4KZZ

Rabbit 40S ribosomal subunit in complex with mRNA, initiator tRNA and eIF1A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.0305 Å
  • R-Value Free: 0.359 
  • R-Value Work: 0.345 

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

  • Primary Citation of Related Structures:  4KZX, 4KZY

  • 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 cuniculusN/A
Find proteins for G1TGI6 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TGI6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
40S Ribosomal Protein S3A
B
264Oryctolagus cuniculusGene Names: LOC100340708 (RPS3A)
Find proteins for G1TN72 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TN72
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
40S Ribosomal Protein S2
C
278Oryctolagus cuniculusN/A
Find proteins for G1U2Z9 (Oryctolagus cuniculus)
Go to UniProtKB:  G1U2Z9
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
40S Ribosomal Protein S3
D
243Oryctolagus cuniculusN/A
Find proteins for G1TNM3 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TNM3
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
40S Ribosomal Protein S4X
E
263Oryctolagus cuniculusGene Names: RPS4X
Find proteins for G1TK17 (Oryctolagus cuniculus)
Go to Gene View: RPS4X
Go to UniProtKB:  G1TK17
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
40S Ribosomal Protein S5
F
204Oryctolagus cuniculusGene 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 cuniculusGene Names: LOC100339133
Find proteins for G1TM55 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TM55
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
40S Ribosomal Protein S7
H
194Oryctolagus cuniculusGene Names: RPS7
Find proteins for G1SVB0 (Oryctolagus cuniculus)
Go to Gene View: RPS7
Go to UniProtKB:  G1SVB0
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
40S Ribosomal Protein S8
I
208Oryctolagus cuniculusGene Names: RPS8
Find proteins for G1TJW1 (Oryctolagus cuniculus)
Go to Gene View: RPS8
Go to UniProtKB:  G1TJW1
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
40S Ribosomal Protein S9
J
194Oryctolagus cuniculusGene 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 cuniculusN/A
Find proteins for G1T168 (Oryctolagus cuniculus)
Go to UniProtKB:  G1T168
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
40S Ribosomal Protein S11
L
158Oryctolagus cuniculusGene 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 cuniculusGene 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 cuniculusGene Names: RPS13
Find proteins for G1SP51 (Oryctolagus cuniculus)
Go to Gene View: RPS13
Go to UniProtKB:  G1SP51
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
40S Ribosomal Protein S14
O
151Oryctolagus cuniculusGene Names: LOC100337691
Find proteins for G1U472 (Oryctolagus cuniculus)
Go to UniProtKB:  G1U472
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
40S Ribosomal Protein S15
P
145Oryctolagus cuniculusGene Names: LOC103349305
Find proteins for G1U0Q2 (Oryctolagus cuniculus)
Go to UniProtKB:  G1U0Q2
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
40S Ribosomal Protein S16
Q
146Oryctolagus cuniculusGene 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 cuniculusGene Names: RPS17
Find proteins for G1TU13 (Oryctolagus cuniculus)
Go to Gene View: RPS17
Go to UniProtKB:  G1TU13
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
40S Ribosomal Protein S18
S
152Oryctolagus cuniculusGene 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 cuniculusGene Names: RPS19
Find proteins for G1TN62 (Oryctolagus cuniculus)
Go to Gene View: RPS19
Go to UniProtKB:  G1TN62
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
40S Ribosomal Protein S20
U
119Oryctolagus cuniculusGene Names: LOC100354063
Find proteins for G1SIZ2 (Oryctolagus cuniculus)
Go to UniProtKB:  G1SIZ2
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
40S Ribosomal Protein S21
V
83Oryctolagus cuniculusGene 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 cuniculusGene 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 cuniculusGene 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 cuniculusGene Names: RPS24
Find proteins for G1TS40 (Oryctolagus cuniculus)
Go to Gene View: RPS24
Go to UniProtKB:  G1TS40
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
40S Ribosomal Protein S25
Z
125Oryctolagus cuniculusGene Names: RPS25
Find proteins for G1TDB3 (Oryctolagus cuniculus)
Go to Gene View: RPS25
Go to UniProtKB:  G1TDB3
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
40S Ribosomal Protein S26
a
115Oryctolagus cuniculusGene Names: RPS26
Find proteins for G1TFE8 (Oryctolagus cuniculus)
Go to Gene View: RPS26
Go to UniProtKB:  G1TFE8
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
40S Ribosomal Protein S27
b
84Oryctolagus cuniculusGene Names: RPS27
Find proteins for G1TZ76 (Oryctolagus cuniculus)
Go to Gene View: RPS27
Go to UniProtKB:  G1TZ76
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
40S Ribosomal Protein S28
c
69Oryctolagus cuniculusGene 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 cuniculusGene Names: LOC100337712
Find proteins for G1U7M4 (Oryctolagus cuniculus)
Go to UniProtKB:  G1U7M4
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
40S Ribosomal Protein S30
e
133Oryctolagus cuniculusGene 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 cuniculusGene Names: RPS27A
Find proteins for G1SK22 (Oryctolagus cuniculus)
Go to Gene View: RPS27A
Go to UniProtKB:  G1SK22
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
40S Ribosomal Protein RACK1
g
317Oryctolagus cuniculusGene Names: GNB2L1
Find proteins for G1SJB4 (Oryctolagus cuniculus)
Go to UniProtKB:  G1SJB4
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
human initiation factor eIF1A
n
144Homo sapiensGene Names: EIF1AX (EIF1A, EIF4C)
Find proteins for P47813 (Homo sapiens)
Go to Gene View: EIF1AX
Go to UniProtKB:  P47813
Entity ID: 34
MoleculeChainsLengthOrganism
18S Ribosomal RNAi1863Oryctolagus cuniculus
Entity ID: 35
MoleculeChainsLengthOrganism
initiator Met-RNA-ij75Homo sapiens
Entity ID: 36
MoleculeChainsLengthOrganism
mRNAk24synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.0305 Å
  • R-Value Free: 0.359 
  • R-Value Work: 0.345 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 297.750α = 90.00
b = 297.750β = 90.00
c = 485.160γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
XDSdata reduction
ADSCdata collection
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



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