7KP7

asymmetric mTNF-alpha hTNFR1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

Starting Model: other
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural insights into the disruption of TNF-TNFR1 signalling by small molecules stabilising a distorted TNF.

McMillan, D.Martinez-Fleites, C.Porter, J.Fox 3rd, D.Davis, R.Mori, P.Ceska, T.Carrington, B.Lawson, A.Bourne, T.O'Connell, J.

(2021) Nat Commun 12: 582-582

  • DOI: https://doi.org/10.1038/s41467-020-20828-3
  • Primary Citation of Related Structures:  
    7KP7, 7KP8, 7KP9

  • PubMed Abstract: 

    Tumour necrosis factor (TNF) is a trimeric protein which signals through two membrane receptors, TNFR1 and TNFR2. Previously, we identified small molecules that inhibit human TNF by stabilising a distorted trimer and reduce the number of receptors bound to TNF from three to two. Here we present a biochemical and structural characterisation of the small molecule-stabilised TNF-TNFR1 complex, providing insights into how a distorted TNF trimer can alter signalling function. We demonstrate that the inhibitors reduce the binding affinity of TNF to the third TNFR1 molecule. In support of this, we show by X-ray crystallography that the inhibitor-bound, distorted, TNF trimer forms a complex with a dimer of TNFR1 molecules. This observation, along with data from a solution-based network assembly assay, leads us to suggest a model for TNF signalling based on TNF-TNFR1 clusters, which are disrupted by small molecule inhibitors.


  • Organizational Affiliation

    UCB Pharma, Slough, SL1 3WE, UK. david.mcmillan@ucb.com.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tumor necrosis factorA [auth B],
B [auth A],
C
148Mus musculusMutation(s): 0 
Gene Names: TnfTnfaTnfsf2
UniProt
Find proteins for P06804 (Mus musculus)
Explore P06804 
Go to UniProtKB:  P06804
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06804
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tumor necrosis factor receptor superfamily member 1AD [auth E],
E [auth D],
F
144Homo sapiensMutation(s): 2 
Gene Names: TNFRSF1ATNFARTNFR1
UniProt & NIH Common Fund Data Resources
Find proteins for P19438 (Homo sapiens)
Explore P19438 
Go to UniProtKB:  P19438
PHAROS:  P19438
GTEx:  ENSG00000067182 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19438
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
FA [auth D],
GA [auth D],
OA [auth F],
Y [auth E],
Z [auth E]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
CA [auth D]
DA [auth D]
EA [auth D]
AA [auth D],
BA [auth D],
CA [auth D],
DA [auth D],
EA [auth D],
G [auth B],
H [auth B],
HA [auth F],
I [auth B],
IA [auth F],
J [auth A],
JA [auth F],
K [auth A],
KA [auth F],
L [auth A],
LA [auth F],
M [auth A],
MA [auth F],
N [auth C],
NA [auth F],
O [auth C],
P [auth C],
Q [auth E],
R [auth E],
S [auth E],
T [auth E],
U [auth E],
V [auth E],
W [auth E],
X [auth E]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.22α = 90
b = 139.22β = 90
c = 138.34γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-13
    Type: Initial release
  • Version 1.1: 2021-02-03
    Changes: Database references
  • Version 1.2: 2024-04-03
    Changes: Data collection, Database references, Refinement description