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
  • Structures With Same Primary Citation

  • 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 sma ...

    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: 2
MoleculeChainsSequence LengthOrganismDetails
40S RIBOSOMAL PROTEIN S8A2, B2208Tetrahymena thermophilaMutation(s): 0 
Find proteins for Q22AV0 (Tetrahymena thermophila (strain SB210))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
RPS7EA3, B3197Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
40S RIBOSOMAL PROTEIN S3AA4, B4265Tetrahymena thermophilaMutation(s): 0 
Find proteins for Q23DE3 (Tetrahymena thermophila (strain SB210))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
RPS27EA6, B681Tetrahymena thermophilaMutation(s): 0 
Find proteins for Q22CK0 (Tetrahymena thermophila (strain SB210))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
PLECTIN/S10 DOMAIN CONTAINING PROTEINA7, B7162Tetrahymena thermophilaMutation(s): 0 
Find proteins for Q24F70 (Tetrahymena thermophila (strain SB210))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
RPS25EA8, B8143Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN S5 CONTAINING PROTEINAE, BE296Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
EIF1AF, BF101Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN S7 CONTAINING PROTEINAG, BG200Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
RPS16E, 40S RIBOSOMAL PROTEIN RPS16EAI, BI145Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN S10 CONTAINING PROTEINAJ, BJ120Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
40S RIBOSOMAL PROTEIN S12AL, BL142Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
RPS18EAM, BM155Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
RPS29EAN, BN55Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
RPS24EAP, BP149Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN S17 CONTAINING PROTEINAQ, BQ157Tetrahymena thermophilaMutation(s): 0 
Find proteins for Q22B78 (Tetrahymena thermophila (strain SB210))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
RPS15EAS, BS144Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
RPS19EAT, BT155Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L7AE CONTAINING PROTEINAU, BU126Tetrahymena thermophilaMutation(s): 0 
Find proteins for Q22W26 (Tetrahymena thermophila (strain SB210))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
40S RIBOSOMAL PROTEIN S4AW, BW260Tetrahymena thermophilaMutation(s): 0 
Find proteins for P0C233 (Tetrahymena thermophila)
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
RPS30EAX, BX80Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
RPS21EAZ, BZ97Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN S28E CONTAINING PROTEINA1, B168Tetrahymena thermophilaMutation(s): 0 
Find proteins for Q234G5 (Tetrahymena thermophila (strain SB210))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
RPS0EAB, BB241Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
KH DOMAIN CONTAINING PROTEINAC, BC243Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN S4 CONTAINING PROTEINAD, BD181Tetrahymena thermophilaMutation(s): 0 
Find proteins for Q230V2 (Tetrahymena thermophila (strain SB210))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN S8 CONTAINING PROTEINAH, BH130Tetrahymena thermophilaMutation(s): 0 
Find proteins for Q238Q8 (Tetrahymena thermophila (strain SB210))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
RPS14EAK, BK151Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
RPS13EAO, BO153Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
RACK1AR, BR343Tetrahymena thermophilaMutation(s): 0 
Find proteins for Q24D42 (Tetrahymena thermophila (strain SB210))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
RPS17EAV, BV130Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
RPS6EAY, BY293Tetrahymena thermophilaMutation(s): 0 
Find proteins for A4VD76 (Tetrahymena thermophila (strain SB210))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN S26E CONTAINING PROTEINA5, B5119Tetrahymena thermophilaMutation(s): 0 
Find proteins for E6PBU4 (Tetrahymena thermophila)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
RPS31EA9, B9189Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 10
MoleculeChainsLengthOrganism
18S RRNAAA, BA1753Tetrahymena thermophila
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
A5, A6, A9, AN, B5, B6, B9, BN
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A4, AA, AL, B4, BA, BD, BW
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 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other