1EXT

EXTRACELLULAR DOMAIN OF THE 55KDA TUMOR NECROSIS FACTOR RECEPTOR. CRYSTALLIZED AT PH3.7 IN P 21 21 21.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structures of the extracellular domain of the type I tumor necrosis factor receptor.

Naismith, J.H.Devine, T.Q.Kohno, T.Sprang, S.R.

(1996) Structure 4: 1251-1262

  • DOI: 10.1016/s0969-2126(96)00134-7
  • Primary Citation of Related Structures:  
    1EXT

  • PubMed Abstract: 
  • Tumor necrosis factor (TNF) is a powerful cytokine that is involved in immune and pro-inflammatory responses. Two TNF receptors that belong to the cysteine-rich low affinity nerve growth factor receptor family (TNF-R1 and TNF-R2) are the sole mediato ...

    Tumor necrosis factor (TNF) is a powerful cytokine that is involved in immune and pro-inflammatory responses. Two TNF receptors that belong to the cysteine-rich low affinity nerve growth factor receptor family (TNF-R1 and TNF-R2) are the sole mediators of TNF signalling. Signalling is thought to occur when a trimer of TNF binds to the extracellular domains of two or three receptor molecules, which permits aggregation and activation of the cytoplasmic domains. The complex is then internalized within an endocytic vesicle, whereupon it dissociates at low pH. Structure of the soluble extracellular domain of the receptor (sTNF-R1) both in the unliganded and TNF-bound state have previously been determined. In both instances, the fourth subdomain of the receptor was found to be partly disordered. In the unliganded state at pH 7.5, the extracellular domain forms two distinct types of dimer, parallel and antiparallel; the antiparallel dimer occludes the TNF-binding.


    Related Citations: 
    • Crystallographic Evidence for Dimerization of Unliganded Tumor Necrosis Factor Receptor
      Naismith, J.H., Devine, T.Q., Brandhuber, B.J., Sprang, S.R.
      (1995) J Biol Chem 270: 13303
    • Two Crystal Forms of the Extracellular Domain of Type I Tumor Necrosis Factor Receptor
      Rodseth, L.E., Brandhuber, B., Devine, T.Q., Eck, M.J., Hale, K., Naismith, J.H., Sprang, S.R.
      (1994) J Mol Biol 239: 332
    • Crystal Structure of the Soluble Human 55 Kd Tnf Receptor-Human Tnf Beta Complex: Implications for Tnf Receptor Activation
      Banner, D.W., D'Arcy, A., Janes, W., Gentz, R., Schoenfeld, H.J., Broger, C., Loetscher, H., Lesslauer, W.
      (1993) Cell 73: 431

    Organizational Affiliation

    Centre for Biomolecular Sciences, Purdie Building, The University, St. Andrews, KY16 9ST, Scotland, UK. naismith@st-andrews.ac.uk



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TUMOR NECROSIS FACTOR RECEPTORAB162Homo sapiensMutation(s): 0 
Gene Names: TNFRSF1ATNFARTNFR1
Find proteins for P19438 (Homo sapiens)
Explore P19438 
Go to UniProtKB:  P19438
NIH Common Fund Data Resources
PHAROS  P19438
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.81α = 90
b = 83.06β = 90
c = 67.9γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-01-11
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance