4U1M

HLA class I micropolymorphisms determine peptide-HLA landscape and dictate differential HIV-1 escape through identical epitopes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.18 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

A molecular switch in immunodominant HIV-1-specific CD8 T-cell epitopes shapes differential HLA-restricted escape.

Klverpris, H.N.Cole, D.K.Fuller, A.Carlson, J.Beck, K.Schauenburg, A.J.Rizkallah, P.J.Buus, S.Sewell, A.K.Goulder, P.

(2015) Retrovirology 12: 20-20

  • DOI: 10.1186/s12977-015-0149-5
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Presentation of identical HIV-1 peptides by closely related Human Leukocyte Antigen class I (HLAI) molecules can select distinct patterns of escape mutation that have a significant impact on viral fitness and disease progression. The molecular mechan ...

    Presentation of identical HIV-1 peptides by closely related Human Leukocyte Antigen class I (HLAI) molecules can select distinct patterns of escape mutation that have a significant impact on viral fitness and disease progression. The molecular mechanisms by which HLAI micropolymorphisms can induce differential HIV-1 escape patterns within identical peptide epitopes remain unknown.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class I histocompatibility antigen, B-42 alpha chain
A
277Homo sapiensMutation(s): 0 
Gene Names: HLA-B (HLAB)
Find proteins for P30480 (Homo sapiens)
Go to Gene View: HLA-B
Go to UniProtKB:  P30480
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B
100Homo sapiensMutation(s): 0 
Gene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Protein Nef
C
9Human immunodeficiency virus type 1 group M subtype BMutation(s): 0 
Gene Names: nef
Find proteins for P03407 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P03407
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B, C
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.18 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.162 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.060α = 90.00
b = 81.340β = 90.00
c = 110.930γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
GDAdata reduction
PHASERphasing
XDSdata reduction
Aimlessdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/H001085/1

Revision History 

  • Version 1.0: 2015-04-08
    Type: Initial release
  • Version 2.0: 2017-08-30
    Type: Advisory, Atomic model, Author supporting evidence, Derived calculations