7SIF

Crystal Structure of HLA B*3505 in complex with NPDIVIYQY, an 9-mer epitope from HIV-I

• PDB DOI: https://doi.org/10.2210/pdb7SIF/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Human immunodeficiency virus 1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-10-14 Released: 2022-11-23 
• Deposition Author(s): Gras, S., Lobos, C.A., Chatzileontiadou, D.S.M.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 0.230 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 

Literature

Molecular insights into the HLA-B35 molecules Px and Py group classification associated with HIV control

Lobos, C.A., Chatzileontiadou, D.S.M., Sok, B., Almedia, C., Halim, H., D'Orsogna, L., Gras, S.

To be published.

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: 45.27 kDa 
• Atom Count: 3,479 
• Modelled Residue Count: 384 
• Deposited Residue Count: 384 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	A	276	Homo sapiens	Mutation(s): 0  Gene Names: HLA-B
UniProt
Find proteins for A0A5H2UI55 (Homo sapiens) Explore A0A5H2UI55  Go to UniProtKB:  A0A5H2UI55

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
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
Reverse transcriptase peptide NPDIVIYQY	C	9	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03366  Go to UniProtKB:  P03366

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BTB	G [auth C]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C8 H19 N O5 OWMVSZAMULFTJU-UHFFFAOYSA-N
TRS	F [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
PEG	D [auth A], E [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 0.230 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.875	α = 90
b = 81.904	β = 90
c = 109.32	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-11-23 
Deposition Author(s): Gras, S., Lobos, C.A., Chatzileontiadou, D.S.M.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	1159272

Revision History  

• Version 1.0: 2022-11-23
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description