4KZX

Rabbit 40S ribosomal subunit in complex with eIF1.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.809 Å
  • R-Value Free: 0.347 
  • R-Value Work: 0.347 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

The initiation of mammalian protein synthesis and mRNA scanning mechanism.

Lomakin, I.B., Steitz, T.A.

(2013) Nature 500: 307-311

  • DOI: 10.1038/nature12355
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • During translation initiation in eukaryotes, the small ribosomal subunit binds messenger RNA at the 5' end and scans in the 5' to 3' direction to locate the initiation codon, form the 80S initiation complex and start protein synthesis. This simple, y ...

    During translation initiation in eukaryotes, the small ribosomal subunit binds messenger RNA at the 5' end and scans in the 5' to 3' direction to locate the initiation codon, form the 80S initiation complex and start protein synthesis. This simple, yet intricate, process is guided by multiple initiation factors. Here we determine the structures of three complexes of the small ribosomal subunit that represent distinct steps in mammalian translation initiation. These structures reveal the locations of eIF1, eIF1A, mRNA and initiator transfer RNA bound to the small ribosomal subunit and provide insights into the details of translation initiation specific to eukaryotes. Conformational changes associated with the captured functional states reveal the dynamics of the interactions in the P site of the ribosome. These results have functional implications for the mechanism of mRNA scanning.

    Organizational Affiliation: 

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, USA. ivan.lomakin@yale.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein SA
A
295Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPSA
Find proteins for G1TGI6 (Oryctolagus cuniculus)
Go to Gene View: RPSA
Go to UniProtKB:  G1TGI6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S3a
B
264Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3A
Find proteins for G1TN72 (Oryctolagus cuniculus)
Go to Gene View: RPS3A
Go to UniProtKB:  G1TN72
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S2
C
278Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1U2Z9 (Oryctolagus cuniculus)
Go to UniProtKB:  G1U2Z9
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S3
D
243Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3
Find proteins for G1TNM3 (Oryctolagus cuniculus)
Go to Gene View: RPS3
Go to UniProtKB:  G1TNM3
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S4X
E
263Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100338112
Find proteins for G1TK17 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TK17
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S5
F
204Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS5
Find proteins for G1TFM5 (Oryctolagus cuniculus)
Go to Gene View: RPS5
Go to UniProtKB:  G1TFM5
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S6
G
249Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TM55 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TM55
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S7
H
194Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SVB0 (Oryctolagus cuniculus)
Go to UniProtKB:  G1SVB0
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S8
I
208Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100352057
Find proteins for G1TJW1 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TJW1
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
40S Ribosomal protein S9
J
194Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS9
Find proteins for B7NZS8 (Oryctolagus cuniculus)
Go to Gene View: RPS9
Go to UniProtKB:  B7NZS8
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S10
K
165Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS10
Find proteins for G1T168 (Oryctolagus cuniculus)
Go to Gene View: RPS10
Go to UniProtKB:  G1T168
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S11
L
158Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS11
Find proteins for G1TRM4 (Oryctolagus cuniculus)
Go to Gene View: RPS11
Go to UniProtKB:  G1TRM4
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S12
M
132Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS12
Find proteins for G1SFR8 (Oryctolagus cuniculus)
Go to Gene View: RPS12
Go to UniProtKB:  G1SFR8
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S13
N
151Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SP51 (Oryctolagus cuniculus)
Go to UniProtKB:  G1SP51
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S14
O
151Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100337691
Find proteins for G1U472 (Oryctolagus cuniculus)
Go to UniProtKB:  G1U472
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S15
P
145Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS15
Find proteins for G1U0Q2 (Oryctolagus cuniculus)
Go to Gene View: RPS15
Go to UniProtKB:  G1U0Q2
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S16
Q
146Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS16
Find proteins for G1SGX4 (Oryctolagus cuniculus)
Go to Gene View: RPS16
Go to UniProtKB:  G1SGX4
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S17
R
135Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100353606 (RPS17)
Find proteins for G1TU13 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TU13
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S18
S
152Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS18
Find proteins for G1TPG3 (Oryctolagus cuniculus)
Go to Gene View: RPS18
Go to UniProtKB:  G1TPG3
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S19
T
145Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100345774
Find proteins for G1TN62 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TN62
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S20
U
119Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS20 (LOC100341365, LOC100348955, LOC100354063)
Find proteins for G1SIZ2 (Oryctolagus cuniculus)
Go to Gene View: RPS20
Go to UniProtKB:  G1SIZ2
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S21
V
83Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS21
Find proteins for G1TM82 (Oryctolagus cuniculus)
Go to Gene View: RPS21
Go to UniProtKB:  G1TM82
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S15A
W
130Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS15A
Find proteins for G1TG89 (Oryctolagus cuniculus)
Go to Gene View: RPS15A
Go to UniProtKB:  G1TG89
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S23
X
143Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS23
Find proteins for G1SZ47 (Oryctolagus cuniculus)
Go to Gene View: RPS23
Go to UniProtKB:  G1SZ47
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S24
Y
133Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TS40 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TS40
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S25
Z
125Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TDB3 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TDB3
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S26
a
115Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100346996
Find proteins for G1TFE8 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TFE8
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S27
b
84Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100345694 (LOC100345044, LOC100348261, RPS27)
Find proteins for G1TZ76 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TZ76
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S28
c
69Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS28
Find proteins for G1TIB4 (Oryctolagus cuniculus)
Go to Gene View: RPS28
Go to UniProtKB:  G1TIB4
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S29
d
56Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100337712
Find proteins for G1U7M4 (Oryctolagus cuniculus)
Go to UniProtKB:  G1U7M4
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S30
e
133Oryctolagus cuniculusMutation(s): 0 
Gene Names: FAU
Find proteins for G1T8A2 (Oryctolagus cuniculus)
Go to Gene View: FAU
Go to UniProtKB:  G1T8A2
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S27A
f
156Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SK22 (Oryctolagus cuniculus)
Go to UniProtKB:  G1SK22
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein RACK1
g
317Oryctolagus cuniculusMutation(s): 0 
Gene Names: RACK1
Find proteins for G1SJB4 (Oryctolagus cuniculus)
Go to Gene View: RACK1
Go to UniProtKB:  G1SJB4
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 1
l
113Homo sapiensMutation(s): 0 
Gene Names: EIF1 (SUI1)
Find proteins for P41567 (Homo sapiens)
Go to Gene View: EIF1
Go to UniProtKB:  P41567
Entity ID: 34
MoleculeChainsLengthOrganism
18S ribosomal RNAi1863Oryctolagus cuniculus
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.809 Å
  • R-Value Free: 0.347 
  • R-Value Work: 0.347 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 292.121α = 90.00
b = 292.121β = 90.00
c = 477.667γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata scaling
XDSdata reduction
CBASSdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-24
    Type: Initial release
  • Version 1.1: 2013-08-07
    Type: Database references
  • Version 1.2: 2013-09-04
    Type: Database references