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- EMDB-8597: 70S ribosome complex with dnaX mRNA stem-loop and E-site tRNA ("o... -

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Basic information

Entry
Database: EMDB / ID: 8597
Title70S ribosome complex with dnaX mRNA stem-loop and E-site tRNA ("out" conformation)
Map data70S ribosome complex with dnaX mRNA stem-loop and E-site tRNA ("out" conformation)
Sample70S-dnaX complex:
(nucleic-acidNucleic acid) x 6 / (50S ribosomal protein ...) x 30 / (30S ribosomal protein ...) x 20 / (ligand) x 2
Function / homologyRibosomal protein S8 superfamily / Ribosomal protein S18 superfamily / RNA-binding S4 domain superfamily / Ribosomal protein S11 superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L14 superfamily / Ribosomal protein L35 superfamily ...Ribosomal protein S8 superfamily / Ribosomal protein S18 superfamily / RNA-binding S4 domain superfamily / Ribosomal protein S11 superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L14 superfamily / Ribosomal protein L35 superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein S20 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein L25, C-terminal / Ribosomal protein L33 superfamily / Ribosomal protein L17 superfamily / Ribosomal protein L14p/L23e / Ribosomal protein S15 / Ribosomal protein L3 / Ribosomal protein L5 / Ribosomal protein L23 / Ribosomal protein S14p/S29e / Ribosomal protein L16p/L10e / Ribosomal protein L22p/L17e / Ribosomal protein L19 superfamily / Ribosomal protein S19 / Ribosomal protein S3, C-terminal domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein S7p/S5e / Ribosomal protein S12/S23 / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein L22/L17 superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein L30p/L7e / Ribosomal protein L4 domain superfamily / Ribosomal protein S16 domain superfamily / Ribosomal protein S7 domain / Ribosomal protein L1-like / Ribosomal protein L1, conserved site / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein L13, conserved site / 30s ribosomal protein S13, C-terminal / Ribosomal protein S14, type Z / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L5 domain superfamily / Ribosomal protein S4/S9 / Ribosomal protein L2, conserved site / Ribosomal protein L2, C-terminal / Ribosomal protein L28/L24 / Ribosomal protein S10 domain / L21-like superfamily / 30S ribosomal protein Thx / Ribosomal protein L29/L35 superfamily / Ribosomal protein L20 signature. / Ribosomal protein S6 superfamily / Ribosomal protein L36 superfamily / Ribosomal protein L20, C-terminal / L28p-like / Ribosomal protein L5, N-terminal / Ribosomal protein L31 type A / Ribosomal protein L5, C-terminal / Ribosomal protein L15 / 30S ribosomal protein / Ribosomal protein L25 / Ribosomal protein L21-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein S2 / Ribosomal protein S5, N-terminal domain / Ribosomal protein L35 / Ribosomal protein S11 signature. / Ribosomal protein S9 signature. / Ribosomal protein L5 signature. / Ribosomal protein S19 signature. / Ribosomal protein S18 signature. / Ribosomal protein S17 signature. / Ribosomal protein S12 signature. / Ribosomal protein S8 signature. / Ribosomal protein S15 signature. / Ribosomal protein S7 signature. / Ribosomal protein L14 signature. / Ribosomal proteins 50S L24/mitochondrial 39S L24 / 30S ribosomal protein Thx / Ribosomal protein TL5, C-terminal domain / KH domain / Ribosomal protein S10 signature. / Ribosomal protein L22 signature. / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein S4 signature. / Ribosomal protein L36 signature. / Ribosomal protein L34 signature. / Ribosomal protein L13 signature. / Ribosomal protein L9 signature. / Ribosomal protein S13 signature. / Ribosomal protein L30 signature. / Ribosomal protein S5 signature. / Ribosomal protein L2 signature.
Function and homology information
SourceThermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) / Escherichia coli K-12 (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / 3.2 Å resolution
AuthorsZhang Y / Hong S / Skiniotis G / Dunham CM
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.
Validation ReportPDB-ID: 5uq8

SummaryFull reportAbout validation report
DateDeposition: Feb 7, 2017 / Header (metadata) release: Mar 7, 2018 / Map release: Mar 7, 2018 / Last update: Mar 21, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5uq8
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8597.map.gz (map file in CCP4 format, 226493 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
384 pix
1 Å/pix.
= 384. Å
384 pix
1 Å/pix.
= 384. Å
384 pix
1 Å/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
Contour Level:0.03 (by author), 0.03 (movie #1):
Minimum - Maximum-0.07980959 - 0.15008026
Average (Standard dev.)-0.00011700496 (0.008379911)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions384384384
Origin0.00.00.0
Limit383.0383.0383.0
Spacing384384384
CellA=B=C: 384.0 Å
α=β=γ: 90.0 deg.

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-0.0800.150-0.000

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Supplemental data

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Sample components

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Entire 70S-dnaX complex

EntireName: 70S-dnaX complex / Number of components: 59

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Component #1: protein, 70S-dnaX complex

ProteinName: 70S-dnaX complex / Recombinant expression: No
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

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Component #2: nucleic-acid, 23S rRNA

Nucleic-acidName: 23S rRNA23S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GUCAAGAUGG UAAGGGCCCA CGGUGGAUGC CUCGGCACCC GAGCCGAUGA AGGACGUGGC UACCUGCGAU AAGCCAGGGG GAGCCGGUAG CGGGCGUGGA UCCCUGGAUG UCCGAAUGGG GGAACCCGGC CGGCGGGAAC GCCGGUCACC GCGCUUUUGC GCGGGGGGAA CCUGGGGAAC UGAAACAUCU CAGUACCCAG AGGAGAGGAA AGAGAAAUCG ACUCCCUGAG UAGCGGCGAG CGAAAGGGGA CCAGCCUAAA CCGUCCGGCU UGUCCGGGCG GGGUCGUGGG GCCCUCGGAC ACCGAAUCCC CAGCCUAGCC GAAGCUGUUG GGAAGCAGCG CCAGAGAGGG UGAAAGCCCC GUAGGCGAAA GGUGGGGGGA UAGGUGAGGG UACCCGAGUA CCCCGUGGUU CGUGGAGCCA UGGGGGAAUC UGGGCGGACC ACCGCCUAAG GCUAAGUACU CCGGGUGACC GAUAGCGCAC CAGUACCGUG AGGGAAAGGU GAAAAGAACC CCGGGAGGGG AGUGAAAUAG AGCCUGAAAC CGUGGGCUUA CAAGCAGUCA CGGCCCCGCA AGGGGUUGUG GCGUGCCUAU UGAAGCAUGA GCCGGCGACU CACGGUCGUG GGCGAGCUUA AGCCGUUGAG GCGGAGGCGU AGGGAAACCG AGUCCGAACA GGGCGCAAGC GGGCCGCACG CGGCCCGCAA AGUCCGCGGC CGUGGACCCG AAACCGGGCG AGCUAGCCCU GGCCAGGGUG AAGCUGGGGU GAGACCCAGU GGAGGCCCGA ACCGGUGGGG GAUGCAAACC CCUCGGAUGA GCUGGGGCUA GGAGUGAAAA GCUAACCGAG CCCGGAGAUA GCUGGUUCUC CCCGAAAUGA CUUUAGGGUC AGCCUCAGGC GCUGACUGGG GCCUGUAGAG CACUGAUAGG GCUAGGGGGC CCACCAGCCU ACCAAACCCU GUCAAACUCC GAAGGGUCCC AGGUGGAGCC UGGGAGUGAG GGCGCGAGCG AUAACGUCCG CGUCCGAGCG CGGGAACAAC CGAGACCGCC AGCUAAGGCC CCCAAGUCUG GGCUAAGUGG UAAAGGAUGU GGCGCCGCGA AGACAGCCAG GAGGUUGGCU UAGAAGCAGC CAUCCUUUAA AGAGUGCGUA AUAGCUCACU GGUCGAGUGG CGCCGCGCCG AAAAUGAUCG GGGCUUAAGC CCAGCGCCGA AGCUGCGGGU CUGGGGGAUG ACCCCAGGCG GUAGGGGAGC GUUCCCGAUG CCGAUGAAGG CCGACCCGCG AGGGCGGCUG GAGGUAAGGG AAGUGCGAAU GCCGGCAUGA GUAACGAUAA AGAGGGUGAG AAUCCCUCUC GCCGUAAGCC CAAGGGUUCC UACGCAAUGG UCGUCAGCGU AGGGUUAGGC GGGACCUAAG GUGAAGCCGA AAGGCGUAGC CGAAGGGCAG CCGGUUAAUA UUCCGGCCCU UCCCGCAGGU GCGAUGGGGG GACGCUCUAG GCUAGGGGGA CCGGAGCCAU GGACGAGCCC GGCCAGAAGC GCAGGGUGGG AGGUAGGCAA AUCCGCCUCC CAACAAGCUC UGCGUGGUGG GGAAGCCCGU ACGGGUGACA ACCCCCCGAA GCCAGGGAGC CAAGAAAAGC CUCUAAGCAC AACCUGCGGG AACCCGUACC GCAAACCGAC ACAGGUGGGC GGGUGCAAGA GCACUCAGGC GCGCGGGAGA ACCCUCGCCA AGGAACUCUG CAAGUUGGCC CCGUAACUUC GGGAGAAGGG GUGCUCCCUG GGGUGAUGAG CCCCGGGGAG CCGCAGUGAA CAGGCUCUGG CGACUGUUUA CCAAAAACAC AGCUCUCUGC GAACUCGUAA GAGGAGGUAU AGGGAGCGAC GCUUGCCCGG UGCCGGAAGG UCAAGGGGAG GGGUGCAAGC CCCGAACCGA AGCCCCGGUG AACGGCGGCC G(PSU)AAC(5MU)A(PSU)AA (4OC)GGUCCUAAG GUAGCGAAA(5MU) UC(5MC)UUGUCGG GUAAGUUCCG AC(5MC)UGCACGA AAAGCGUAAC GACCGGAGCG CUGUCUCGGC GAGGGACCCG GUGAAAUUGA ACUGGCCGUG AAGAUGCGGC CUACCCGUGG CAGGACGAAA AGACCCCGUG GAGCUUUACU GCAGCCUGGU GUUGGCUCUU GGUCGCGCCU GCGUAGGAUA GGUGGGAGCC UGUGAACCCC CGCCUCCGGG UGGGGGGGAG GCGCCGGUGA AAUACCACCC UGGCGCGGCU GGGGGCCUAA CCCUCGGAUG GGGGGACAGC GCUUGGCGGG CAGUUUGACU G(OMG)GGCGGUCG CCUCCUAAAA GGUAACGGAG GCGCCCAAAG GUCCCCUCAG GCGGGACGGA AAUCCGCCGG AGAGCGCAAG GGUAGAAGGG GGCCUGACUG CGAGGCCUGC AAGCCGAGCA GGGGCGAAAG CCGGGCCUAG UGAACCGGUG GUCCCGUGUG GAAGGGCCAU CGAUCAACGG AUAAAAGUUA CCCCGGGGAU AACAGGCUGA UCUCCCCCGA GCGUCCACAG CGGCGGGGAG GUUUGGCACC UCG(2MA)UGUCGG CUCGUCGCAU CCUGGGGCUG AAGAAGGUCC CAAGGGUUGG GC(2MU)GUUCGCC CAUUAAAGCG GCACGCGAGC UGGGUUCAGA ACGUCGUGAG ACAGU(PSU)CGGU CUCUAUCCGC CACGGGCGCA GGAGGCUUGA GGGGGGCUCU UCCUAGUACG AGAGGACCGG AAGGGACGCA CCUCUGGUUU CCCAGCUGUC CCUCCAGGGG CAUAAGCUGG GUAGCCAUGU GCGGAAGGGA UAACCGCUGA AAGCAUCUAA GCGGGAAGCC CGCCCCAAGA UGAGGCCUCC CACGGCGUCA AGCCGGUAAG GACCCGGGAA GACCACCCGG UGGAUGGGCC GGGGGUGUAA GCGCCGCGAG GCGUUGAGCC GACCGGUCCC AAUCGUCCGA GGUCUUGACC CCUCC
MassTheoretical: 948.035625 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #3: nucleic-acid, 5S rRNA

Nucleic-acidName: 5S rRNA5S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UCCCCCGUGC CCAUAGCGGC GUGGAACCAC CCGUUCCCAU UCCGAACACG GAAGUGAAAC GCGCCAGCGC CGAUGGUACU GGGCGGGCGA CCGCCUGGGA GAGUAGGUCG GUGCGGGGGA
MassTheoretical: 38.882207 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #4: protein, 50S ribosomal protein L2

ProteinName: 50S ribosomal protein L2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.401355 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #5: protein, 50S ribosomal protein L3

ProteinName: 50S ribosomal protein L3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.249953 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #6: protein, 50S ribosomal protein L4

ProteinName: 50S ribosomal protein L4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.512023 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #7: protein, 50S ribosomal protein L5

ProteinName: 50S ribosomal protein L5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.9304 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #8: protein, 50S ribosomal protein L6

ProteinName: 50S ribosomal protein L6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.893082 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #9: protein, 50S ribosomal protein L9

ProteinName: 50S ribosomal protein L9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.164937 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #10: protein, 50S ribosomal protein L13

ProteinName: 50S ribosomal protein L13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.927903 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #11: protein, 50S ribosomal protein L14

ProteinName: 50S ribosomal protein L14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.323612 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #12: protein, 50S ribosomal protein L15

ProteinName: 50S ribosomal protein L15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.248062 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #13: protein, 50S ribosomal protein L16

ProteinName: 50S ribosomal protein L16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.993909 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #14: protein, 50S ribosomal protein L17

ProteinName: 50S ribosomal protein L17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.750148 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #15: protein, 50S ribosomal protein L18

ProteinName: 50S ribosomal protein L18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.43757 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #16: protein, 50S ribosomal protein L19

ProteinName: 50S ribosomal protein L19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.503017 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #17: protein, 50S ribosomal protein L20

ProteinName: 50S ribosomal protein L20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.591028 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #18: protein, 50S ribosomal protein L21

ProteinName: 50S ribosomal protein L21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.069153 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #19: protein, 50S ribosomal protein L22

ProteinName: 50S ribosomal protein L22 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.678874 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #20: protein, 50S ribosomal protein L23

ProteinName: 50S ribosomal protein L23 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.64665 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #21: protein, 50S ribosomal protein L24

ProteinName: 50S ribosomal protein L24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.72628 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #22: protein, 50S ribosomal protein L25

ProteinName: 50S ribosomal protein L25 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.139299 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #23: protein, 50S ribosomal protein L27

ProteinName: 50S ribosomal protein L27 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.689006 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #24: protein, 50S ribosomal protein L28

ProteinName: 50S ribosomal protein L28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.872965 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #25: protein, 50S ribosomal protein L29

ProteinName: 50S ribosomal protein L29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.485077 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #26: protein, 50S ribosomal protein L30

ProteinName: 50S ribosomal protein L30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.667931 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #27: protein, 50S ribosomal protein L31

ProteinName: 50S ribosomal protein L31 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.086297 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #28: protein, 50S ribosomal protein L32

ProteinName: 50S ribosomal protein L32 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.590854 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #29: protein, 50S ribosomal protein L33

ProteinName: 50S ribosomal protein L33 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.5017 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #30: protein, 50S ribosomal protein L34

ProteinName: 50S ribosomal protein L34 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.975255 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #31: protein, 50S ribosomal protein L35

ProteinName: 50S ribosomal protein L35 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.374981 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #32: protein, 50S ribosomal protein L36

ProteinName: 50S ribosomal protein L36 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 4.435411 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #33: nucleic-acid, 16S rRNA

Nucleic-acidName: 16S rRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UUGUUGGAGA GUUUGAUCCU GGCUCAGGGU GAACGCUGGC GGCGUGCCUA AGACAUGCAA GUCGUGCGGG CCGCGGGGUU UUACUCCGUG GUCAGCGGCG GACGGGUGAG UAACGCGUGG GUGACCUACC CGGAAGAGGG GGACAACCCG GGGAAACUCG GGCUAAUCCC CCAUGUGGAC CCGCCCCUUG GGGUGUGUCC AAAGGGCUUU GCCCGCUUCC GGAUGGGCCC GCGUCCCAUC AGCUAGUUGG UGGGGUAAUG GCCCACCAAG GCGACGACGG GUAGCCGGUC UGAGAGGAUG GCCGGCCACA GGGGCACUGA GACACGGGCC CCACUCCUAC GGGAGGCAGC AGUUAGGAAU CUUCCGCAAU GGGCGCAAGC CUGACGGAGC GACGCCGCUU GGAGGAAGAA GCCCUUCGGG GUGUAAACUC CUGAACCCGG GACGAAACCC CCGACGAGGG GACUGACGGU ACCGGGGUAA UAGCGCCGGC CAACUCCG(PSU)G CCAGCAGCC(7MG) CGGUAAUACG GAGGGCGCGA GCGUUACCCG GAUUCACUGG GCGUAAAGGG CGUGUAGGCG GCCUGGGGCG UCCCAUGUGA AAGACCACGG CUCAACCGUG GGGGAGCGUG GGAUACGCUC AGGCUAGACG GUGGGAGAGG GUGGUGGAAU UCCCGGAGUA GCGGUGAAAU GCGCAGAUAC CGGGAGGAAC GCCGAUGGCG AAGGCAGCCA CCUGGUCCAC CCGUGACGCU GAGGCGCGAA AGCGUGGGGA GCAAACCGGA UUAGAUACCC GGGUAGUCCA CGCCCUAAAC GAUGCGCGCU AGGUCUCUGG GUCUCCUGGG GGCCGAAGCU AACGCGUUAA GCGCGCCGCC UGGGGAGUAC GGCCGCAAGG CUGAAACUCA AAGGAAUUGA CGGGGGCCCG CACAAGCGGU GGAGCAUGUG GUUUAAUUCG AA(M2G)(5MC)AACGCG AAGAACCUUA CCAGGCCUUG ACAUGCUAGG GAACCCGGGU GAAAGCCUGG GGUGCCCCGC GAGGGGAGCC CUAGCACAGG UGCUGCAUGG CCGUCGUCAG CUCGUGCCGU GAGGUGUUGG GUUAAGUCCC GCAACGAGCG CAACCCCCGC CGUUAGUUGC CAGCGGUUCG GCCGGGCACU CUAACGGGAC UGCCCGCGAA AGCGGGAGGA AGGAGGGGAC GACGUCUGGU CAGCAUG(2MG)CC CUUACGGCCU GGGCGACACA CGUGCUACAA UGCCCACUAC AAAGCGAUGC CACCCGGCAA CGGGGAGCUA AUCGCAAAAA GGUGGGCCCA GUUCGGAUUG GGGUCUGCAA CCCGACCCCA UGAAGCCGGA AUCGCUAGUA AUCGCGGAUC AGCCAUGCCG CGGUGAAUAC GUUCCCGGGC CUUGUACACA C(5MC)G(4OC)C(5MC)GU(5MC)A CGCCAUGGGA GCGGGCUCUA CCCGAAGUCG CCGGGAGCCU ACGGGCAGGC GCCGAGGGUA GGGCCCGUGA CUGGGGCGAA GUCG(UR3)AACAA GGUAGCUGUA CCGG(MA6)(MA6)GGUG CGGCUGGAUC ACCUCCUUGC U
MassTheoretical: 493.903656 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #34: protein, 30S ribosomal protein S2

ProteinName: 30S ribosomal protein S2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.646852 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #35: protein, 30S ribosomal protein S3

ProteinName: 30S ribosomal protein S3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.86243 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

+
Component #36: protein, 30S ribosomal protein S4

ProteinName: 30S ribosomal protein S4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.242254 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

+
Component #37: protein, 30S ribosomal protein S5

ProteinName: 30S ribosomal protein S5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.144848 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

+
Component #38: protein, 30S ribosomal protein S6

ProteinName: 30S ribosomal protein S6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.917675 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

+
Component #39: protein, 30S ribosomal protein S7

ProteinName: 30S ribosomal protein S7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.919775 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

+
Component #40: protein, 30S ribosomal protein S8

ProteinName: 30S ribosomal protein S8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.737372 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

+
Component #41: protein, 30S ribosomal protein S9

ProteinName: 30S ribosomal protein S9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.122225 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

+
Component #42: protein, 30S ribosomal protein S10

ProteinName: 30S ribosomal protein S10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.056838 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

+
Component #43: protein, 30S ribosomal protein S11

ProteinName: 30S ribosomal protein S11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.032662 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

+
Component #44: protein, 30S ribosomal protein S12

ProteinName: 30S ribosomal protein S12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.650211 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

+
Component #45: protein, 30S ribosomal protein S13

ProteinName: 30S ribosomal protein S13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.067221 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

+
Component #46: protein, 30S ribosomal protein S14 type Z

ProteinName: 30S ribosomal protein S14 type ZRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.027529 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

+
Component #47: protein, 30S ribosomal protein S15

ProteinName: 30S ribosomal protein S15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.447213 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

+
Component #48: protein, 30S ribosomal protein S16

ProteinName: 30S ribosomal protein S16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.795354 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

+
Component #49: protein, 30S ribosomal protein S17

ProteinName: 30S ribosomal protein S17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.722904 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

+
Component #50: protein, 30S ribosomal protein S18

ProteinName: 30S ribosomal protein S18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.897451 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

+
Component #51: protein, 30S ribosomal protein S19

ProteinName: 30S ribosomal protein S19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.455995 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

+
Component #52: protein, 30S ribosomal protein S20

ProteinName: 30S ribosomal protein S20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.876067 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

+
Component #53: protein, 30S ribosomal protein Thx

ProteinName: 30S ribosomal protein ThxRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.831295 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

+
Component #54: nucleic-acid, P-site tRNA fMet

Nucleic-acidName: P-site tRNA fMet / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
CGCGGGGUGG AGCAGCCCGG UAGCUCGUCG GGCUCAUAAC CCGAAGGUCG UCGGUUCAAA UCCGGCCCCC GCAACCA
MassTheoretical: 24.801801 kDa
SourceSpecies: Escherichia coli K-12 (bacteria) / Strain: K-12

+
Component #55: protein, 50S ribosomal protein L1

ProteinName: 50S ribosomal protein L1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.513211 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

+
Component #56: nucleic-acid, E-site tRNA Phe

Nucleic-acidName: E-site tRNA Phe / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GCCCGGAUAG CUCAGUCGGU AGAGCAGGGG AUUGAAAAUC CCCGUGUCCU UGGUUCGAUU CCGAGUCCGG GCACCA
MassTheoretical: 24.485539 kDa
SourceSpecies: Escherichia coli K-12 (bacteria) / Strain: K-12

+
Component #57: nucleic-acid, messenger RNA

Nucleic-acidName: messenger RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UAAGGAAAUA AAAAUGUUUA GUGAACCGGC AGCCGCUACC CGCGCGCGGC CGGUA
MassTheoretical: 17.773668 kDa
SourceSpecies: synthetic construct (others)

+
Component #58: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

+
Component #59: ligand, IRON/SULFUR CLUSTER

LigandName: IRON/SULFUR CLUSTERIron–sulfur cluster / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.35164 kDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 3 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 36361
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL
Output model

+
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