5XS3 | pdb_00005xs3

Crystal structure of HLA Class I antigen

• PDB DOI: https://doi.org/10.2210/pdb5XS3/pdb

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


• Deposited: 2017-06-12 Released: 2017-09-13 
• Deposition Author(s): Wei, P.C., Yang, Y., Liu, Z.X., Luo, Z.Q., Tu, W.Y., Han, J.Y., Deng, Y.H., Yin, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.272 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

Characterization of Autoantigen Presentation by HLA-C*06:02 in Psoriasis

Wei, P., Yang, Y., Liu, Z., Luo, Z., Tu, W., Han, J., Deng, Y., Yin, L.

(2017) J Invest Dermatol 137: 2238-2241

• PubMed: 28655516 
• DOI: https://doi.org/10.1016/j.jid.2017.05.036
• Primary Citation Related Structures: 
  5XS3

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Organizational Affiliation: 
• State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, Hubei, China.
Department of Immunology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
Department of Dermatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, Hubei, China. Electronic address: [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 44.51 kDa 
• Atom Count: 3,134 
• Modeled Residue Count: 378 
• Deposited Residue Count: 380 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy Chain	A	273	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light Chain	B	98	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
P	C	9	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.272 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.21	α = 90
b = 81.1	β = 90
c = 117.19	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-09-13 
Deposition Author(s): Wei, P.C., Yang, Y., Liu, Z.X., Luo, Z.Q., Tu, W.Y., Han, J.Y., Deng, Y.H., Yin, L.

Revision History  

• Version 1.0: 2017-09-13
  Type: Initial release
  
• Version 1.1: 2017-10-11
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Advisory, Data collection, Database references, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary