVHN VLAKAYGSTN PINVVRATID GLENMNSPEM VAAKRGKSVE E IL

+
Macromolecule #42: 30S ribosomal protein S6, non-modified isoform

MacromoleculeName: 30S ribosomal protein S6, non-modified isoform / type: protein_or_peptide / ID: 42 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 15.201021 KDa
SequenceString:
MRHYEIVFMV HPDQSEQVPG MIERYTAAIT GAEGKIHRLE DWGRRQLAYP INKLHKAHYV LMNVEAPQEV IDELETTFRF NDAVIRSMV MRTKHAVTEA SSMVKAKDER RERRDDFANE TADDAEAGDS EE

+
Macromolecule #43: 30S ribosomal protein S7

MacromoleculeName: 30S ribosomal protein S7 / type: protein_or_peptide / ID: 43 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 17.618398 KDa
SequenceString:
MPRRRVIGQR KILPDPKFGS ELLAKFVNIL MVDGKKSTAE SIVYSALETL AQRSGKSELE AFEVALENVR PTVEVKSHRV GGSTYQVPV EVRPVRRNAL AMRWIVEAAR KRGDKSMALR LANELSDAAE NKGTAVKKRE DVHRMAEANK AFAHYRW

+
Macromolecule #44: 30S ribosomal protein S8

MacromoleculeName: 30S ribosomal protein S8 / type: protein_or_peptide / ID: 44 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 14.146557 KDa
SequenceString:
MSMQDPIADM LTRIRNGQAA NKAAVTMPSS KLKVAIANVL KEEGFIEDFK VEGDTKPELE LTLKYFQGKA VVESIQRVSR PGLRIYKRK DELPKVMAGL GIAVVSTSKG VMTDRAARQA GLGGEIICYV A

+
Macromolecule #45: 30S ribosomal protein S9

MacromoleculeName: 30S ribosomal protein S9 / type: protein_or_peptide / ID: 45 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 14.872244 KDa
SequenceString:
MADNQYYGTG RRKSSAARVF IKPGNGKIVI NQRSLEQYFG RETARMVVRQ PLELVDMVEK LDLYITVKGG GISGQAGAIR HGITRALME YDESLRSELR KAGFVTRDAR QVERKKVGLR KARRRPQFSK R

+
Macromolecule #46: 30S ribosomal protein S10

MacromoleculeName: 30S ribosomal protein S10 / type: protein_or_peptide / ID: 46 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 11.755597 KDa
SequenceString:
MQNQRIRIRL KAFDHRLIDQ ATAEIVETAK RTGAQVRGPI PLPTRKERFT VLISPHVNKD ARDQYEIRTH LRLVDIVEPT EKTVDALMR LDLAAGVDVQ ISLG

+
Macromolecule #47: 30S ribosomal protein S11

MacromoleculeName: 30S ribosomal protein S11 / type: protein_or_peptide / ID: 47 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 13.844938 KDa
SequenceString:
MAKAAIRARK RVRKQVSDGV AHIHASFNNT IVTITDRQGN ALGWATAGGS GFRGSRKSTP FAAQVAAERC ADAVKEYGIK NLEVMVKGP GPGRESTIRA LNAAGFRITN ITDVTPIPHN GCRPPKKRRV

+
Macromolecule #48: 30S ribosomal protein S12

MacromoleculeName: 30S ribosomal protein S12 / type: protein_or_peptide / ID: 48 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 13.768157 KDa
SequenceString:
MATVNQLVRK PRARKVAKSN VPALEACPQK RGVCTRVYTT TPKKPNSALR KVCRVRLTNG FEVTSYIGGE GHNLQEHSVI LIRGGRVKD LPGVRYHTVR GALDCSGVKD RKQARSKYGV KRPKA

+
Macromolecule #49: 30S ribosomal protein S13

MacromoleculeName: 30S ribosomal protein S13 / type: protein_or_peptide / ID: 49 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 13.096402 KDa
SequenceString:
VARIAGINIP DHKHAVIALT SIYGVGKTRS KAILAAAGIA EDVKISELSE GQIDTLRDEV AKFVVEGDLR REISMSIKRL MDLGCYRGL RHRRGLPVRG QRTKTNARTR KGPRKPIKK

+
Macromolecule #50: 30S ribosomal protein S14

MacromoleculeName: 30S ribosomal protein S14 / type: protein_or_peptide / ID: 50 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 11.56255 KDa
SequenceString:
MAKQSMKARE VKRVALADKY FAKRAELKAI ISDVNASDEA RWNAVLKLQT LPRDSSPSRQ RNRCRQTGRP HGFLRKFGLS RIKVREAAM RGEIPGLKKA SW

+
Macromolecule #51: 30S ribosomal protein S15

MacromoleculeName: 30S ribosomal protein S15 / type: protein_or_peptide / ID: 51 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 10.290816 KDa
SequenceString:
MSLSTEATAK IVSEFGRDAN DTGSTEVQVA LLTAQINHLQ GHFAEHKKDH HSRRGLLRMV SQRRKLLDYL KRKDVARYTQ LIERLGLRR

+
Macromolecule #52: 30S ribosomal protein S16

MacromoleculeName: 30S ribosomal protein S16 / type: protein_or_peptide / ID: 52 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 9.207572 KDa
SequenceString:
MVTIRLARHG AKKRPFYQVV VADSRNARNG RFIERVGFFN PIASEKEEGT RLDLDRIAHW VGQGATISDR VAALIKEVNK AA

+
Macromolecule #53: 30S ribosomal protein S17

MacromoleculeName: 30S ribosomal protein S17 / type: protein_or_peptide / ID: 53 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 9.694465 KDa
SequenceString:
MADKIRTLQG RVVSDKMEKS IVVAIERFVK HPIYGKFIKR TTKLHVHDEN NECGIGDVVE IRECRPLSKT KSWTLVRVVE KAVL

+
Macromolecule #54: 30S ribosomal protein S18

MacromoleculeName: 30S ribosomal protein S18 / type: protein_or_peptide / ID: 54 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 9.0065 KDa
SequenceString:
MARYFRRRKF CRFTTEGVVE IDYKDIATLK NYITESGKIV PSRITGTRAK YQRQLARAIK RARYLSLLPY TDRHQ

+
Macromolecule #55: 30S ribosomal protein S19

MacromoleculeName: 30S ribosomal protein S19 / type: protein_or_peptide / ID: 55 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 10.586505 KDa
SequenceString:
MPRSLKKGPF IDLHLLKKVE KAVESGDKKP LRTWSRRSTI FPNMIGLTIA VHNGRQHVPV FVTDEMVGHK LGEFAPTRTY RYYAADKKA KKK

+
Macromolecule #56: 30S ribosomal protein S20

MacromoleculeName: 30S ribosomal protein S20 / type: protein_or_peptide / ID: 56 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 9.690425 KDa
SequenceString:
LANIKSAKKR AIQSEKARKH NASRRSMMRT FIKKVYAAIE AGDKAAAQKA FNEMQPIVDR QAAKGLIHKN KAARHKANLT AQINKLA

+
Macromolecule #57: 30S ribosomal protein S21

MacromoleculeName: 30S ribosomal protein S21 / type: protein_or_peptide / ID: 57 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 10.257935 KDa
SequenceString:
MPVIKVRENE PFDVALRRFK RSCEKAGVLA EVRRREFYEK PTTERKRAKA SAVKRHAKNT RRNWLAKTHA ALVCTNSPRA LLSDQTEL

+
Macromolecule #58: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 58 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #59: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 59 / Number of copies: 1 / Formula: K
Molecular weightTheoretical: 39.098 Da

+
Macromolecule #60: water

MacromoleculeName: water / type: ligand / ID: 60 / Number of copies: 9 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5nwy

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 75081

+
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