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- PDB-6o7k: 30S initiation complex -

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Basic information

Entry
Database: PDB / ID: 6o7k
Title30S initiation complex
Components
  • (30S ribosomal protein ...) x 20
  • (Translation initiation factor IF- ...) x 2
  • 16S ribosomal RNA
  • mRNAMessenger RNA
  • tRNATransfer RNA
KeywordsRIBOSOME / 30S Initiation complex with IF1 / IF2 and P/I tRNA
Function / homology
Function and homology information


translation initiation factor activity / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / small ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation ...translation initiation factor activity / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / small ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / GTPase activity / GTP binding / cytosol / cytoplasm
Similarity search - Function
Initiation factor 2 associated domain, bacterial / Bacterial translation initiation factor IF-2 associated region / Translation initiation factor IF-2, N-terminal / Translation initiation factor IF-2, N-terminal region / Translation initiation factor IF-2, domain II / Initiation factor 2 signature. / Translation initiation factor IF-2, bacterial-like / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / Translation initiation factor IF- 2 ...Initiation factor 2 associated domain, bacterial / Bacterial translation initiation factor IF-2 associated region / Translation initiation factor IF-2, N-terminal / Translation initiation factor IF-2, N-terminal region / Translation initiation factor IF-2, domain II / Initiation factor 2 signature. / Translation initiation factor IF-2, bacterial-like / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / Translation initiation factor IF- 2 / Translation initiation factor IF-2, domain 3 superfamily / Putative DNA-binding domain superfamily / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein S21 / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 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 / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S15, bacterial-type / Ribosomal protein S2 signature 2. / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / K Homology domain / K homology RNA-binding domain / Ribosomal protein S3, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S10, conserved site / : / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / KH domain / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S10 / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3 signature. / Ribosomal protein S10 signature. / Ribosomal protein S14 signature. / Ribosomal protein S7, conserved site / K homology domain superfamily, prokaryotic type / Ribosomal protein S17, conserved site / Ribosomal protein S19 / Ribosomal protein S2 signature 1. / Ribosomal protein S2, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S2 / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S14 / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S4, conserved site / Type-2 KH domain profile. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S13/S18 / Ribosomal protein S4/S9 / Ribosomal protein S19 signature. / K homology domain-like, alpha/beta / Ribosomal protein S14p/S29e / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S5
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Translation initiation factor IF-2 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS14 / 30S ribosomal protein S21 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Translation initiation factor IF-2 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS14 / 30S ribosomal protein S21 / Small ribosomal subunit protein uS13 / 30S ribosomal protein S3 / 30S ribosomal protein S5 / Small ribosomal subunit protein bS16 / 30S ribosomal protein S10 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS8 / 30S ribosomal protein S19 / 30S ribosomal protein S18 / 30S ribosomal protein S4 / Small ribosomal subunit protein uS11 / 30S ribosomal protein S6 / 30S ribosomal protein S7 / 30S ribosomal protein S20 / 30S ribosomal protein S9 / Small ribosomal subunit protein uS2 / 30S ribosomal protein S12
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsFrank, J. / Gonzalez Jr., R.L. / kaledhonkar, S. / Fu, Z. / Caban, K. / Li, W. / Chen, B. / Sun, M.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01 GM29169 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01 GM55440 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01 GM 084288 United States
American Cancer Society125201 United States
CitationJournal: Nature / Year: 2019
Title: Late steps in bacterial translation initiation visualized using time-resolved cryo-EM.
Authors: Sandip Kaledhonkar / Ziao Fu / Kelvin Caban / Wen Li / Bo Chen / Ming Sun / Ruben L Gonzalez / Joachim Frank /
Abstract: The initiation of bacterial translation involves the tightly regulated joining of the 50S ribosomal subunit to an initiator transfer RNA (fMet-tRNA)-containing 30S ribosomal initiation complex to ...The initiation of bacterial translation involves the tightly regulated joining of the 50S ribosomal subunit to an initiator transfer RNA (fMet-tRNA)-containing 30S ribosomal initiation complex to form a 70S initiation complex, which subsequently matures into a 70S elongation-competent complex. Rapid and accurate formation of the 70S initiation complex is promoted by initiation factors, which must dissociate from the 30S initiation complex before the resulting 70S elongation-competent complex can begin the elongation of translation. Although comparisons of the structures of the 30S and 70S initiation complexes have revealed that the ribosome, initiation factors and fMet-tRNA can acquire different conformations in these complexes, the timing of conformational changes during formation of the 70S initiation complex, the structures of any intermediates formed during these rearrangements, and the contributions that these dynamics might make to the mechanism and regulation of initiation remain unknown. Moreover, the absence of a structure of the 70S elongation-competent complex formed via an initiation-factor-catalysed reaction has precluded an understanding of the rearrangements to the ribosome, initiation factors and fMet-tRNA that occur during maturation of a 70S initiation complex into a 70S elongation-competent complex. Here, using time-resolved cryogenic electron microscopy, we report the near-atomic-resolution view of how a time-ordered series of conformational changes drive and regulate subunit joining, initiation factor dissociation and fMet-tRNA positioning during formation of the 70S elongation-competent complex. Our results demonstrate the power of time-resolved cryogenic electron microscopy to determine how a time-ordered series of conformational changes contribute to the mechanism and regulation of one of the most fundamental processes in biology.
History
DepositionMar 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 29, 2020Group: Structure summary / Category: entity / Item: _entity.pdbx_description

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Structure visualization

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Assembly

Deposited unit
5: Translation initiation factor IF-1
f: Translation initiation factor IF-2
g: 16S ribosomal RNA
P: 30S ribosomal protein S17
r: 30S ribosomal protein S10
q: 30S ribosomal protein S11
t: 30S ribosomal protein S12
s: 30S ribosomal protein S13
w: 30S ribosomal protein S14
u: 30S ribosomal protein S15
y: 30S ribosomal protein S16
1: 30S ribosomal protein S18
z: 30S ribosomal protein S19
j: 30S ribosomal protein S2
3: 30S ribosomal protein S20
2: 30S ribosomal protein S21
h: 30S ribosomal protein S3
l: 30S ribosomal protein S4
k: 30S ribosomal protein S5
n: 30S ribosomal protein S6
m: 30S ribosomal protein S7
p: 30S ribosomal protein S8
o: 30S ribosomal protein S9
v: tRNA
N: mRNA


Theoretical massNumber of molelcules
Total (without water)853,18125
Polymers853,18125
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Translation initiation factor IF- ... , 2 types, 2 molecules 5f

#1: Protein Translation initiation factor IF-1


Mass: 8116.468 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#2: Protein Translation initiation factor IF-2


Mass: 54866.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A069XYI1

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RNA chain , 3 types, 3 molecules gvN

#3: RNA chain 16S ribosomal RNA /


Mass: 498725.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1338015391
#24: RNA chain tRNA / Transfer RNA


Mass: 24786.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 817573384
#25: RNA chain mRNA / Messenger RNA


Mass: 1900.198 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)

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30S ribosomal protein ... , 20 types, 20 molecules Prqtswuy1zj32hlknmpo

#4: Protein 30S ribosomal protein S17 /


Mass: 9263.946 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A080IK26
#5: Protein 30S ribosomal protein S10 /


Mass: 11196.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7X302
#6: Protein 30S ribosomal protein S11 / / Small ribosomal subunit protein uS11


Mass: 12487.200 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7R9
#7: Protein 30S ribosomal protein S12 /


Mass: 13636.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: V6FZ95
#8: Protein 30S ribosomal protein S13 /


Mass: 12625.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A1X3KX08
#9: Protein 30S ribosomal protein S14 /


Mass: 11489.390 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A090BZT4
#10: Protein 30S ribosomal protein S15 /


Mass: 10159.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7XN21
#11: Protein 30S ribosomal protein S16 /


Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MIU7
#12: Protein 30S ribosomal protein S18 /


Mass: 6466.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: L3BXG0
#13: Protein 30S ribosomal protein S19 /


Mass: 9057.626 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: F4SQ43
#14: Protein 30S ribosomal protein S2 /


Mass: 24253.943 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: U9ZNW8
#15: Protein 30S ribosomal protein S20 /


Mass: 9506.190 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: T6N332
#16: Protein 30S ribosomal protein S21 /


Mass: 6067.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A0K5Z365
#17: Protein 30S ribosomal protein S3 /


Mass: 23078.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A376HTV6
#18: Protein 30S ribosomal protein S4 /


Mass: 23383.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: L3PZ69
#19: Protein 30S ribosomal protein S5 /


Mass: 15804.282 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B6I217
#20: Protein 30S ribosomal protein S6 /


Mass: 11669.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: S1CG62
#21: Protein 30S ribosomal protein S7 /


Mass: 16861.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: S1D5F0
#22: Protein 30S ribosomal protein S8 /


Mass: 14015.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D8A1L7
#23: Protein 30S ribosomal protein S9 /


Mass: 14554.882 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: T9TH92

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 70S elongation competent ribosome / Type: RIBOSOME / Entity ID: all / Source: NATURAL
Source (natural)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: DARK FIELD
Image recordingElectron dose: 35 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: MDFF / Category: model fitting
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 86367 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 2AVY

2avy
PDB Unreleased entry

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