6Q3K | pdb_00006q3k

Engineered Human HLA_A2 MHC Class I molecule in complex with NV9 peptide

• PDB DOI: https://doi.org/10.2210/pdb6Q3K/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Cytomegalovirus
• Expression System: Escherichia coli, synthetic construct
• Mutation(s): No 


• Deposited: 2018-12-04 Released: 2019-07-24 
• Deposition Author(s): Meijers, R., Anjanappa, R., Springer, S., Garcia-Alai, M.
• Funding Organization(s): European Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.200 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

Engineered Human HLA_A2MHC Class I molecule in complex with NV9 peptide

Meijers, R., Anjanappa, R., Springer, S., Garcia-Alai, M.

(2019) Sci Immunol 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Macromolecule Content 

• Total Structure Weight: 45.34 kDa 
• Atom Count: 3,787 
• Modeled Residue Count: 384 
• Deposited Residue Count: 385 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen, A-2 alpha chain	A	276	Homo sapiens	Mutation(s): 0  Gene Names: HLA-A, HLAA
UniProt & NIH Common Fund Data Resources
Find proteins for P04439 (Homo sapiens) Explore P04439  Go to UniProtKB:  P04439
PHAROS:  P04439 GTEx:  ENSG00000206503

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	100	Homo sapiens	Mutation(s): 0  Gene Names: B2M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769
PHAROS:  P61769 GTEx:  ENSG00000166710

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ASN-LEU-VAL-PRO-MET-VAL-ALA-THR-VAL	C [auth P]	9	Cytomegalovirus	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A], L [auth P]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CO	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth B]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.200 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.158	α = 90
b = 80.575	β = 90
c = 109.693	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-07-24 
Deposition Author(s): Meijers, R., Anjanappa, R., Springer, S., Garcia-Alai, M.

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Funding Organization	Location	Grant Number
European Commission		653706

Revision History  

• Version 1.0: 2019-07-24
  Type: Initial release
  
• Version 1.1: 2019-11-20
  Changes: Derived calculations
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary