5IM7 | pdb_00005im7

Crystal structure of HLA-B5801, a protective HLA allele for HIV-1 infection

• PDB DOI: https://doi.org/10.2210/pdb5IM7/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-03-05 Released: 2016-10-05 
• Deposition Author(s): Li, X., Wang, J.-H.
• Funding Organization(s): Ragon Institute of MGH, MIT and Harvard

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of HLA-B*5801, a protective HLA allele for HIV-1 infection.

Li, X., Lamothe, P.A., Ng, R., Xu, S., Teng, M., Walker, B.D., Wang, J.H.

(2016) Protein Cell 7: 761-765

• PubMed: 27638468 
• DOI: https://doi.org/10.1007/s13238-016-0309-y
• Primary Citation of Related Structures:  
  5IM7, 5INC, 5IND

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Organizational Affiliation: 
• School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China.
Department of Medical Oncology and Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA.
Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, Harvard University, Boston, MA, 02139, USA.
Biomarin Pharmaceutical, 790 Lincoln Ave, San Rafael, CA, 94901, USA.
Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, Harvard University, Boston, MA, 02139, USA. [e-mail].
Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA. [e-mail].
School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China. [e-mail].
Department of Medical Oncology and Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA. [e-mail].
Department of Pediatrics and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA. [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 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 89.63 kDa 
• Atom Count: 6,521 
• Modeled Residue Count: 770 
• Deposited Residue Count: 770 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA-B*58:01 Heavy Chain	A, C	277	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01889 (Homo sapiens) Explore P01889  Go to UniProtKB:  P01889
PHAROS:  P01889 GTEx:  ENSG00000234745

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B, D	99	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
GLN-ALA-SER-GLN-GLU-VAL-LYS-ASN-TRP	E, F	9	synthetic construct	Mutation(s): 0
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04585  Go to UniProtKB:  P04585

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.439	α = 90
b = 81.956	β = 90
c = 157.123	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-10-05 
Deposition Author(s): Li, X., Wang, J.-H.

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Funding Organization	Location	Grant Number
Ragon Institute of MGH, MIT and Harvard	United States	--

Revision History  

• Version 1.0: 2016-10-05
  Type: Initial release
  
• Version 1.1: 2016-10-19
  Changes: Database references
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary