5UUI | pdb_00005uui

Crystal Structure of Spin-Labeled T77C TNFa

• PDB DOI: https://doi.org/10.2210/pdb5UUI/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-02-16 Released: 2017-08-02 
• Deposition Author(s): Horanyi, P.S., Dranow, D.M., Ceska, T.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.170 (Depositor), 0.168 (DCC) 
• R-Value Work: 
  0.139 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.148 (Depositor) 

Starting Model: experimental

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

• PubMed: 28746848 
• DOI: https://doi.org/10.1016/j.bpj.2017.06.007
• Primary Citation Related Structures: 
  5UUI


• 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 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: [e-mail].
Department of Inorganic Chemistry, University of Oxford, Oxford, United Kingdom.
Beryllium, Bainbridge Island, Washington.
UCB Celltech, Slough, United Kingdom.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 17.72 kDa 
• Atom Count: 1,080 
• Modeled Residue Count: 134 
• Deposited Residue Count: 158 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor necrosis factor	A	158	Homo sapiens	Mutation(s): 1  Gene Names: TNF, TNFA, TNFSF2
UniProt & NIH Common Fund Data Resources
Find proteins for P01375 (Homo sapiens) Explore P01375  Go to UniProtKB:  P01375
PHAROS:  P01375 GTEx:  ENSG00000232810

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MTN	B [auth A]	S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate C10 H18 N O3 S2 MXZPGYFBZHBAQM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.170 (Depositor), 0.168 (DCC) 
• R-Value Work:  0.139 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.148 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.66	α = 90
b = 65.66	β = 90
c = 84.09	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-02 
Deposition Author(s): Horanyi, P.S., Dranow, D.M., Ceska, T.

Revision History  

• Version 1.0: 2017-08-02
  Type: Initial release
  
• Version 1.1: 2017-08-09
  Changes: Database references
• Version 1.2: 2024-01-17
  Changes: Advisory, Data collection, Database references, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary