Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 44.79 kDa 
• Atom Count: 3548 
• Residue Count: 382 
• Unique protein chains: 3

4HX1

Structure of HLA-A68 complexed with a tumor antigen derived peptide

• DOI: 10.2210/pdb4HX1/pdb

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


• Deposited: 2012-11-09 Released: 2013-10-02 
• Deposition Author(s): Niu, L., Cheng, H., Zhang, S., Tan, S., Zhang, Y., Qi, J., Liu, J., Gao, G.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.226 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 

Literature

Structural basis for the differential classification of HLA-A*6802 and HLA-A*6801 into the A2 and A3 supertypes

Niu, L., Cheng, H., Zhang, S., Tan, S., Zhang, Y., Qi, J., Liu, J., Gao, G.F.

(2013) Mol Immunol 55: 381-392

• PubMed: 23566939 
• DOI: 10.1016/j.molimm.2013.03.015
• Primary Citation of Related Structures:  
  4I48, 4HWZ, 4HX1


• PubMed Abstract: 
  

High polymorphism is one of the most important features of human leukocyte antigen (HLA) alleles, which were initially classified by serotyping but have recently been re-grouped into supertypes according to their peptide presentation properties. Two relatively prevalent HLA alleles HLA-A*6801 and HLA-A*6802, are classified into the same serotype HLA-A68. However, based on their distinct peptide-binding characteristics, HLA-A*6801 is grouped into A3 supertype, whereas HLA-A*6802 belongs to A2 supertype, similar to HLA-A*0201. Thusfar, the structural basis of the different supertype definitions of these serotyping-identical HLA alleles remains largely unknown. Herein, we determined the structures of HLA-A*6801 and HLA-A*6802 presenting three typical A3 and A2 supertype-restricted peptides, respectively. The binding capabilities of these peptides to HLA-A*6801, HLA-A*6802, and HLA-A*0201 were analyzed. These data indicate that the similar conformations of the residues within the F pocket contribute to close-related peptide binding features of HLA-A*6802 and HLA-A*0201. However, the overall structure and the peptide conformation of HLA-A*6802 are more similar to HLA-A*6801 rather than HLA-A*0201 which illuminates the similar serotype grouping of HLA-A*6802 and HLA-A*6801. Our findings are helpful for understanding the divergent peptide presentation and virus-specific CTL responses impacted by MHC micropolymorphisms and also elucidate the molecular basis of HLA supertype definitions.

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Organizational Affiliation: 

CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	A	274	Homo sapiens	Mutation(s): 0  Gene Names: HLA-A, HLAA
Find proteins for P04439 (Homo sapiens) Explore P04439  Go to UniProtKB:  P04439
NIH Common Fund Data Resources
PHAROS  P04439 GTEx  ENSG00000206503

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	99	Homo sapiens	Mutation(s): 0  Gene Names: B2M, CDABP0092, HDCMA22P
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769
NIH Common Fund Data Resources
PHAROS  P61769 GTEx  ENSG00000166710

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
9-mer peptide from Tyrosinase-related protein-2	C	9	Homo sapiens	Mutation(s): 0  Gene Names: DCT, TYRP2 EC: 5.3.3.12
Find proteins for P40126 (Homo sapiens) Explore P40126  Go to UniProtKB:  P40126
NIH Common Fund Data Resources
PHAROS  P40126 GTEx  ENSG00000080166

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	A	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.226 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.237	α = 90
b = 37.857	β = 120.04
c = 108.323	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-11-09 
• Released Date: 2013-10-02 
Deposition Author(s): Niu, L., Cheng, H., Zhang, S., Tan, S., Zhang, Y., Qi, J., Liu, J., Gao, G.F.

Revision History 

• Version 1.0: 2013-10-02
  Type: Initial release