4BTS

THE CRYSTAL STRUCTURE OF THE EUKARYOTIC 40S RIBOSOMAL SUBUNIT IN COMPLEX WITH EIF1 AND EIF1A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The crystal structure of the eukaryotic 40S ribosomal subunit in complex with eIF1 and eIF1A.

Weisser, M.Voigts-Hoffmann, F.Rabl, J.Leibundgut, M.Ban, N.

(2013) Nat Struct Mol Biol 20: 1015-1017

  • DOI: 10.1038/nsmb.2622
  • Primary Citation of Related Structures:  
    4BTS

  • PubMed Abstract: 
  • Eukaryotic translation initiation factors (eIFs) 1A and 1 are central players in the complex process of start-codon recognition. To improve mechanistic understanding of this process, we determined the crystal structure of the 40S ribosomal subunit in complex with eIF1A and eIF1 from Tetrahymena thermophila at a resolution of 3 ...

    Eukaryotic translation initiation factors (eIFs) 1A and 1 are central players in the complex process of start-codon recognition. To improve mechanistic understanding of this process, we determined the crystal structure of the 40S ribosomal subunit in complex with eIF1A and eIF1 from Tetrahymena thermophila at a resolution of 3.7 Å. It reveals the positions of the two factors on the 40S and the conformational changes that accompany their binding.


    Organizational Affiliation

    Institute of Molecular Biology and Biophysics, Swiss Federal Institute of Technology (ETH Zürich), Zürich, Switzerland.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TRANSLATION INITIATION FACTOR EIF-1A FAMILY PROTEINA [auth A0], KA [auth B0], UB [auth C0], ED [auth D0]211Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00497990
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS28EB [auth A1], LA [auth B1], VB [auth C1], FD [auth D1]68Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S8C [auth A2], MA [auth B2], WB [auth C2], GD [auth D2]208Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS7ED [auth A3], NA [auth B3], XB [auth C3], HD [auth D3]197Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S3AE [auth A4], OA [auth B4], YB [auth C4], ID [auth D4]265Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS26EF [auth A5], PA [auth B5], ZB [auth C5], JD [auth D5]119Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S27G [auth A6], QA [auth B6], AC [auth C6], KD [auth D6]81Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS10EH [auth A7], RA [auth B7], BC [auth C7], LD [auth D7]162Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS25EI [auth A8], SA [auth B8], CC [auth C8], MD [auth D8]143Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS31EJ [auth A9], TA [auth B9], DC [auth C9], ND [auth D9]189Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN SAL [auth AB], VA [auth BB], FC [auth CB], PD [auth DB]241Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS3EM [auth AC], WA [auth BC], GC [auth CC], QD [auth DC]243Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS9EN [auth AD], XA [auth BD], HC [auth CD], RD [auth DD]181Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS2EO [auth AE], YA [auth BE], IC [auth CE], SD [auth DE]296Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
EIF1P [auth AF], ZA [auth BF], JC [auth CF], TD [auth DF]101Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS5EQ [auth AG], AB [auth BG], KC [auth CG], UD [auth DG]200Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS22ER [auth AH], BB [auth BH], LC [auth CH], VD [auth DH]130Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS16ES [auth AI], CB [auth BI], MC [auth CI], WD [auth DI]145Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS20ET [auth AJ], DB [auth BJ], NC [auth CJ], XD [auth DJ]120Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS14EU [auth AK], EB [auth BK], OC [auth CK], YD [auth DK]151Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S12V [auth AL], FB [auth BL], PC [auth CL], ZD [auth DL]142Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS18EW [auth AM], GB [auth BM], QC [auth CM], AE [auth DM]155Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS29EX [auth AN], HB [auth BN], RC [auth CN], BE [auth DN]55Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS13EY [auth AO], IB [auth BO], SC [auth CO], CE [auth DO]153Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S24Z [auth AP], JB [auth BP], TC [auth CP], DE [auth DP]149Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS11EAA [auth AQ], KB [auth BQ], UC [auth CQ], EE [auth DQ]157Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RACK1BA [auth AR], LB [auth BR], VC [auth CR], FE [auth DR]343Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS15ECA [auth AS], MB [auth BS], WC [auth CS], GE [auth DS]144Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS19EDA [auth AT], NB [auth BT], XC [auth CT], HE [auth DT]155Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS12EEA [auth AU], OB [auth BU], YC [auth CU], IE [auth DU]126Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS17EFA [auth AV], PB [auth BV], ZC [auth CV], JE [auth DV]130Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS4EGA [auth AW], QB [auth BW], AD [auth CW], KE [auth DW]259Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS30EHA [auth AX], RB [auth BX], BD [auth CX], LE [auth DX]80Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S6IA [auth AY], SB [auth BY], CD [auth CY], ME [auth DY]293Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS21EJA [auth AZ], TB [auth BZ], DD [auth CZ], NE [auth DZ]97Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 11
MoleculeChainsLengthOrganismImage
18S ribosomal RNAK [auth AA], UA [auth BA], EC [auth CA], OD [auth DA]1753Tetrahymena thermophila
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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AL [auth C9] , CO [auth CN] , DO [auth D5] , EO [auth D6] , FO [auth D9] , HR [auth DN] , OE [auth A5] , PE [auth A6] , 
AL [auth C9],  CO [auth CN],  DO [auth D5],  EO [auth D6],  FO [auth D9],  HR [auth DN],  OE [auth A5],  PE [auth A6],  QE [auth A9],  SH [auth AN],  TH [auth B5],  UH [auth B6],  VH [auth B9],  XK [auth BN],  YK [auth C5],  ZK [auth C6]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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AF [auth AA] , AG [auth AA] , AH [auth AA] , AI [auth BA] , AJ [auth BA] , AK [auth BA] , AM [auth CA] , AN [auth CA] , 
AF [auth AA],  AG [auth AA],  AH [auth AA],  AI [auth BA],  AJ [auth BA],  AK [auth BA],  AM [auth CA],  AN [auth CA],  AO [auth CA],  AP [auth DA],  AQ [auth DA],  AR [auth DA],  BF [auth AA],  BG [auth AA],  BH [auth AA],  BI [auth BA],  BJ [auth BA],  BK [auth BA],  BL [auth CA],  BM [auth CA],  BN [auth CA],  BO [auth CA],  BP [auth DA],  BQ [auth DA],  BR [auth DA],  CF [auth AA],  CG [auth AA],  CH [auth AA],  CI [auth BA],  CJ [auth BA],  CK [auth BA],  CL [auth CA],  CM [auth CA],  CN [auth CA],  CP [auth DA],  CQ [auth DA],  CR [auth DA],  DF [auth AA],  DG [auth AA],  DH [auth AA],  DI [auth BA],  DJ [auth BA],  DK [auth BA],  DL [auth CA],  DM [auth CA],  DN [auth CA],  DP [auth DA],  DQ [auth DA],  DR [auth DA],  EF [auth AA],  EG [auth AA],  EH [auth AA],  EI [auth BA],  EJ [auth BA],  EK [auth BA],  EL [auth CA],  EM [auth CA],  EN [auth CA],  EP [auth DA],  EQ [auth DA],  ER [auth DA],  FF [auth AA],  FG [auth AA],  FH [auth AA],  FI [auth BA],  FJ [auth BA],  FK [auth BA],  FL [auth CA],  FM [auth CA],  FN [auth CA],  FP [auth DA],  FQ [auth DA],  FR [auth DA],  GF [auth AA],  GG [auth AA],  GH [auth AA],  GI [auth BA],  GJ [auth BA],  GK [auth BA],  GL [auth CA],  GM [auth CA],  GN [auth CA],  GO [auth DA],  GP [auth DA],  GQ [auth DA],  GR [auth DA],  HF [auth AA],  HG [auth AA],  HH [auth AA],  HI [auth BA],  HJ [auth BA],  HK [auth BA],  HL [auth CA],  HM [auth CA],  HN [auth CA],  HO [auth DA],  HP [auth DA],  HQ [auth DA],  IF [auth AA],  IG [auth AA],  IH [auth AA],  II [auth BA],  IJ [auth BA],  IK [auth BA],  IL [auth CA],  IM [auth CA],  IN [auth CA],  IO [auth DA],  IP [auth DA],  IQ [auth DA],  JF [auth AA],  JG [auth AA],  JH [auth AA],  JI [auth BA],  JJ [auth BA],  JK [auth BA],  JL [auth CA],  JM [auth CA],  JN [auth CA],  JO [auth DA],  JP [auth DA],  JQ [auth DA],  KF [auth AA],  KG [auth AA],  KH [auth AA],  KI [auth BA],  KJ [auth BA],  KK [auth BA],  KL [auth CA],  KM [auth CA],  KN [auth CA],  KO [auth DA],  KP [auth DA],  KQ [auth DA],  LF [auth AA],  LG [auth AA],  LH [auth AA],  LI [auth BA],  LJ [auth BA],  LK [auth BA],  LL [auth CA],  LM [auth CA],  LN [auth CA],  LO [auth DA],  LP [auth DA],  LQ [auth DA],  MF [auth AA],  MG [auth AA],  MH [auth AA],  MI [auth BA],  MJ [auth BA],  MK [auth BA],  ML [auth CA],  MM [auth CA],  MN [auth CA],  MO [auth DA],  MP [auth DA],  MQ [auth DA],  NF [auth AA],  NG [auth AA],  NH [auth AA],  NI [auth BA],  NJ [auth BA],  NK [auth BA],  NL [auth CA],  NM [auth CA],  NN [auth CA],  NO [auth DA],  NP [auth DA],  NQ [auth DA],  OF [auth AA],  OG [auth AA],  OH [auth AA],  OI [auth BA],  OJ [auth BA],  OK [auth BA],  OL [auth CA],  OM [auth CA],  ON [auth CA],  OO [auth DA],  OP [auth DA],  OQ [auth DA],  PF [auth AA],  PG [auth AA],  PH [auth AA],  PI [auth BA],  PJ [auth BA],  PK [auth BA],  PL [auth CA],  PM [auth CA],  PN [auth CA],  PO [auth DA],  PP [auth DA],  PQ [auth DA],  QF [auth AA],  QG [auth AA],  QH [auth AA],  QI [auth BA],  QJ [auth BA],  QK [auth BA],  QL [auth CA],  QM [auth CA],  QN [auth CA],  QO [auth DA],  QP [auth DA],  QQ [auth DA],  RE [auth AA],  RF [auth AA],  RG [auth AA],  RH [auth AA],  RI [auth BA],  RJ [auth BA],  RK [auth BA],  RL [auth CA],  RM [auth CA],  RN [auth CA],  RO [auth DA],  RP [auth DA],  RQ [auth DA],  SE [auth AA],  SF [auth AA],  SG [auth AA],  SI [auth BA],  SJ [auth BA],  SK [auth BA],  SL [auth CA],  SM [auth CA],  SN [auth CA],  SO [auth DA],  SP [auth DA],  SQ [auth DA],  TE [auth AA],  TF [auth AA],  TG [auth AA],  TI [auth BA],  TJ [auth BA],  TK [auth BA],  TL [auth CA],  TM [auth CA],  TN [auth CA],  TO [auth DA],  TP [auth DA],  TQ [auth DA],  UE [auth AA],  UF [auth AA],  UG [auth AA],  UI [auth BA],  UJ [auth BA],  UK [auth BA],  UL [auth CA],  UM [auth CA],  UN [auth CA],  UO [auth DA],  UP [auth DA],  UQ [auth DA],  VE [auth AA],  VF [auth AA],  VG [auth AA],  VI [auth BA],  VJ [auth BA],  VK [auth BA],  VL [auth CA],  VM [auth CA],  VN [auth CA],  VO [auth DA],  VP [auth DA],  VQ [auth DA],  WE [auth AA],  WF [auth AA],  WG [auth AA],  WH [auth BA],  WI [auth BA],  WJ [auth BA],  WK [auth BA],  WL [auth CA],  WM [auth CA],  WN [auth CA],  WO [auth DA],  WP [auth DA],  WQ [auth DA],  XE [auth AA],  XF [auth AA],  XG [auth AA],  XH [auth BA],  XI [auth BA],  XJ [auth BA],  XL [auth CA],  XM [auth CA],  XN [auth CA],  XO [auth DA],  XP [auth DA],  XQ [auth DA],  YE [auth AA],  YF [auth AA],  YG [auth AA],  YH [auth BA],  YI [auth BA],  YJ [auth BA],  YL [auth CA],  YM [auth CA],  YN [auth CA],  YO [auth DA],  YP [auth DA],  YQ [auth DA],  ZE [auth AA],  ZF [auth AA],  ZG [auth AA],  ZH [auth BA],  ZI [auth BA],  ZJ [auth BA],  ZL [auth CA],  ZM [auth CA],  ZN [auth CA],  ZO [auth DA],  ZP [auth DA],  ZQ [auth DA]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 209.99α = 90
b = 471.55β = 91.02
c = 298.54γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-17
    Type: Initial release
  • Version 1.1: 2013-07-24
    Changes: Database references
  • Version 1.2: 2014-06-25
    Changes: Database references
  • Version 1.3: 2014-12-10
    Changes: Other
  • Version 1.4: 2018-03-07
    Changes: Database references, Source and taxonomy, Structure summary