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 

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:  

  • 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

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN S28E CONTAINING PROTEIN
A1, B1
68Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Find proteins for Q234G5 (Tetrahymena thermophila (strain SB210))
Go to UniProtKB:  Q234G5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
40S RIBOSOMAL PROTEIN S8
A2, B2
208Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Find proteins for Q22AV0 (Tetrahymena thermophila (strain SB210))
Go to UniProtKB:  Q22AV0
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
RPS7E
A3, B3
197N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
40S RIBOSOMAL PROTEIN S3A
A4, B4
265Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Find proteins for Q23DE3 (Tetrahymena thermophila (strain SB210))
Go to UniProtKB:  Q23DE3
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN S26E CONTAINING PROTEIN
A5, B5
119Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Find proteins for Q23PT4 (Tetrahymena thermophila (strain SB210))
Go to UniProtKB:  Q23PT4
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
RPS27E
A6, B6
81Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Find proteins for Q22CK0 (Tetrahymena thermophila (strain SB210))
Go to UniProtKB:  Q22CK0
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
PLECTIN/S10 DOMAIN CONTAINING PROTEIN
A7, B7
162Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Find proteins for Q24F70 (Tetrahymena thermophila (strain SB210))
Go to UniProtKB:  Q24F70
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
RPS25E
A8, B8
143N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
RPS31E
A9, B9
189N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
RPS0E
AB, BB
241N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
KH DOMAIN CONTAINING PROTEIN
AC, BC
243Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Find proteins for Q22AV9 (Tetrahymena thermophila (strain SB210))
Go to UniProtKB:  Q22AV9
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN S4 CONTAINING PROTEIN
AD, BD
181Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Find proteins for Q230V2 (Tetrahymena thermophila (strain SB210))
Go to UniProtKB:  Q230V2
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN S5 CONTAINING PROTEIN
AE, BE
296Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Find proteins for Q23KG1 (Tetrahymena thermophila (strain SB210))
Go to UniProtKB:  Q23KG1
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
EIF1
AF, BF
101N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN S7 CONTAINING PROTEIN
AG, BG
200Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Find proteins for Q22WU7 (Tetrahymena thermophila (strain SB210))
Go to UniProtKB:  Q22WU7
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN S8 CONTAINING PROTEIN
AH, BH
130Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Find proteins for Q238Q8 (Tetrahymena thermophila (strain SB210))
Go to UniProtKB:  Q238Q8
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
RPS16E, 40S RIBOSOMAL PROTEIN RPS16E
AI, BI
145N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN S10 CONTAINING PROTEIN
AJ, BJ
120Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Find proteins for Q22DC6 (Tetrahymena thermophila (strain SB210))
Go to UniProtKB:  Q22DC6
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
RPS14E
AK, BK
151N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
40S RIBOSOMAL PROTEIN S12
AL, BL
142Tetrahymena thermophilaMutation(s): 0 
Find proteins for P06147 (Tetrahymena thermophila)
Go to UniProtKB:  P06147
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
RPS18E
AM, BM
155N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
RPS29E
AN, BN
55Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Find proteins for Q22MB0 (Tetrahymena thermophila (strain SB210))
Go to UniProtKB:  Q22MB0
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
RPS13E
AO, BO
153N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
RPS24E
AP, BP
149Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Find proteins for Q22MB0 (Tetrahymena thermophila (strain SB210))
Go to UniProtKB:  Q22MB0
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN S17 CONTAINING PROTEIN
AQ, BQ
157Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Find proteins for Q22B78 (Tetrahymena thermophila (strain SB210))
Go to UniProtKB:  Q22B78
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
RACK1
AR, BR
343Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Find proteins for Q24D42 (Tetrahymena thermophila (strain SB210))
Go to UniProtKB:  Q24D42
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
RPS15E
AS, BS
144N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
RPS19E
AT, BT
155N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L7AE CONTAINING PROTEIN
AU, BU
126Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Find proteins for Q22W26 (Tetrahymena thermophila (strain SB210))
Go to UniProtKB:  Q22W26
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
RPS17E
AV, BV
130N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
40S RIBOSOMAL PROTEIN S4
AW, BW
260Tetrahymena thermophilaMutation(s): 0 
Find proteins for P0C233 (Tetrahymena thermophila)
Go to UniProtKB:  P0C233
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
RPS30E
AX, BX
80N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
RPS6E
AY, BY
293Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Find proteins for A4VD76 (Tetrahymena thermophila (strain SB210))
Go to UniProtKB:  A4VD76
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
RPS21E
AZ, BZ
97N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 10
MoleculeChainsLengthOrganism
18S RRNAAA,BA1753Tetrahymena thermophila
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
A4, AA, AL, B4, BA, BD, BW
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
A9, B9
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.93 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.206 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 320.520α = 90.00
b = 362.210β = 109.61
c = 412.110γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXphasing
SHARPphasing
CNSphasing
PHASERmodel building
PHASERphasing
CNSrefinement
DMmodel building
SHARPmodel building
PHENIXmodel building
XDSdata reduction
CNSmodel building
DMphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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