3ALQ

Crystal structure of TNF-TNFR2 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Solution of the Structure of the TNF-TNFR2 Complex

Mukai, Y.Nakamura, T.Yoshikawa, M.Yoshioka, Y.Tsunoda, S.I.Nakagawa, S.Yamagata, Y.Tsutsumi, Y.

(2010) Sci Signal 3: ra83-ra83

  • DOI: 10.1126/scisignal.2000954
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Tumor necrosis factor (TNF) is an inflammatory cytokine that has important roles in various immune responses, which are mediated through its two receptors, TNF receptor 1 (TNFR1) and TNFR2. Antibody-based therapy against TNF is used clinically to tre ...

    Tumor necrosis factor (TNF) is an inflammatory cytokine that has important roles in various immune responses, which are mediated through its two receptors, TNF receptor 1 (TNFR1) and TNFR2. Antibody-based therapy against TNF is used clinically to treat several chronic autoimmune diseases; however, such treatment sometimes results in serious side effects, which are thought to be caused by the blocking of signals from both TNFRs. Therefore, knowledge of the structural basis for the recognition of TNF by each receptor would be invaluable in designing TNFR-selective drugs. Here, we solved the 3.0 angstrom resolution structure of the TNF-TNFR2 complex, which provided insight into the molecular recognition of TNF by TNFR2. Comparison to the known TNFR1 structure highlighted several differences between the ligand-binding interfaces of the two receptors. Additionally, we also demonstrated that TNF-TNFR2 formed aggregates on the surface of cells, which may be required for signal initiation. These results may contribute to the design of therapeutics for autoimmune diseases.


    Organizational Affiliation

    Laboratory of Biopharmaceutical Research, National Institute of Biomedical Innovation, Osaka, Japan. yohe@phs.osaka-u.ac.jp



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tumor necrosis factorA, B, C, D, E, F157Homo sapiensMutation(s): 6 
Gene Names: TNFTNFATNFSF2
Find proteins for P01375 (Homo sapiens)
Explore P01375 
Go to UniProtKB:  P01375
NIH Common Fund Data Resources
PHAROS  P01375
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Tumor necrosis factor receptor superfamily member 1BR, S, T, U, V, W173Homo sapiensMutation(s): 0 
Gene Names: TNFBRTNFR2TNFRSF1B
Find proteins for P20333 (Homo sapiens)
Explore P20333 
Go to UniProtKB:  P20333
NIH Common Fund Data Resources
PHAROS  P20333
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CO
Query on CO

Download CCD File 
R, S, T, U, V, W
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.220 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.47α = 90
b = 117.356β = 90
c = 246.835γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-11-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance