4PDC | pdb_00004pdc

Crystal structure of Cowpox virus CPXV018 (OMCP) bound to human NKG2D

• PDB DOI: https://doi.org/10.2210/pdb4PDC/pdb

• Classification: IMMUNE SYSTEM/VIRAL PROTEIN
• Organism(s): Homo sapiens, Cowpox virus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-04-17 Released: 2014-05-21 
• Deposition Author(s): Lazear, E., Nelson, C.A., Fremont, D.H., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 
  0.214 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Models: experimental

Literature

Structural basis of cowpox evasion of NKG2D immunosurveillance

Lazear, E., Sun, M.M., Wang, X., Geurs, T.L., Nelson, C.A., Campbell, J.A., Lippold, D., Krupnick, A.S., Davis, R.S., Carayannopoulos, L.N., French, A.R., Fremont, D.H.

(2019) bioRxiv 

• DOI: https://doi.org/10.1101/796862

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 92.77 kDa 
• Atom Count: 7,151 
• Modeled Residue Count: 791 
• Deposited Residue Count: 792 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NKG2-D type II integral membrane protein	A, B, C, D	123	Homo sapiens	Mutation(s): 0  Gene Names: KLRK1, D12S2489E, NKG2D
UniProt & NIH Common Fund Data Resources
Find proteins for P26718 (Homo sapiens) Explore P26718  Go to UniProtKB:  P26718
PHAROS:  P26718 GTEx:  ENSG00000213809

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CPXV018 protein	E, F	150	Cowpox virus	Mutation(s): 2  Gene Names: CPXV018 CDS
UniProt
Find proteins for Q8QN43 (Cowpox virus (strain Brighton Red)) Explore Q8QN43  Go to UniProtKB:  Q8QN43

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free:  0.214 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.315	α = 90
b = 101.11	β = 91.63
c = 91.368	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-05-21 
Deposition Author(s): Lazear, E., Nelson, C.A., Fremont, D.H., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI073552
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI057160

Revision History  

• Version 1.0: 2014-05-21
  Type: Initial release
  
• Version 1.1: 2014-07-30
  Changes: Database references
• Version 1.2: 2017-08-09
  Changes: Database references, Derived calculations, Other, Source and taxonomy
• Version 1.3: 2017-09-13
  Changes: Author supporting evidence
• Version 1.4: 2017-11-22
  Changes: Refinement description
• Version 1.5: 2019-11-06
  Changes: Data collection, Database references
• Version 1.6: 2019-12-11
  Changes: Author supporting evidence
• Version 1.7: 2023-09-27
  Changes: Data collection, Database references, Refinement description
• Version 1.8: 2024-10-30
  Changes: Structure summary