6VQE | pdb_00006vqe

HLA-B*27:05 presenting an HIV-1 13mer peptide

• PDB DOI: https://doi.org/10.2210/pdb6VQE/pdb

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


• Deposited: 2020-02-05 Released: 2021-02-10 
• Deposition Author(s): Pymm, P., Tenzer, S., Wee, E., Weimershaus, M., Burgevin, A., Kollnberger, S., Gerstoft, J., Josephs, T.M., Ladell, K., Mclaren, J.E., Appay, V., Price, D.A., Fugger, L., Bell, J.I., Hansjorg, S., Van Endert, P., Harkiolaki, M., Iversen, A.K.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 
  0.186 (Depositor), 0.187 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

Epitope length variants balance protective immune responses and viral escape in HIV-1 infection

Pymm, P., Tenzer, S., Wee, E., Weimershaus, M., Burgevin, A., Kollnberger, S., Gerstoft, J., Josephs, T.M., Ladell, K., McLaren, J.E., Appay, V., Price, D.A., Fugger, L., Bell, J.I., Schild, H., van Endert, P., Harkiolaki, M., Iversen, A.K.

(2022) Cell Rep 38

• DOI: https://doi.org/10.1016/j.celrep.2022.110449

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: 45.6 kDa 
• Atom Count: 3,640 
• Modeled Residue Count: 386 
• Deposited Residue Count: 389 
• 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 O78189 (Homo sapiens) Explore O78189  Go to UniProtKB:  O78189

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
13-mer peptide	C	13	Human immunodeficiency virus 1	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A], E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free:  0.186 (Depositor), 0.187 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.94	α = 90
b = 82.782	β = 90
c = 109.426	γ = 90

Software Package:

Software Name	Purpose
xia2	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-02-10 
Deposition Author(s): Pymm, P., Tenzer, S., Wee, E., Weimershaus, M., Burgevin, A., Kollnberger, S., Gerstoft, J., Josephs, T.M., Ladell, K., Mclaren, J.E., Appay, V., Price, D.A., Fugger, L., Bell, J.I., Hansjorg, S., Van Endert, P., Harkiolaki, M., Iversen, A.K.N.

Revision History  

• Version 1.0: 2021-02-10
  Type: Initial release
  
• Version 1.1: 2022-03-09
  Changes: Database references
• Version 1.2: 2023-10-11
  Changes: Data collection, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary