3IT8

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

• PDB DOI: https://doi.org/10.2210/pdb3IT8/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Yaba-like disease virus
• Expression System: Escherichia coli, Trichoplusia ni
• Mutation(s): No 


• Deposited: 2009-08-27 Released: 2009-10-20 
• Deposition Author(s): Yang, Z., West Jr., A.P., Bjorkman, P.J.

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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 

Starting Models: experimental

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

• PubMed: 19838188 
• DOI: https://doi.org/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. 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 335.67 kDa 
• Atom Count: 22,002 
• Modelled Residue Count: 2,706 
• Deposited Residue Count: 2,910 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor necrosis factor	A, B, C, G, H, I	161	Homo sapiens	Mutation(s): 0  Gene Names: TNF
UniProt & NIH Common Fund Data Resources
Find proteins for P01375 (Homo sapiens) Explore P01375  Go to UniProtKB:  P01375
GTEx:  ENSG00000232810

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
2L protein	D, E, F, J, K, L	324	Yaba-like disease virus	Mutation(s): 0  Gene Names: 2L
UniProt
Find proteins for Q9DHW0 (Yaba-like disease virus) Explore Q9DHW0  Go to UniProtKB:  Q9DHW0
Glycosylation
Glycosylation Sites: 3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	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

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 = 101.656	α = 90
b = 170.295	β = 92.04
c = 122.002	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
Web-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-20 
Deposition Author(s): Yang, Z., West Jr., A.P., Bjorkman, P.J.

Revision History  

• 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
• Version 1.5: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary