1CVJ | pdb_00001cvj

X-RAY CRYSTAL STRUCTURE OF THE POLY(A)-BINDING PROTEIN IN COMPLEX WITH POLYADENYLATE RNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.304 (Depositor) 
  • R-Value Work: 
    0.230 (Depositor) 
  • R-Value Observed: 
    0.230 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1CVJ

This is version 2.0 of the entry. See complete history. 

Literature

Recognition of polyadenylate RNA by the poly(A)-binding protein.

Deo, R.C., Bonanno, J.B., Sonenberg, N., Burley, S.K.

(1999) Cell 98: 835-845

  • DOI: https://doi.org/10.1016/s0092-8674(00)81517-2
  • Primary Citation Related Structures: 
    1CVJ

  • PubMed Abstract: 

    The cocrystal structure of human poly(A)-binding protein (PABP) has been determined at 2.6 A resolution. PABP recognizes the 3' mRNA poly(A) tail and plays critical roles in eukaryotic translation initiation and mRNA stabilization/degradation. The minimal PABP used in this study consists of the N-terminal two RRM-type RNA-binding domains connected by a short linker (RRM1/2). These two RRMs form a continuous RNA-binding trough, lined by an antiparallel beta sheet backed by four alpha helices. The polyadenylate RNA adopts an extended conformation running the length of the molecular trough. Adenine recognition is primarily mediated by contacts with conserved residues found in the RNP motifs of the two RRMs. The convex dorsum of RRM1/2 displays a phylogenetically conserved hydrophobic/acidic portion, which may interact with translation initiation factors and regulatory proteins.

    • Organizational Affiliation: 
    • Laboratories of Molecular Biophysics, The Rockefeller University, New York, New York 10021, USA.

Macromolecule Content 

  • Total Structure Weight: 203.1 kDa 
  • Atom Count: 11,162 
  • Modeled Residue Count: 1,304 
  • Deposited Residue Count: 1,608 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:
|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
POLYADENYLATE BINDING PROTEIN 1190Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P11940 (Homo sapiens)
Explore P11940 
Go to UniProtKB:  P11940
PHAROS:  P11940
GTEx:  ENSG00000070756 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11940
Sequence Annotations
Expand
Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 1
MoleculeChains LengthOrganismImage
5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'11N/A
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.304 (Depositor) 
  • R-Value Work:  0.230 (Depositor) 
  • R-Value Observed: 0.230 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.557α = 90
b = 176.797β = 117.67
c = 82.489γ = 90
Software Package:
Software NamePurpose
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-10-04
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-02-03
    Changes: Advisory, Database references, Derived calculations, Structure summary
  • Version 1.4: 2024-02-07
    Changes: Advisory, Data collection, Database references
  • Version 2.0: 2024-05-29
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary