5LMN

Structure of bacterial 30S-IF1-IF3-mRNA translation pre-initiation complex (state-1A)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.55 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Large-Scale Movements of IF3 and tRNA during Bacterial Translation Initiation.

Hussain, T.Llacer, J.L.Wimberly, B.T.Kieft, J.S.Ramakrishnan, V.

(2016) Cell 167: 133-144.e13

  • DOI: 10.1016/j.cell.2016.08.074
  • Primary Citation of Related Structures:  
    5LMO, 5LMN, 5LMQ, 5LMP, 5LMS, 5LMR, 5LMU, 5LMT, 5LMV

  • PubMed Abstract: 
  • In bacterial translational initiation, three initiation factors (IFs 1-3) enable the selection of initiator tRNA and the start codon in the P site of the 30S ribosomal subunit. Here, we report 11 single-particle cryo-electron microscopy (cryoEM) reconstructions of the complex of bacterial 30S subunit with initiator tRNA, mRNA, and IFs 1-3, representing different steps along the initiation pathway ...

    In bacterial translational initiation, three initiation factors (IFs 1-3) enable the selection of initiator tRNA and the start codon in the P site of the 30S ribosomal subunit. Here, we report 11 single-particle cryo-electron microscopy (cryoEM) reconstructions of the complex of bacterial 30S subunit with initiator tRNA, mRNA, and IFs 1-3, representing different steps along the initiation pathway. IF1 provides key anchoring points for IF2 and IF3, thereby enhancing their activities. IF2 positions a domain in an extended conformation appropriate for capturing the formylmethionyl moiety charged on tRNA. IF3 and tRNA undergo large conformational changes to facilitate the accommodation of the formylmethionyl-tRNA (fMet-tRNA(fMet)) into the P site for start codon recognition.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK. Electronic address: ramak@mrc-lmb.cam.ac.uk.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2B256Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsBrps2TTHA0861
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3C239Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsCrps3TTHA1686
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4D209Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5E162Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsETTHA1675
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6F101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S7G156Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsGrps7TTHA1696
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8H138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsHTTHA1678
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9I128Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S10J105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJTTHA1693
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S11K129Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsKrps11TTHA1666
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S12L132Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsLTTHA1697
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S13M126Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZN61Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsZrpsNTTHA1679
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S15O89Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsOTTHA1138
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S16P88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsPTTHA1035
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17Q105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsQTTHA1683
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S18R88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsRTTHA0243
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19S93Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsSTTHA1688
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S20T106Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein ThxU [auth V]27Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsUTTHA1396
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Translation initiation factor IF-1V [auth W]72Thermus thermophilus HB8Mutation(s): 0 
Gene Names: infATTHA1669
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Translation initiation factor IF-3W [auth X]171Thermus thermophilus HB8Mutation(s): 0 
Gene Names: infCTTHA0551
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S ribosomal RNAA1522Thermus thermophilus HB8
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Entity ID: 24
MoleculeChainsLengthOrganismImage
mRNAX [auth Y]42Thermus thermophilus HB8
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
UE [auth D], WE [auth N]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth A] , AB [auth A] , AC [auth A] , AD [auth A] , AE [auth A] , BA [auth A] , BB [auth A] , BC [auth A] , 
AA [auth A],  AB [auth A],  AC [auth A],  AD [auth A],  AE [auth A],  BA [auth A],  BB [auth A],  BC [auth A],  BD [auth A],  BE [auth A],  CA [auth A],  CB [auth A],  CC [auth A],  CD [auth A],  CE [auth A],  DA [auth A],  DB [auth A],  DC [auth A],  DD [auth A],  DE [auth A],  EA [auth A],  EB [auth A],  EC [auth A],  ED [auth A],  EE [auth A],  FA [auth A],  FB [auth A],  FC [auth A],  FD [auth A],  FE [auth A],  GA [auth A],  GB [auth A],  GC [auth A],  GD [auth A],  GE [auth A],  HA [auth A],  HB [auth A],  HC [auth A],  HD [auth A],  HE [auth A],  IA [auth A],  IB [auth A],  IC [auth A],  ID [auth A],  IE [auth A],  JA [auth A],  JB [auth A],  JC [auth A],  JD [auth A],  JE [auth A],  KA [auth A],  KB [auth A],  KC [auth A],  KD [auth A],  KE [auth A],  LA [auth A],  LB [auth A],  LC [auth A],  LD [auth A],  LE [auth A],  MA [auth A],  MB [auth A],  MC [auth A],  MD [auth A],  ME [auth A],  NA [auth A],  NB [auth A],  NC [auth A],  ND [auth A],  NE [auth A],  OA [auth A],  OB [auth A],  OC [auth A],  OD [auth A],  OE [auth A],  PA [auth A],  PB [auth A],  PC [auth A],  PD [auth A],  PE [auth A],  QA [auth A],  QB [auth A],  QC [auth A],  QD [auth A],  QE [auth A],  RA [auth A],  RB [auth A],  RC [auth A],  RD [auth A],  RE [auth A],  SA [auth A],  SB [auth A],  SC [auth A],  SD [auth A],  SE [auth A],  TA [auth A],  TB [auth A],  TC [auth A],  TD [auth A],  TE [auth A],  UA [auth A],  UB [auth A],  UC [auth A],  UD [auth A],  VA [auth A],  VB [auth A],  VC [auth A],  VD [auth A],  VE [auth N],  WA [auth A],  WB [auth A],  WC [auth A],  WD [auth A],  XA [auth A],  XB [auth A],  XC [auth A],  XD [auth A],  Y [auth A],  YA [auth A],  YB [auth A],  YC [auth A],  YD [auth A],  Z [auth A],  ZA [auth A],  ZB [auth A],  ZC [auth A],  ZD [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.55 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMC_U105184332
Wellcome TrustUnited KingdomWT096570
HHMIUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-05
    Type: Initial release
  • Version 1.1: 2016-10-26
    Changes: Structure summary
  • Version 1.2: 2017-08-02
    Changes: Data collection, Derived calculations
  • Version 1.3: 2018-11-21
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.4: 2019-10-02
    Changes: Data collection, Other