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- EMDB-4475: Structure of tmRNA SmpB bound in A site of T. thermophilus 70S ri... -

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Basic information

Entry
Database: EMDB / ID: 4475
TitleStructure of tmRNA SmpB bound in A site of T. thermophilus 70S ribosome
Map data
Sample70S ribosome bound by tmRNA-SmpB in the A site:
(nucleic-acidNucleic acid) x 7 / (30S ribosomal protein ...) x 20 / (50S ribosomal protein ...) x 31 / SsrA-binding protein / Nascent peptide MET-ALA / (ligand) x 2
Function / homologyRibosomal protein L20, C-terminal / Ribosomal protein L14 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 S18 superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein L25, C-terminal ...Ribosomal protein L20, C-terminal / Ribosomal protein L14 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 S18 superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein L25, C-terminal / 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 L22/L17 superfamily / RNA-binding S4 domain superfamily / Ribosomal protein L35 superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein L22p/L17e / Ribosomal protein L3 / Ribosomal protein L5 / Ribosomal protein L23 / Ribosomal protein S14p/S29e / Ribosomal protein L16p/L10e / Ribosomal protein L14p/L23e / Ribosomal protein S19 / Ribosomal protein L33 superfamily / 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 L19 superfamily / Ribosomal protein L17 superfamily / L21-like superfamily / Ribosomal protein S2 / Ribosomal protein L13, conserved site / Ribosomal protein L1-like / Ribosomal protein L1, conserved site / Small protein B / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein L4 domain superfamily / Ribosomal protein S14, type Z / Ribosomal protein S16 domain superfamily / 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 Proteins L2, RNA binding domain / Ribosomal protein S7 domain / Ribosomal protein L28/L24 / Ribosomal protein L29/L35 superfamily / Ribosomal protein L5, N-terminal / Ribosomal protein S8 superfamily / Ribosomal protein S6 superfamily / Ribosomal protein L36 superfamily / Ribosomal protein L20 signature. / L28p-like / 30S ribosomal protein Thx / Ribosomal protein L5, C-terminal / 30s ribosomal protein S13, C-terminal / Ribosomal protein L15 / 30S ribosomal protein / Ribosomal protein L25 / Ribosomal protein L21-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L31 type A / Ribosomal protein S10 domain / Ribosomal protein S15 / Ribosomal protein L30p/L7e / Ribosomal protein L18e/L15P / Ribosomal protein S8 signature. / Ribosomal protein L5 signature. / Ribosomal protein S19 signature. / Ribosomal protein S18 signature. / Ribosomal protein S17 signature. / Ribosomal protein S12 signature. / Ribosomal protein S11 signature. / Ribosomal protein S7 signature. / Ribosomal protein S10 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 L9, C-terminal domain / Ribosomal protein S9 signature. / Ribosomal protein S15 signature. / Ribosomal protein S5, 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.
Function and homology information
SourceThermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) / Escherichia coli (E. coli) / Thermus thermophilus HB27 (bacteria) / Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Methodsingle particle reconstruction / cryo EM / 3.7 Å resolution
AuthorsRae CD
CitationJournal: Science / Year: 2019
Title: How a circularized tmRNA moves through the ribosome.
Authors: Christopher D Rae / Yuliya Gordiyenko / V Ramakrishnan
Abstract: During trans-translation, transfer-messenger RNA (tmRNA) and small protein B (SmpB) together rescue ribosomes stalled on a truncated mRNA and tag the nascent polypeptide for degradation. We used ...During trans-translation, transfer-messenger RNA (tmRNA) and small protein B (SmpB) together rescue ribosomes stalled on a truncated mRNA and tag the nascent polypeptide for degradation. We used cryo-electron microscopy to determine the structures of three key states of the tmRNA-SmpB-ribosome complex during trans translation at resolutions of 3.7 to 4.4 angstroms. The results show how tmRNA and SmpB act specifically on stalled ribosomes and how the circularized complex moves through the ribosome, enabling translation to switch from the old defective message to the reading frame on tmRNA.
Validation ReportPDB-ID: 6q95

SummaryFull reportAbout validation report
DateDeposition: Dec 17, 2018 / Header (metadata) release: Feb 27, 2019 / Map release: Feb 27, 2019 / Last update: Feb 27, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6q95
  • Surface level: 0.05
  • 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_4475.map.gz (map file in CCP4 format, 186625 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
360 pix
1.34 Å/pix.
= 482.4 Å
360 pix
1.34 Å/pix.
= 482.4 Å
360 pix
1.34 Å/pix.
= 482.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density
Contour Level:0.05 (by author), 0.05 (movie #1):
Minimum - Maximum-0.20200269 - 0.4199737
Average (Standard dev.)0.0009820506 (0.01193797)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions360360360
Origin0.00.00.0
Limit359.0359.0359.0
Spacing360360360
CellA=B=C: 482.40002 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z482.400482.400482.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ364364364
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.2020.4200.001

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Supplemental data

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Sample components

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Entire 70S ribosome bound by tmRNA-SmpB in the A site

EntireName: 70S ribosome bound by tmRNA-SmpB in the A site / Number of components: 69

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Component #1: protein, 70S ribosome bound by tmRNA-SmpB in the A site

ProteinName: 70S ribosome bound by tmRNA-SmpB in the A site / Recombinant expression: No

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Component #2: protein, 70S ribosome bound by tmRNA-SmpB in the A site

ProteinName: 70S ribosome bound by tmRNA-SmpB in the A site / Recombinant expression: No
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, 70S ribosome bound by tmRNA-SmpB in the A site

ProteinName: 70S ribosome bound by tmRNA-SmpB in the A site / Recombinant expression: No
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: protein, 70S ribosome bound by tmRNA-SmpB in the A site

ProteinName: 70S ribosome bound by tmRNA-SmpB in the A site / Recombinant expression: No
SourceSpecies: Thermus thermophilus HB27 (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #5: protein, 70S ribosome bound by tmRNA-SmpB in the A site

ProteinName: 70S ribosome bound by tmRNA-SmpB in the A site / Recombinant expression: No
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

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Component #6: protein, 70S ribosome bound by tmRNA-SmpB in the A site

ProteinName: 70S ribosome bound by tmRNA-SmpB in the A site / Recombinant expression: No
SourceSpecies: Escherichia coli (E. coli)

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Component #7: protein, 70S ribosome bound by tmRNA-SmpB in the A site

ProteinName: 70S ribosome bound by tmRNA-SmpB in the A site / Recombinant expression: No
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: synthetic construct (others)

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Component #8: nucleic-acid, 16S RIBOSOMAL RNA

Nucleic-acidName: 16S RIBOSOMAL RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UUUGUUGGAG AGUUUGAUCC UGGCUCAGGG UGAACGCUGG CGGCGUGCCU AAGACAUGCA AGUCGUGCGG GCCGCGGGGU UUUACUCCGU GGUCAGCGGC GGACGGGUGA GUAACGCGUG GGUGACCUAC CCGGAAGAGG GGGACAACCC GGGGAAACUC GGGCUAAUCC CCCAUGUGGA CCCGCCCCUU GGGGUGUGUC CAAAGGGCUU UGCCCGCUUC CGGAUGGGCC CGCGUCCCAU CAGCUAGUUG GUGGGGUAAU GGCCCACCAA GGCGACGACG GGUAGCCGGU CUGAGAGGAU GGCCGGCCAC AGGGGCACUG AGACACGGGC CCCACUCCUA CGGGAGGCAG CAGUUAGGAA UCUUCCGCAA UGGGCGCAAG CCUGACGGAG CGACGCCGCU UGGAGGAAGA AGCCCUUCGG GGUGUAAACU CCUGAACCCG GGACGAAACC CCCGACGAGG GGACUGACGG UACCGGGGUA AUAGCGCCGG CCAACUCCGU GCCAGCAGCC GCGGUAAUAC GGAGGGCGCG AGCGUUACCC GGAUUCACUG GGCGUAAAGG GCGUGUAGGC GGCCUGGGGC GUCCCAUGUG AAAGACCACG GCUCAACCGU GGGGGAGCGU GGGAUACGCU CAGGCUAGAC GGUGGGAGAG GGUGGUGGAA UUCCCGGAGU AGCGGUGAAA UGCGCAGAUA CCGGGAGGAA CGCCGAUGGC GAAGGCAGCC ACCUGGUCCA CCCGUGACGC UGAGGCGCGA AAGCGUGGGG AGCAAACCGG AUUAGAUACC CGGGUAGUCC ACGCCCUAAA CGAUGCGCGC UAGGUCUCUG GGUCUCCUGG GGGCCGAAGC UAACGCGUUA AGCGCGCCGC CUGGGGAGUA CGGCCGCAAG GCUGAAACUC AAAGGAAUUG ACGGGGGCCC GCACAAGCGG UGGAGCAUGU GGUUUAAUUC GAAGCAACGC GAAGAACCUU ACCAGGCCUU GACAUGCUAG GGAACCCGGG UGAAAGCCUG GGGUGCCCCG CGAGGGGAGC CCUAGCACAG GUGCUGCAUG GCCGUCGUCA GCUCGUGCCG UGAGGUGUUG GGUUAAGUCC CGCAACGAGC GCAACCCCCG CCGUUAGUUG CCAGCGGUUC GGCCGGGCAC UCUAACGGGA CUGCCCGCGA AAGCGGGAGG AAGGAGGGGA CGACGUCUGG UCAGCAUGGC CCUUACGGCC UGGGCGACAC ACGUGCUACA AUGCCCACUA CAAAGCGAUG CCACCCGGCA ACGGGGAGCU AAUCGCAAAA AGGUGGGCCC AGUUCGGAUU GGGGUCUGCA ACCCGACCCC AUGAAGCCGG AAUCGCUAGU AAUCGCGGAU CAGCCAUGCC GCGGUGAAUA CGUUCCCGGG CCUUGUACAC ACCGCCCGUC ACGCCAUGGG AGCGGGCUCU ACCCGAAGUC GCCGGGAGCC UACGGGCAGG CGCCGAGGGU AGGGCCCGUG ACUGGGGCGA AGUCGUAACA AGGUAGCUGU ACCGGAAGGU GCGGCUGGAU CACCUCCUUU CU
MassTheoretical: 493.958281 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

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Component #9: protein, 30S ribosomal protein S2

ProteinName: 30S ribosomal protein S2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.116385 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

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Component #10: protein, 30S ribosomal protein S3

ProteinName: 30S ribosomal protein S3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.975588 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

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Component #11: 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)

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Component #12: protein, 30S ribosomal protein S5

ProteinName: 30S ribosomal protein S5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.460193 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

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Component #13: protein, 30S ribosomal protein S6

ProteinName: 30S ribosomal protein S6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.988753 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

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Component #14: 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)

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Component #15: protein, 30S ribosomal protein S8

ProteinName: 30S ribosomal protein S8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.86857 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

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Component #16: protein, 30S ribosomal protein S9

ProteinName: 30S ribosomal protein S9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.298466 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

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Component #17: protein, 30S ribosomal protein S10

ProteinName: 30S ribosomal protein S10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.398308 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

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Component #18: protein, 30S ribosomal protein S11

ProteinName: 30S ribosomal protein S11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.606369 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

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Component #19: protein, 30S ribosomal protein S12

ProteinName: 30S ribosomal protein S12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.875388 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

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Component #20: protein, 30S ribosomal protein S13

ProteinName: 30S ribosomal protein S13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.62392 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

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Component #21: 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)

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Component #22: 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)

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Component #23: protein, 30S ribosomal protein S16

ProteinName: 30S ribosomal protein S16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.995546 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

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Component #24: protein, 30S ribosomal protein S17

ProteinName: 30S ribosomal protein S17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.880098 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

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Component #25: protein, 30S ribosomal protein S18

ProteinName: 30S ribosomal protein S18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.155812 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

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Component #26: protein, 30S ribosomal protein S19

ProteinName: 30S ribosomal protein S19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.006486 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

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Component #27: protein, 30S ribosomal protein S20

ProteinName: 30S ribosomal protein S20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.921086 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

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Component #28: protein, 30S ribosomal protein Thx

ProteinName: 30S ribosomal protein ThxRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 3.089655 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

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Component #29: nucleic-acid, tRNA-fMet

Nucleic-acidName: tRNA-fMet / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
CGCGGGGUGG AGCAGCCUGG UAGCUCGUCG GGCUCAUAAC CCGAAGGUCG UCGG(5MU)UCAAA UCCGGCCCCC GCAACCA
MassTheoretical: 24.816811 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #30: nucleic-acid, tRNA-Phe

Nucleic-acidName: tRNA-Phe / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GCCCGGAUAG CUCAGUCGGU AGAGCAGGGG AUUUUUAAUC CCCGUGUCCU UGGUUCGAUU CCGAGUCCGG GCACCA
MassTheoretical: 24.400418 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #31: nucleic-acid, mRNA

Nucleic-acidName: mRNAMessenger RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UUCAUG
MassTheoretical: 1.853133 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #32: protein, 50S ribosomal protein L27

ProteinName: 50S ribosomal protein L27 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.529074 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

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Component #33: protein, 50S ribosomal protein L28

ProteinName: 50S ribosomal protein L28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.985846 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

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Component #34: protein, 50S ribosomal protein L29

ProteinName: 50S ribosomal protein L29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.112247 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

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Component #35: protein, 50S ribosomal protein L30

ProteinName: 50S ribosomal protein L30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.799126 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

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Component #36: protein, 50S ribosomal protein L31

ProteinName: 50S ribosomal protein L31 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.640646 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

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Component #37: 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)

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Component #38: protein, 50S ribosomal protein L33

ProteinName: 50S ribosomal protein L33 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.602612 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

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Component #39: protein, 50S ribosomal protein L34

ProteinName: 50S ribosomal protein L34 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.132449 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

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Component #40: 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)

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Component #41: nucleic-acid, 23S RIBOSOMAL RNA

Nucleic-acidName: 23S RIBOSOMAL RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GGUCAAGAUG GUAAGGGCCC ACGGUGGAUG CCUCGGCACC CGAGCCGAUG AAGGACGUGG CUACCUGCGA UAAGCCAGGG GGAGCCGGUA GCGGGCGUGG AUCCCUGGAU GUCCGAAUGG GGGAACCCGG CCGGCGGGAA CGCCGGUCAC CGCGCUUUUG CGCGGGGGGA ACCUGGGGAA CUGAAACAUC UCAGUACCCA GAGGAGAGGA AAGAGAAAUC GACUCCCUGA GUAGCGGCGA GCGAAAGGGG ACCAGCCUAA ACCGUCCGGC UUGUCCGGGC GGGGUCGUGG GGCCCUCGGA CACCGAAUCC CCAGCCUAGC CGAAGCUGUU GGGAAGCAGC GCCAGAGAGG GUGAAAGCCC CGUAGGCGAA AGGUGGGGGG AUAGGUGAGG GUACCCGAGU ACCCCGUGGU UCGUGGAGCC AUGGGGGAAU CUGGGCGGAC CACCGCCUAA GGCUAAGUAC UCCGGGUGAC CGAUAGCGCA CCAGUACCGU GAGGGAAAGG UGAAAAGAAC CCCGGGAGGG GAGUGAAAUA GAGCCUGAAA CCGUGGGCUU ACAAGCAGUC ACGGCCCCGC AAGGGGUUGU GGCGUGCCUA UUGAAGCAUG AGCCGGCGAC UCACGGUCGU GGGCGAGCUU AAGCCGUUGA GGCGGAGGCG UAGGGAAACC GAGUCCGAAC AGGGCGCAAG CGGGCCGCAC GCGGCCCGCA AAGUCCGCGG CCGUGGACCC GAAACCGGGC GAGCUAGCCC UGGCCAGGGU GAAGCUGGGG UGAGACCCAG UGGAGGCCCG AACCGGUGGG GGAUGCAAAC CCCUCGGAUG AGCUGGGGCU AGGAGUGAAA AGCUAACCGA GCCCGGAGAU AGCUGGUUCU CCCCGAAAUG ACUUUAGGGU CAGCCUCAGG CGCUGACUGG GGCCUGUAGA GCACUGAUAG GGCUAGGGGG CCCACCAGCC UACCAAACCC UGUCAAACUC CGAAGGGUCC CAGGUGGAGC CUGGGAGUGA GGGCGCGAGC GAUAACGUCC GCGUCCGAGC GCGGGAACAA CCGAGACCGC CAGCUAAGGC CCCCAAGUCU GGGCUAAGUG GUAAAGGAUG UGGCGCCGCG AAGACAGCCA GGAGGUUGGC UUAGAAGCAG CCAUCCUUUA AAGAGUGCGU AAUAGCUCAC UGGUCGAGUG GCGCCGCGCC GAAAAUGAUC GGGGCUUAAG CCCAGCGCCG AAGCUGCGGG UCUGGGGGAU GACCCCAGGC GGUAGGGGAG CGUUCCCGAU GCCGAUGAAG GCCGACCCGC GAGGGCGGCU GGAGGUAAGG GAAGUGCGAA UGCCGGCAUG AGUAACGAUA AAGAGGGUGA GAAUCCCUCU CGCCGUAAGC CCAAGGGUUC CUACGCAAUG GUCGUCAGCG UAGGGUUAGG CGGGACCUAA GGUGAAGCCG AAAGGCGUAG CCGAAGGGCA GCCGGUUAAU AUUCCGGCCC UUCCCGCAGG UGCGAUGGGG GGACGCUCUA GGCUAGGGGG ACCGGAGCCA UGGACGAGCC CGGCCAGAAG CGCAGGGUGG GAGGUAGGCA AAUCCGCCUC CCAACAAGCU CUGCGUGGUG GGGAAGCCCG UACGGGUGAC AACCCCCCGA AGCCAGGGAG CCAAGAAAAG CCUCUAAGCA CAACCUGCGG GAACCCGUAC CGCAAACCGA CACAGGUGGG CGGGUGCAAG AGCACUCAGG CGCGCGGGAG AACCCUCGCC AAGGAACUCU GCAAGUUGGC CCCGUAACUU CGGGAGAAGG GGUGCUCCCU GGGGUGAUGA GCCCCGGGGA GCCGCAGUGA ACAGGCUCUG GCGACUGUUU ACCAAAAACA CAGCUCUCUG CGAACUCGUA AGAGGAGGUA UAGGGAGCGA CGCUUGCCCG GUGCCGGAAG GUCAAGGGGA GGGGUGCAAG CCCCGAACCG AAGCCCCGGU GAACGGCGGC CGUAACUAUA ACGGUCCUAA GGUAGCGAAA UUCCUUGUCG GGUAAGUUCC GACCUGCACG AAAAGCGUAA CGACCGGAGC GCUGUCUCGG CGAGGGACCC GGUGAAAUUG AACUGGCCGU GAAGAUGCGG CCUACCCGUG GCAGGACGAA AAGACCCCGU GGAGCUUUAC UGCAGCCUGG UGUUGGCUCU UGGUCGCGCC UGCGUAGGAU AGGUGGGAGC CUGUGAACCC CCGCCUCCGG GUGGGGGGGA GGCGCCGGUG AAAUACCACC CUGGCGCGGC UGGGGGCCUA ACCCUCGGAU GGGGGGACAG CGCUUGGCGG GCAGUUUGAC UGGGGCGGUC GCCUCCUAAA AGGUAACGGA GGCGCCCAAA GGUCCCCUCA GGCGGGACGG AAAUCCGCCG GAGAGCGCAA GGGUAGAAGG GGGCCUGACU GCGAGGCCUG CAAGCCGAGC AGGGGCGAAA GCCGGGCCUA GUGAACCGGU GGUCCCGUGU GGAAGGGCCA UCGAUCAACG GAUAAAAGUU ACCCCGGGGA UAACAGGCUG AUCUCCCCCG AGCGUCCACA GCGGCGGGGA GGUUUGGCAC CUCGAUGUCG GCUCGUCGCA UCCUGGGGCU GAAGAAGGUC CCAAGGGUUG GGCUGUUCGC CCAUUAAAGC GGCACGCGAG CUGGGUUCAG AACGUCGUGA GACAGUUCGG UCUCUAUCCG CCACGGGCGC AGGAGGCUUG AGGGGGGCUC UUCCUAGUAC GAGAGGACCG GAAGGGACGC ACCUCUGGUU UCCCAGCUGU CCCUCCAGGG GCAUAAGCUG GGUAGCCAUG UGCGGAAGGG AUAACCGCUG AAAGCAUCUA AGCGGGAAGC CCGCCCCAAG AUGAGGCCUC CCACGGCGUC AAGCCGGUAA GGACCCGGGA AGACCACCCG GUGGAUGGGC CGGGGGUGUA AGCGCCGCGA GGCGUUGAGC CGACCGGUCC CAAUCGUCCG AGGUCUUGAC CCCUC
MassTheoretical: 947.935438 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

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Component #42: nucleic-acid, 5S RIBOSOMAL RNA

Nucleic-acidName: 5S RIBOSOMAL RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UCCCCCGUGC CCAUAGCGGC GUGGAACCAC CCGUUCCCAU UCCGAACACG GAAGUGAAAC GCGCCAGCGC CGAUGGUACU GGGCGGGCGA CCGCCUGGGA GAGUAGGUCG GUGCGGGGG
MassTheoretical: 38.553 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

+
Component #43: protein, 50S ribosomal protein L1

ProteinName: 50S ribosomal protein L1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.872721 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

+
Component #44: protein, 50S ribosomal protein L2

ProteinName: 50S ribosomal protein L2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.985799 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

+
Component #45: protein, 50S ribosomal protein L3

ProteinName: 50S ribosomal protein L3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.321031 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

+
Component #46: protein, 50S ribosomal protein L4

ProteinName: 50S ribosomal protein L4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.071721 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

+
Component #47: 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)

+
Component #48: protein, 50S ribosomal protein L6

ProteinName: 50S ribosomal protein L6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.476279 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

+
Component #49: protein, 50S ribosomal protein L9

ProteinName: 50S ribosomal protein L9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.536709 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

+
Component #50: protein, 50S ribosomal protein L13

ProteinName: 50S ribosomal protein L13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.828771 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

+
Component #51: 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)

+
Component #52: protein, 50S ribosomal protein L15

ProteinName: 50S ribosomal protein L15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.858526 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

+
Component #53: protein, 50S ribosomal protein L16

ProteinName: 50S ribosomal protein L16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.36405 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

+
Component #54: protein, 50S ribosomal protein L17

ProteinName: 50S ribosomal protein L17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.618952 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

+
Component #55: protein, 50S ribosomal protein L18

ProteinName: 50S ribosomal protein L18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.998918 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

+
Component #56: protein, 50S ribosomal protein L19

ProteinName: 50S ribosomal protein L19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.289891 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

+
Component #57: protein, 50S ribosomal protein L20

ProteinName: 50S ribosomal protein L20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.648081 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

+
Component #58: 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)

+
Component #59: protein, 50S ribosomal protein L22

ProteinName: 50S ribosomal protein L22 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.808055 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

+
Component #60: protein, 50S ribosomal protein L23

ProteinName: 50S ribosomal protein L23 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.386274 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

+
Component #61: protein, 50S ribosomal protein L24

ProteinName: 50S ribosomal protein L24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.181658 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

+
Component #62: protein, 50S ribosomal protein L25

ProteinName: 50S ribosomal protein L25 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.954641 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

+
Component #63: protein, SsrA-binding protein

ProteinName: SsrA-binding protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.78549 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #64: protein, Nascent peptide MET-ALA

ProteinName: Nascent peptide MET-ALA / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.220289 kDa
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #65: 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 HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #66: protein, 50S RIBOSOMAL PROTEIN L10 AND L11

ProteinName: 50S RIBOSOMAL PROTEIN L10 AND L11Ribosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 11.932701 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

+
Component #67: nucleic-acid, transfer-messenger RNA (tmRNA)

Nucleic-acidName: transfer-messenger RNA (tmRNA) / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GGGGGUGAAA CGGUCUCGAC GGGGGUCGCC GAGGGCGUGG CUGCGCGCCG AGGUGCGGGU GGCCUCGUAA AAACCCGCAA CGGCAUAACU GCCAACACCA ACUACGCUCU CGCGGCUUAA UGACCGCGAC CUCGCCCGGU AGCCCUGCCG GGGGCUCACC GGAAGCGGGG ACACAAACCC GGCUAGCCCG GGGCCACGCC CUCUAACCCC GGGCGAAGCU UGAAGGGGGC UCGCUCCUGG CCGCCCGUCC GCGGGCCAAG CCAGGAGGAC ACGCGAAACG CGGACUACGC GCGUAGAGGC CCGCCGUAGG GACCUUCGGA CGGGGGUUCG ACUCCCCCCA CCUCCACCA
MassTheoretical: 112.818945 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

+
Component #68: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 637 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

+
Component #69: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

-
Experimental details

-
Sample preparation

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

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 42 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 24400
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Output model

+
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