5UUI

Crystal Structure of Spin-Labeled T77C TNFa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.139 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Natural Conformational Sampling of Human TNF alpha Visualized by Double Electron-Electron Resonance.

Carrington, B.Myers, W.K.Horanyi, P.Calmiano, M.Lawson, A.D.G.

(2017) Biophys. J. 113: 371-380

  • DOI: 10.1016/j.bpj.2017.06.007

  • PubMed Abstract: 
  • Double electron-electron resonance in conjunction with site-directed spin labeling has been used to probe natural conformational sampling of the human tumor necrosis factor α trimer. We suggest a previously unreported, predeoligomerization conformati ...

    Double electron-electron resonance in conjunction with site-directed spin labeling has been used to probe natural conformational sampling of the human tumor necrosis factor α trimer. We suggest a previously unreported, predeoligomerization conformation of the trimer that has been shown to be sampled at low frequency. A model of this trimeric state has been constructed based on crystal structures using the double-electron-electron-resonance distances. The model shows one of the protomers to be rotated and tilted outward at the tip end, leading to a breaking of the trimerous symmetry and distortion at a receptor-binding interface. The new structure offers opportunities to modulate the biological activity of tumor necrosis factor α through stabilization of the distorted trimer with small molecules.


    Organizational Affiliation

    UCB Celltech, Slough, United Kingdom. Electronic address: bruce.carrington@ucb.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tumor necrosis factor
A
158Homo sapiensMutation(s): 1 
Gene Names: TNF (TNFA, TNFSF2)
Find proteins for P01375 (Homo sapiens)
Go to Gene View: TNF
Go to UniProtKB:  P01375
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MTN
Query on MTN

Download SDF File 
Download CCD File 
A
S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate
MTSL
C10 H18 N O3 S2
MXZPGYFBZHBAQM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.139 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 65.660α = 90.00
b = 65.660β = 90.00
c = 84.090γ = 120.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-08-02
    Type: Initial release
  • Version 1.1: 2017-08-09
    Type: Database references