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⇱ RCSB PDB - 1D0J: STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 IN COMPLEX WITH A M4-1BB PEPTIDE

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255,630
Structures from the PDB archive		1,062,058
Computed Structure Models (CSM)

 1D0J | pdb_00001d0j

STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 IN COMPLEX WITH A M4-1BB PEPTIDE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.270 (Depositor) 
  • R-Value Work: 
    0.227 (Depositor) 
  • R-Value Observed: 
    0.227 (Depositor) 

This is version 1.4 of the entry. See complete history. 

Literature

The structural basis for the recognition of diverse receptor sequences by TRAF2.

Ye, H., Park, Y.C., Kreishman, M., Kieff, E., Wu, H.

(1999) Mol Cell 4: 321-330

  • DOI: https://doi.org/10.1016/s1097-2765(00)80334-2
  • Primary Citation Related Structures: 
    1CZY, 1CZZ, 1D00, 1D01, 1D0A, 1D0J

  • PubMed Abstract: 

    Many members of the tumor necrosis factor receptor (TNFR) superfamily initiate intracellular signaling by recruiting TNFR-associated factors (TRAFs) through their cytoplasmic tails. TRAFs apparently recognize highly diverse receptor sequences. Crystal structures of the TRAF domain of human TRAF2 in complex with peptides from the TNFR family members CD40, CD30, Ox40, 4-1BB, and the EBV oncoprotein LMP1 revealed a conserved binding mode. A major TRAF2-binding consensus sequence, (P/S/A/T)x(Q/E)E, and a minor consensus motif, PxQxxD, can be defined from the structural analysis, which encompass all known TRAF2-binding sequences. The structural information provides a template for the further dissection of receptor binding specificity of TRAF2 and for the understanding of the complexity of TRAF-mediated signal transduction.

    • Organizational Affiliation: 
    • Department of Biochemistry, Weill Medical College, New York, New York, USA.

Macromolecule Content 

  • Total Structure Weight: 117.19 kDa 
  • Atom Count: 8,112 
  • Modeled Residue Count: 1,036 
  • Deposited Residue Count: 1,043 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
A, B, C, D, E
A, B, C, D, E, F
168Homo sapiensMutation(s): 0 
EC: 2.3.2.27
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UniProt & NIH Common Fund Data Resources
Find proteins for Q12933 (Homo sapiens)
Explore Q12933 
Go to UniProtKB:  Q12933
PHAROS:  Q12933
GTEx:  ENSG00000127191 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12933
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
4-1BB LIGAND RECEPTOR
G, H, I, J, K
7N/AMutation(s): 0 
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UniProt & NIH Common Fund Data Resources
Find proteins for P20334 (Mus musculus)
Explore P20334 
Go to UniProtKB:  P20334
IMPC:  MGI:1101059
Entity Groups
UniProt GroupP20334
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.270 (Depositor) 
  • R-Value Work:  0.227 (Depositor) 
  • R-Value Observed: 0.227 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.9α = 90
b = 85.6β = 119.1
c = 124.1γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-03-08
    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: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.