4V5O

CRYSTAL STRUCTURE OF THE EUKARYOTIC 40S RIBOSOMAL SUBUNIT IN COMPLEX WITH INITIATION FACTOR 1.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.93 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal Structure of the Eukaryotic 40S Ribosomal Subunit in Complex with Initiation Factor 1.

Rabl, J.Leibundgut, M.Ataide, S.F.Haag, A.Ban, N.

(2011) Science 331: 730

  • DOI: 10.1126/science.1198308
  • Primary Citation of Related Structures:  
    4V5O

  • PubMed Abstract: 
  • Eukaryotic ribosomes are substantially larger and more complex than their bacterial counterparts. Although their core function is conserved, bacterial and eukaryotic protein synthesis differ considerably at the level of initiation. The eukaryotic small ribosomal subunit (40S) plays a central role in this process; it binds initiation factors that facilitate scanning of messenger RNAs and initiation of protein synthesis ...

    Eukaryotic ribosomes are substantially larger and more complex than their bacterial counterparts. Although their core function is conserved, bacterial and eukaryotic protein synthesis differ considerably at the level of initiation. The eukaryotic small ribosomal subunit (40S) plays a central role in this process; it binds initiation factors that facilitate scanning of messenger RNAs and initiation of protein synthesis. We have determined the crystal structure of the Tetrahymena thermophila 40S ribosomal subunit in complex with eukaryotic initiation factor 1 (eIF1) at a resolution of 3.9 angstroms. The structure reveals the fold of the entire 18S ribosomal RNA and of all ribosomal proteins of the 40S subunit, and defines the interactions with eIF1. It provides insights into the eukaryotic-specific aspects of protein synthesis, including the function of eIF1 as well as signaling and regulation mediated by the ribosomal proteins RACK1 and rpS6e.


    Organizational Affiliation

    Institute of Molecular Biology and Biophysics, ETH Zürich, Schafmattstrasse 20, 8093 Zürich, Switzerland.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S28E CONTAINING PROTEINA [auth A1], JA [auth B1]68Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S8B [auth A2], KA [auth B2]208Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
RPS7EC [auth A3], LA [auth B3]197Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S3AD [auth A4], MA [auth B4]265Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S26E CONTAINING PROTEINE [auth A5], NA [auth B5]119Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
RPS27EF [auth A6], OA [auth B6]81Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
PLECTIN/S10 DOMAIN CONTAINING PROTEING [auth A7], PA [auth B7]162Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
RPS25EH [auth A8], QA [auth B8]143Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
RPS31EI [auth A9], RA [auth B9]189Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
RPS0EK [auth AB], TA [auth BB]241Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
KH DOMAIN CONTAINING PROTEINL [auth AC], UA [auth BC]243Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S4 CONTAINING PROTEINM [auth AD], VA [auth BD]181Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S5 CONTAINING PROTEINN [auth AE], WA [auth BE]296Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
EIF1O [auth AF], XA [auth BF]101Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S7 CONTAINING PROTEINP [auth AG], YA [auth BG]200Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S8 CONTAINING PROTEINQ [auth AH], ZA [auth BH]130Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
RPS16E, 40S RIBOSOMAL PROTEIN RPS16ER [auth AI], AB [auth BI]145Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S10 CONTAINING PROTEINS [auth AJ], BB [auth BJ]120Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
RPS14ET [auth AK], CB [auth BK]151Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S12U [auth AL], DB [auth BL]142Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
RPS18EV [auth AM], EB [auth BM]155Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
RPS29EW [auth AN], FB [auth BN]55Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
RPS13EX [auth AO], GB [auth BO]153Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
RPS24EY [auth AP], HB [auth BP]149Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S17 CONTAINING PROTEINZ [auth AQ], IB [auth BQ]157Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
RACK1AA [auth AR], JB [auth BR]343Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
RPS15EBA [auth AS], KB [auth BS]144Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
RPS19ECA [auth AT], LB [auth BT]155Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L7AE CONTAINING PROTEINDA [auth AU], MB [auth BU]126Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
RPS17EEA [auth AV], NB [auth BV]130Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S4FA [auth AW], OB [auth BW]260Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
RPS30EGA [auth AX], PB [auth BX]80Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
RPS6EHA [auth AY], QB [auth BY]293Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
RPS21EIA [auth AZ], RB [auth BZ]97Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 10
MoleculeChainsLengthOrganismImage
18S RRNAJ [auth AA], SA [auth BA]1753Tetrahymena thermophila
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AJ [auth BN], JF [auth AN], LF [auth B5], MF [auth B6], NF [auth B9], TB [auth A5], UB [auth A6], VB [auth A9]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AC [auth AA] , AD [auth AA] , AE [auth AA] , AF [auth AA] , AG [auth BA] , AH [auth BA] , AI [auth BA] , BC [auth AA] , 
AC [auth AA],  AD [auth AA],  AE [auth AA],  AF [auth AA],  AG [auth BA],  AH [auth BA],  AI [auth BA],  BC [auth AA],  BD [auth AA],  BE [auth AA],  BF [auth AA],  BG [auth BA],  BH [auth BA],  BI [auth BA],  BJ [auth BW],  CC [auth AA],  CD [auth AA],  CE [auth AA],  CF [auth AA],  CG [auth BA],  CH [auth BA],  CI [auth BA],  DC [auth AA],  DD [auth AA],  DE [auth AA],  DF [auth AA],  DG [auth BA],  DH [auth BA],  DI [auth BA],  EC [auth AA],  ED [auth AA],  EE [auth AA],  EF [auth AA],  EG [auth BA],  EH [auth BA],  EI [auth BA],  FC [auth AA],  FD [auth AA],  FE [auth AA],  FF [auth AA],  FG [auth BA],  FH [auth BA],  FI [auth BA],  GC [auth AA],  GD [auth AA],  GE [auth AA],  GF [auth AA],  GG [auth BA],  GH [auth BA],  GI [auth BA],  HC [auth AA],  HD [auth AA],  HE [auth AA],  HF [auth AA],  HG [auth BA],  HH [auth BA],  HI [auth BA],  IC [auth AA],  ID [auth AA],  IE [auth AA],  IF [auth AL],  IG [auth BA],  IH [auth BA],  II [auth BA],  JC [auth AA],  JD [auth AA],  JE [auth AA],  JG [auth BA],  JH [auth BA],  JI [auth BA],  KC [auth AA],  KD [auth AA],  KE [auth AA],  KF [auth B4],  KG [auth BA],  KH [auth BA],  KI [auth BA],  LC [auth AA],  LD [auth AA],  LE [auth AA],  LG [auth BA],  LH [auth BA],  LI [auth BA],  MC [auth AA],  MD [auth AA],  ME [auth AA],  MG [auth BA],  MH [auth BA],  MI [auth BA],  NC [auth AA],  ND [auth AA],  NE [auth AA],  NG [auth BA],  NH [auth BA],  NI [auth BA],  OC [auth AA],  OD [auth AA],  OE [auth AA],  OF [auth BA],  OG [auth BA],  OH [auth BA],  OI [auth BA],  PC [auth AA],  PD [auth AA],  PE [auth AA],  PF [auth BA],  PG [auth BA],  PH [auth BA],  PI [auth BA],  QC [auth AA],  QD [auth AA],  QE [auth AA],  QF [auth BA],  QG [auth BA],  QH [auth BA],  QI [auth BA],  RC [auth AA],  RD [auth AA],  RE [auth AA],  RF [auth BA],  RG [auth BA],  RH [auth BA],  RI [auth BA],  SB [auth A4],  SC [auth AA],  SD [auth AA],  SE [auth AA],  SF [auth BA],  SG [auth BA],  SH [auth BA],  SI [auth BA],  TC [auth AA],  TD [auth AA],  TE [auth AA],  TF [auth BA],  TG [auth BA],  TH [auth BA],  TI [auth BA],  UC [auth AA],  UD [auth AA],  UE [auth AA],  UF [auth BA],  UG [auth BA],  UH [auth BA],  UI [auth BA],  VC [auth AA],  VD [auth AA],  VE [auth AA],  VF [auth BA],  VG [auth BA],  VH [auth BA],  VI [auth BA],  WB [auth AA],  WC [auth AA],  WD [auth AA],  WE [auth AA],  WF [auth BA],  WG [auth BA],  WH [auth BA],  WI [auth BA],  XB [auth AA],  XC [auth AA],  XD [auth AA],  XE [auth AA],  XF [auth BA],  XG [auth BA],  XH [auth BA],  XI [auth BA],  YB [auth AA],  YC [auth AA],  YD [auth AA],  YE [auth AA],  YF [auth BA],  YG [auth BA],  YH [auth BA],  YI [auth BA],  ZB [auth AA],  ZC [auth AA],  ZD [auth AA],  ZE [auth AA],  ZF [auth BA],  ZG [auth BA],  ZH [auth BA],  ZI [auth BD]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.93 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 320.52α = 90
b = 362.21β = 109.61
c = 412.11γ = 90
Software Package:
Software NamePurpose
SHARPmodel building
PHASERmodel building
DMmodel building
CNSmodel building
PHENIXmodel building
CNSrefinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
PHASERphasing
DMphasing
CNSphasing
PHENIXphasing

Structure Validation

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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