1GH6 | pdb_00001gh6

RETINOBLASTOMA POCKET COMPLEXED WITH SV40 LARGE T ANTIGEN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.314 (Depositor) 
  • R-Value Work: 
    0.248 (Depositor) 
  • R-Value Observed: 
    0.248 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 1GH6

This is version 1.4 of the entry. See complete history

Literature

Structural basis for the inactivation of retinoblastoma tumor suppressor by SV40 large T antigen.

Kim, H.Y.Ahn, B.Y.Cho, Y.

(2001) EMBO J 20: 295-304

  • DOI: https://doi.org/10.1093/emboj/20.1.295
  • Primary Citation Related Structures: 
    1GH6

  • PubMed Abstract: 

    Inactivation of the retinoblastoma (Rb) tumor suppressor by Simian virus 40 (SV40) large T antigen is one of the central features of tumorigenesis induced by SV40. Both the N-terminal J domain and the LxCxE motif of large T antigen are required for inactivation of Rb. The crystal structure of the N-terminal region (residues 7-117) of SV40 large T antigen bound to the pocket domain of Rb reveals that large T antigen contains a four-helix bundle, and residues from helices alpha2 and alpha4 and from a loop containing the LxCxE motif participate in the interactions with Rb. The two central helices and a connecting loop in large T antigen have structural similarities with the J domains of the molecular chaperones DnaJ and HDJ-1, suggesting that large T antigen may use a chaperone mechanism for its biological function. However, there are significant differences between large T antigen and the molecular chaperones in other regions and these differences are likely to provide the specificity needed for large T antigen to inactivate Rb.


  • Organizational Affiliation
    • Division of Molecular and Life Science, Pohang University of Science and Technology, Hyo-ja dong, San31, Pohang, Seoul, South Korea.

Macromolecule Content 

  • Total Structure Weight: 52.46 kDa 
  • Atom Count: 3,627 
  • Modeled Residue Count: 440 
  • Deposited Residue Count: 447 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Large T antigen114Betapolyomavirus macacaeMutation(s): 0 
EC: 3.6.4 (PDB Primary Data), 5.6.2.4 (UniProt)
UniProt
Find proteins for P03070 (Simian virus 40)
Explore P03070 
Go to UniProtKB:  P03070
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03070
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Retinoblastoma-associated protein333Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P06400 (Homo sapiens)
Explore P06400 
Go to UniProtKB:  P06400
PHAROS:  P06400
GTEx:  ENSG00000139687 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06400
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.314 (Depositor) 
  • R-Value Work:  0.248 (Depositor) 
  • R-Value Observed: 0.248 (Depositor) 
Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.13α = 90
b = 127.13β = 90
c = 96.19γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-11-15
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-06-28
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.4: 2023-08-09
    Changes: Data collection, Database references, Refinement description