4V4A

Crystal Structure of the Wild Type Ribosome from E. Coli 70S Ribosome.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 9.50 Å
  • R-Value Free: 0.407 
  • R-Value Work: 0.389 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

X-ray crystal structures of the WT and a hyper-accurate ribosome from Escherichia coli

Vila-Sanjurjo, A.Ridgeway, W.K.Seymaner, V.Zhang, W.Santoso, S.Yu, K.Cate, J.H.D.

(2003) Proc Natl Acad Sci U S A 100: 8682-8687

  • DOI: 10.1073/pnas.1133380100
  • Primary Citation of Related Structures:  
    4V4A, 4V49

  • PubMed Abstract: 
  • Protein biosynthesis on the ribosome requires accurate reading of the genetic code in mRNA. Two conformational rearrangements in the small ribosomal subunit, a closing of the head and body around the incoming tRNA and an RNA helical switch near the mRNA decoding site, have been proposed to select for complementary base-pairing between mRNA codons and tRNA anticodons ...

    Protein biosynthesis on the ribosome requires accurate reading of the genetic code in mRNA. Two conformational rearrangements in the small ribosomal subunit, a closing of the head and body around the incoming tRNA and an RNA helical switch near the mRNA decoding site, have been proposed to select for complementary base-pairing between mRNA codons and tRNA anticodons. We determined x-ray crystal structures of the WT and a hyper-accurate variant of the Escherichia coli ribosome at resolutions of 10 and 9 A, respectively, revealing that formation of the intact 70S ribosome from its two subunits closes the conformation of the head of the small subunit independent of mRNA decoding. Moreover, no change in the conformation of the switch helix is observed in two steps of tRNA discrimination. These 70S ribosome structures indicate that mRNA decoding is coupled primarily to movement of the small subunit body, consistent with previous proposals, whereas closing of the head and the helical switch may function in other steps of protein synthesis.


    Organizational Affiliation

    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2 AB234Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3 AC206Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4 AD208Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5 AE150Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6 AF101Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S7 AG155Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8 AH138Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9 AI127Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S10 AJ98Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S11 AK119Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S12 AL124Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S13 AM125Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S14 AN60Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S15 AO88Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S16 AP83Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17 AQ104Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S18 AR73Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19 AS80Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S20 AT99Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2 BA270Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3 BB205Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4 BC197Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5 BD178Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6 BE177Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L9 BF52Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L11 BG143Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13 BH143Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14 BI132Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15 BJ141Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L16 BK124Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L17 BL114Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18 BM111Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19 BN125Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L20 BO117Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21 BP100Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L22 BQ130Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23 BR93Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24 BS113Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
general stress protein Ctc BT173Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L27 BU86Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L28 BV16Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29 BW65Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30 BX55Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L31 BY73Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32 BZ58Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L33 B153Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34 B246Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L35 B363Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L36 B435Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L1P B5217Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
16S RIBOSOMAL RNAAA1537Escherichia coli
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 21
MoleculeChainsLengthOrganismImage
23S RIBOSOMAL RNAB02887Escherichia coli
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 22
MoleculeChainsLengthOrganismImage
5S RIBOSOMAL RNAB9118Escherichia coli
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
B5L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 9.50 Å
  • R-Value Free: 0.407 
  • R-Value Work: 0.389 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 683.89α = 90
b = 683.89β = 90
c = 386.72γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



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