3IT8

Crystal structure of TNF alpha complexed with a poxvirus MHC-related TNF binding protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.236 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Crystal structure of TNFalpha complexed with a poxvirus MHC-related TNF binding protein

Yang, Z.West, A.P.Bjorkman, P.J.

(2009) Nat Struct Mol Biol 16: 1189-1191

  • DOI: 10.1038/nsmb.1683
  • Primary Citation of Related Structures:  
    3IT8

  • PubMed Abstract: 
  • The poxvirus 2L protein binds tumor necrosis factor-alpha (TNFalpha) to inhibit host antiviral and immune responses. The 2.8-A 2L-TNFalpha structure reveals three symmetrically arranged 2L molecules per TNFalpha trimer. 2L resembles class I major histocompatibility complex (MHC) molecules but lacks a peptide-binding groove and beta2-microglobulin light chain ...

    The poxvirus 2L protein binds tumor necrosis factor-alpha (TNFalpha) to inhibit host antiviral and immune responses. The 2.8-A 2L-TNFalpha structure reveals three symmetrically arranged 2L molecules per TNFalpha trimer. 2L resembles class I major histocompatibility complex (MHC) molecules but lacks a peptide-binding groove and beta2-microglobulin light chain. Overlap between the 2L and host TNF receptor-binding sites on TNFalpha rationalizes 2L inhibition of TNFalpha-TNF receptor interactions and prevention of TNFalpha-induced immune responses.


    Organizational Affiliation

    Division of Biology 114-96, California Institute of Technology, Pasadena, California, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tumor necrosis factor
A, B, C, G, H, I
A, B, C, G, H, I
161Homo sapiensMutation(s): 0 
Gene Names: TNFTNFATNFSF2
UniProt & NIH Common Fund Data Resources
Find proteins for P01375 (Homo sapiens)
Explore P01375 
Go to UniProtKB:  P01375
PHAROS:  P01375
GTEx:  ENSG00000232810 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01375
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
2L protein
D, E, F, J, K, L
D, E, F, J, K, L
324Yaba-like disease virusMutation(s): 0 
Gene Names: 2L
UniProt
Find proteins for Q9DHW0 (Yaba-like disease virus)
Explore Q9DHW0 
Go to UniProtKB:  Q9DHW0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9DHW0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth K],
BA [auth L],
CA [auth L],
DA [auth L],
M [auth D],
AA [auth K],
BA [auth L],
CA [auth L],
DA [auth L],
M [auth D],
N [auth D],
O [auth D],
P [auth E],
Q [auth E],
R [auth E],
S [auth F],
T [auth F],
U [auth F],
V [auth J],
W [auth J],
X [auth J],
Y [auth K],
Z [auth K]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.236 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.656α = 90
b = 170.295β = 92.04
c = 122.002γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
Web-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-10-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2015-12-09
    Changes: Database references
  • Version 1.3: 2017-11-01
    Changes: Refinement description
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary