4V8Z

Cryo-EM reconstruction of the 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation Complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 4.0 of the entry. See complete history


Literature

Molecular architecture of a eukaryotic translational initiation complex.

Fernandez, I.S.Bai, X.C.Hussain, T.Kelley, A.C.Lorsch, J.R.Ramakrishnan, V.Scheres, S.H.W.

(2013) Science 342: 1240585-1240585

  • DOI: 10.1126/science.1240585
  • Primary Citation of Related Structures:  
    4V8Y, 4V8Z

  • PubMed Abstract: 
  • The last step in eukaryotic translational initiation involves the joining of the large and small subunits of the ribosome, with initiator transfer RNA (Met-tRNA(i)(Met)) positioned over the start codon of messenger RNA in the P site. This step is catalyzed by initiation factor eIF5B ...

    The last step in eukaryotic translational initiation involves the joining of the large and small subunits of the ribosome, with initiator transfer RNA (Met-tRNA(i)(Met)) positioned over the start codon of messenger RNA in the P site. This step is catalyzed by initiation factor eIF5B. We used recent advances in cryo-electron microscopy (cryo-EM) to determine a structure of the eIF5B initiation complex to 6.6 angstrom resolution from <3% of the population, comprising just 5143 particles. The structure reveals conformational changes in eIF5B, initiator tRNA, and the ribosome that provide insights into the role of eIF5B in translational initiation. The relatively high resolution obtained from such a small fraction of a heterogeneous sample suggests a general approach for characterizing the structure of other dynamic or transient biological complexes.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, CB2 0QH, United Kingdom.



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40S RIBOSOMAL PROTEIN S27-AB [auth A1]82Saccharomyces cerevisiaeMutation(s): 0 
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40S RIBOSOMAL PROTEIN S28-AC [auth A2]67Saccharomyces cerevisiaeMutation(s): 0 
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40S RIBOSOMAL PROTEIN S29-AD [auth A3]56Saccharomyces cerevisiaeMutation(s): 0 
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40S RIBOSOMAL PROTEIN S30-AE [auth A4]63Saccharomyces cerevisiaeMutation(s): 0 
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GUANINE NUCLEOTIDE-BINDING PROTEIN SUBUNIT BETA-LIKE PROTEING [auth A6]319Saccharomyces cerevisiaeMutation(s): 0 
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40S RIBOSOMAL PROTEIN S21-ADA [auth AV]87Saccharomyces cerevisiaeMutation(s): 0 
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40S RIBOSOMAL PROTEIN S22-AEA [auth AW]130Saccharomyces cerevisiaeMutation(s): 0 
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40S RIBOSOMAL PROTEIN S23-AFA [auth AX]145Saccharomyces cerevisiaeMutation(s): 0 
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40S RIBOSOMAL PROTEIN S25-AHA [auth AZ]108Saccharomyces cerevisiaeMutation(s): 0 
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60S RIBOSOMAL PROTEIN L2-BIA [auth BA]253Saccharomyces cerevisiaeMutation(s): 0 
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60S RIBOSOMAL PROTEIN L3JA [auth BB]386Saccharomyces cerevisiaeMutation(s): 0 
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60S RIBOSOMAL PROTEIN L4-AKA [auth BC]361Saccharomyces cerevisiaeMutation(s): 0 
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60S RIBOSOMAL PROTEIN L5LA [auth BD]296Saccharomyces cerevisiaeMutation(s): 0 
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60S RIBOSOMAL PROTEIN L6-AMA [auth BE]175Saccharomyces cerevisiaeMutation(s): 0 
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60S RIBOSOMAL PROTEIN L7-ANA [auth BF]243Saccharomyces cerevisiaeMutation(s): 0 
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60S RIBOSOMAL PROTEIN L8-AOA [auth BG]255Saccharomyces cerevisiaeMutation(s): 0 
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60S RIBOSOMAL PROTEIN L11-ARA [auth BJ]173Saccharomyces cerevisiaeMutation(s): 0 
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60S RIBOSOMAL PROTEIN L19-BZA [auth BR]188Saccharomyces cerevisiaeMutation(s): 0 
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60S RIBOSOMAL PROTEIN L20-BAB [auth BS]172Saccharomyces cerevisiaeMutation(s): 0 
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60S RIBOSOMAL PROTEIN L21-ABB [auth BT]159Saccharomyces cerevisiaeMutation(s): 0 
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60S RIBOSOMAL PROTEIN L23-ADB [auth BV]136Saccharomyces cerevisiaeMutation(s): 0 
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60S RIBOSOMAL PROTEIN L24-AEB [auth BW]155Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L25FB [auth BX]141Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 59
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60S RIBOSOMAL PROTEIN L26-AGB [auth BY]126Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 60
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60S RIBOSOMAL PROTEIN L27-AHB [auth BZ]135Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 61
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60S RIBOSOMAL PROTEIN L28IB [auth Ba]148Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 62
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60S RIBOSOMAL PROTEIN L29JB [auth Bb]58Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L30KB [auth Bc]104Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 64
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60S RIBOSOMAL PROTEIN L31-ALB [auth Bd]112Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 65
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60S RIBOSOMAL PROTEIN L32MB [auth Be]129Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 66
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60S RIBOSOMAL PROTEIN L33-ANB [auth Bf]106Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 67
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60S RIBOSOMAL PROTEIN L34-AOB [auth Bg]120Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 68
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60S RIBOSOMAL PROTEIN L35-BPB [auth Bh]119Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 69
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60S RIBOSOMAL PROTEIN L36-AQB [auth Bi]99Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 70
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60S RIBOSOMAL PROTEIN L37-ARB [auth Bj]87Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 71
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60S RIBOSOMAL PROTEIN L38SB [auth Bk]77Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L39TB [auth Bl]50Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 73
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UBIQUITIN-60S RIBOSOMAL PROTEIN L40UB [auth Bm]128Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 74
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60S RIBOSOMAL PROTEIN L41-BVB [auth Bn]25Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L42-AWB [auth Bo]105Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetailsImage
60S ACIDIC RIBOSOMAL PROTEIN P0XB [auth Bq]312Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetailsImage
60S ACIDIC RIBOSOMAL PROTEIN P1YB [auth Br]47Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 78
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60S ACIDIC RIBOSOMAL PROTEIN P2ZB [auth Bs]46Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 83
MoleculeChainsSequence LengthOrganismDetailsImage
EUKARYOTIC TRANSLATION INITIATION FACTOR 5B, PROBABLE TRANSLATION INITIATION FACTOR IF-2EC [auth CV]586Saccharomyces cerevisiaeMethanothermobacter thermautotrophicus
This entity is chimeric
Mutation(s): 0 
EC: 3.6.5.3
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Find proteins for O26359 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H))
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Entity ID: 79
MoleculeChainsLengthOrganismImage
18S RIBOSOMAL RNAAC [auth B2]1800Saccharomyces cerevisiae
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Entity ID: 80
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25S RIBOSOMAL RNABC [auth B5]3396Saccharomyces cerevisiae
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Entity ID: 81
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5S RIBOSOMAL RNACC [auth B7]121Saccharomyces cerevisiae
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Entity ID: 82
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5.8S RIBOSOMAL RNADC [auth B8]158Saccharomyces cerevisiae
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Entity ID: 84
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EUKARYOTIC RIBOSOMAL PI TRNAFC [auth CW]76Saccharomyces cerevisiae
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  • Entity ID: 85
    MoleculeChainsLengthOrganismImage
    5'-R(*AP*UP*GP)-3'GC [auth CX]3Saccharomyces cerevisiae
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    Small Molecules
    Ligands 4 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    GCP
    Query on GCP

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    FT [auth CV]PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
    C11 H18 N5 O13 P3
    PHBDHXOBFUBCJD-KQYNXXCUSA-N
     Ligand Interaction
    OHX
    Query on OHX

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    AD [auth AI] , AE [auth B2] , AF [auth B2] , AG [auth B2] , AH [auth B2] , AI [auth B2] , AJ [auth B2] , AK [auth B2] , 
    AD [auth AI],  AE [auth B2],  AF [auth B2],  AG [auth B2],  AH [auth B2],  AI [auth B2],  AJ [auth B2],  AK [auth B2],  BE [auth B2],  BF [auth B2],  BG [auth B2],  BH [auth B2],  BI [auth B2],  BJ [auth B2],  BK [auth B2],  BS [auth B7],  CE [auth B2],  CF [auth B2],  CG [auth B2],  CH [auth B2],  CI [auth B2],  CJ [auth B2],  CK [auth B2],  DD [auth AL],  DE [auth B2],  DF [auth B2],  DG [auth B2],  DH [auth B2],  DI [auth B2],  DJ [auth B2],  DK [auth B2],  DS [auth B7],  EE [auth B2],  EF [auth B2],  EG [auth B2],  EH [auth B2],  EI [auth B2],  EJ [auth B2],  EK [auth B2],  ES [auth B7],  ET [auth CV],  FE [auth B2],  FF [auth B2],  FG [auth B2],  FH [auth B2],  FI [auth B2],  FJ [auth B2],  FK [auth B2],  GD [auth AN],  GE [auth B2],  GF [auth B2],  GG [auth B2],  GH [auth B2],  GI [auth B2],  GJ [auth B2],  GK [auth B2],  HE [auth B2],  HF [auth B2],  HG [auth B2],  HH [auth B2],  HI [auth B2],  HJ [auth B2],  HK [auth B2],  HT [auth CX],  ID [auth AP],  IE [auth B2],  IF [auth B2],  IG [auth B2],  IH [auth B2],  II [auth B2],  IJ [auth B2],  IK [auth B2],  IS [auth B7],  JE [auth B2],  JF [auth B2],  JG [auth B2],  JH [auth B2],  JI [auth B2],  JJ [auth B2],  JK [auth B2],  JS [auth B7],  KE [auth B2],  KF [auth B2],  KG [auth B2],  KH [auth B2],  KI [auth B2],  KJ [auth B2],  KK [auth B2],  KR [auth B5],  KS [auth B7],  LE [auth B2],  LF [auth B2],  LG [auth B2],  LH [auth B2],  LI [auth B2],  LJ [auth B2],  LK [auth B2],  LR [auth B5],  MC [auth A3],  ME [auth B2],  MF [auth B2],  MG [auth B2],  MH [auth B2],  MI [auth B2],  MJ [auth B2],  MK [auth B2],  MR [auth B5],  NE [auth B2],  NF [auth B2],  NG [auth B2],  NH [auth B2],  NI [auth B2],  NJ [auth B2],  NK [auth B2],  OE [auth B2],  OF [auth B2],  OG [auth B2],  OH [auth B2],  OI [auth B2],  OJ [auth B2],  OK [auth B2],  PE [auth B2],  PF [auth B2],  PG [auth B2],  PH [auth B2],  PI [auth B2],  PJ [auth B2],  PK [auth B2],  QE [auth B2],  QF [auth B2],  QG [auth B2],  QH [auth B2],  QI [auth B2],  QJ [auth B2],  QK [auth B2],  QR [auth B7],  RD [auth BR],  RE [auth B2],  RF [auth B2],  RG [auth B2],  RH [auth B2],  RI [auth B2],  RJ [auth B2],  RK [auth B2],  RR [auth B7],  SC [auth A6],  SE [auth B2],  SF [auth B2],  SG [auth B2],  SH [auth B2],  SI [auth B2],  SJ [auth B2],  SK [auth B2],  SR [auth B7],  TE [auth B2],  TF [auth B2],  TG [auth B2],  TH [auth B2],  TI [auth B2],  TJ [auth B2],  TK [auth B2],  TR [auth B7],  UC [auth AC],  UE [auth B2],  UF [auth B2],  UG [auth B2],  UH [auth B2],  UI [auth B2],  UJ [auth B2],  UK [auth B2],  UR [auth B7],  VE [auth B2],  VF [auth B2],  VG [auth B2],  VH [auth B2],  VI [auth B2],  VJ [auth B2],  VK [auth B2],  VR [auth B7],  WE [auth B2],  WF [auth B2],  WG [auth B2],  WH [auth B2],  WI [auth B2],  WJ [auth B2],  WK [auth B2],  XD [auth Bn],  XE [auth B2],  XF [auth B2],  XG [auth B2],  XH [auth B2],  XI [auth B2],  XJ [auth B2],  XK [auth B2],  YD [auth B2],  YE [auth B2],  YF [auth B2],  YG [auth B2],  YH [auth B2],  YI [auth B2],  YJ [auth B2],  ZC [auth AI],  ZD [auth B2],  ZE [auth B2],  ZF [auth B2],  ZG [auth B2],  ZH [auth B2],  ZI [auth B2],  ZJ [auth B2],  ZR [auth B7]
    osmium (III) hexammine
    H12 N6 Os
    OWCQTVJQFLTQTE-UHFFFAOYSA-N
     Ligand Interaction
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    HC [auth A0], KC [auth A1], LC [auth A3], QC [auth A5], VD [auth Bj], WD [auth Bm]ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    AL [auth B2] , AM [auth B2] , AN [auth B2] , AO [auth B2] , AP [auth B2] , AQ [auth B2] , AR [auth B2] , AS [auth B7] , 
    AL [auth B2],  AM [auth B2],  AN [auth B2],  AO [auth B2],  AP [auth B2],  AQ [auth B2],  AR [auth B2],  AS [auth B7],  AT [auth B7],  BD [auth AI],  BL [auth B2],  BM [auth B2],  BN [auth B2],  BO [auth B2],  BP [auth B2],  BQ [auth B2],  BR [auth B2],  BT [auth B7],  CD [auth AJ],  CL [auth B2],  CM [auth B2],  CN [auth B2],  CO [auth B2],  CP [auth B2],  CQ [auth B2],  CR [auth B2],  CS [auth B7],  CT [auth B7],  DL [auth B2],  DM [auth B2],  DN [auth B2],  DO [auth B2],  DP [auth B2],  DQ [auth B2],  DR [auth B2],  DT [auth B7],  ED [auth AL],  EL [auth B2],  EM [auth B2],  EN [auth B2],  EO [auth B2],  EP [auth B2],  EQ [auth B2],  ER [auth B2],  FD [auth AL],  FL [auth B2],  FM [auth B2],  FN [auth B2],  FO [auth B2],  FP [auth B2],  FQ [auth B2],  FR [auth B2],  FS [auth B7],  GL [auth B2],  GM [auth B2],  GN [auth B2],  GO [auth B2],  GP [auth B2],  GQ [auth B2],  GR [auth B2],  GS [auth B7],  GT [auth CW],  HD [auth AN],  HL [auth B2],  HM [auth B2],  HN [auth B2],  HO [auth B2],  HP [auth B2],  HQ [auth B2],  HR [auth B2],  HS [auth B7],  IC [auth A0],  IL [auth B2],  IM [auth B2],  IN [auth B2],  IO [auth B2],  IP [auth B2],  IQ [auth B2],  IR [auth B2],  JC [auth A0],  JD [auth AP],  JL [auth B2],  JM [auth B2],  JN [auth B2],  JO [auth B2],  JP [auth B2],  JQ [auth B2],  JR [auth B2],  KD [auth AS],  KL [auth B2],  KM [auth B2],  KN [auth B2],  KO [auth B2],  KP [auth B2],  KQ [auth B2],  LD [auth AU],  LL [auth B2],  LM [auth B2],  LN [auth B2],  LO [auth B2],  LP [auth B2],  LQ [auth B2],  LS [auth B7],  MD [auth BD],  ML [auth B2],  MM [auth B2],  MN [auth B2],  MO [auth B2],  MP [auth B2],  MQ [auth B2],  MS [auth B7],  NC [auth A3],  ND [auth BD],  NL [auth B2],  NM [auth B2],  NN [auth B2],  NO [auth B2],  NP [auth B2],  NQ [auth B2],  NR [auth B5],  NS [auth B7],  OC [auth A3],  OD [auth BD],  OL [auth B2],  OM [auth B2],  ON [auth B2],  OO [auth B2],  OP [auth B2],  OQ [auth B2],  OR [auth B5],  OS [auth B7],  PC [auth A3],  PD [auth BD],  PL [auth B2],  PM [auth B2],  PN [auth B2],  PO [auth B2],  PP [auth B2],  PQ [auth B2],  PR [auth B5],  PS [auth B7],  QD [auth BF],  QL [auth B2],  QM [auth B2],  QN [auth B2],  QO [auth B2],  QP [auth B2],  QQ [auth B2],  QS [auth B7],  RC [auth A5],  RL [auth B2],  RM [auth B2],  RN [auth B2],  RO [auth B2],  RP [auth B2],  RQ [auth B2],  RS [auth B7],  SD [auth BS],  SL [auth B2],  SM [auth B2],  SN [auth B2],  SO [auth B2],  SP [auth B2],  SQ [auth B2],  SS [auth B7],  TC [auth AB],  TD [auth BS],  TL [auth B2],  TM [auth B2],  TN [auth B2],  TO [auth B2],  TP [auth B2],  TQ [auth B2],  TS [auth B7],  UD [auth BS],  UL [auth B2],  UM [auth B2],  UN [auth B2],  UO [auth B2],  UP [auth B2],  UQ [auth B2],  US [auth B7],  VC [auth AC],  VL [auth B2],  VM [auth B2],  VN [auth B2],  VO [auth B2],  VP [auth B2],  VQ [auth B2],  VS [auth B7],  WC [auth AC],  WL [auth B2],  WM [auth B2],  WN [auth B2],  WO [auth B2],  WP [auth B2],  WQ [auth B2],  WR [auth B7],  WS [auth B7],  XC [auth AE],  XL [auth B2],  XM [auth B2],  XN [auth B2],  XO [auth B2],  XP [auth B2],  XQ [auth B2],  XR [auth B7],  XS [auth B7],  YC [auth AG],  YK [auth B2],  YL [auth B2],  YM [auth B2],  YN [auth B2],  YO [auth B2],  YP [auth B2],  YQ [auth B2],  YR [auth B7],  YS [auth B7],  ZK [auth B2],  ZL [auth B2],  ZM [auth B2],  ZN [auth B2],  ZO [auth B2],  ZP [auth B2],  ZQ [auth B2],  ZS [auth B7]
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Modified Residues  1 Unique
    IDChainsTypeFormula2D DiagramParent
    HSO
    Query on HSO
    EC [auth CV]L-PEPTIDE LINKINGC6 H12 N3 OHIS
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 6.60 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2014-07-09
      Type: Initial release
    • Version 1.1: 2014-12-10
      Changes: Other
    • Version 1.2: 2015-04-22
      Changes: Other
    • Version 2.0: 2017-08-02
      Changes: Advisory, Atomic model, Data collection, Derived calculations
    • Version 3.0: 2018-04-18
      Changes: Atomic model, Data collection, Database references, Other, Structure summary
    • Version 3.1: 2019-08-21
      Changes: Data collection, Database references, Derived calculations
    • Version 3.2: 2019-10-09
      Changes: Data collection, Source and taxonomy, Structure summary
    • Version 3.3: 2019-10-23
      Changes: Data collection, Database references
    • Version 4.0: 2019-12-11
      Changes: Other, Polymer sequence