4U1L

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: 2.06 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.173 

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-81 alpha chain
A, D
277Homo sapiensMutation(s): 0 
Gene Names: HLA-B (HLAB)
Find proteins for Q31610 (Homo sapiens)
Go to Gene View: HLA-B
Go to UniProtKB:  Q31610
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B, E
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, F
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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.173 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 46.020α = 91.13
b = 49.060β = 93.53
c = 107.840γ = 95.70
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
REFMACrefinement
GDAdata reduction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

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: Atomic model, Author supporting evidence, Derived calculations