Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 45191.21 
• Atom Count: 3195 
• Residue Count: 387 
• Unique protein chains: 3

5T6Y

HLA-B*57:01 presenting TSTFEDVKILAF

• DOI: 10.2210/pdb5T6Y/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21


• Deposited: 2016-09-02 Released: 2017-03-01 
• Deposition Author(s): Pymm, P., Rossjohn, J., Vivian, J.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.219 
• R-Value Work: 0.178 

Literature

MHC-I peptides get out of the groove and enable a novel mechanism of HIV-1 escape.

Pymm, P., Illing, P.T., Ramarathinam, S.H., O'Connor, G.M., Hughes, V.A., Hitchen, C., Price, D.A., Ho, B.K., McVicar, D.W., Brooks, A.G., Purcell, A.W., Rossjohn, J., Vivian, J.P.

(2017) Nat. Struct. Mol. Biol. 24: 387-394

• PubMed: 28218747 
• DOI: 10.1038/nsmb.3381
• Primary Citation of Related Structures:  
  5T70, 5T6Z, 5T6X, 5T6W


• PubMed Abstract: 
  

Major histocompatibility complex class I (MHC-I) molecules play a crucial role in immunity by capturing peptides for presentation to T cells and natural killer (NK) cells. The peptide termini are tethered within the MHC-I antigen-binding groove, but it is unknown whether other presentation modes occur. Here we show that 20% of the HLA-B*57:01 peptide repertoire comprises N-terminally extended sets characterized by a common motif at position 1 (P1) to P2. Structures of HLA-B*57:01 presenting N-terminally extended peptides, including the immunodominant HIV-1 Gag epitope TW10 (TSTLQEQIGW), showed that the N terminus protrudes from the peptide-binding groove. The common escape mutant TSNLQEQIGW bound HLA-B*57:01 canonically, adopting a dramatically different conformation than the TW10 peptide. This affected recognition by killer cell immunoglobulin-like receptor (KIR) 3DL1 expressed on NK cells. We thus define a previously uncharacterized feature of the human leukocyte antigen class I (HLA-I) immunopeptidome that has implications for viral immune escape. We further suggest that recognition of the HLA-B*57:01-TW10 epitope is governed by a 'molecular tension' between the adaptive and innate immune systems.

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Organizational Affiliation: 

Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
HLA class I histocompatibility antigen, B-57 alpha chain	A	276	Homo sapiens	Mutation(s): 0  Gene Names: HLA-B (HLAB)
Find proteins for P01889 (Homo sapiens) Go to Gene View: HLA-B Go to UniProtKB:  P01889

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Beta-2-microglobulin	B	99	Homo sapiens	Mutation(s): 0  Gene Names: B2M
Find proteins for P61769 (Homo sapiens) Go to Gene View: B2M Go to UniProtKB:  P61769

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Decapeptide: THR-SER-THR-PHE-GLU-ASP-VAL-LYS-ILE-LEU-ALA-PHE	C	12	Homo sapiens	Mutation(s): 0  Gene Names: THADA (GITA, KIAA1767)
Find proteins for Q6YHU6 (Homo sapiens) Go to Gene View: THADA Go to UniProtKB:  Q6YHU6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ACT	A	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
GOL	A, B	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.219 
• R-Value Work: 0.178 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 50.707	α = 90.00
b = 82.043	β = 90.00
c = 110.095	γ = 90.00

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
SCALA	data scaling
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-09-02 
• Released Date: 2017-03-01 
• Deposition Author(s): Pymm, P., Rossjohn, J., Vivian, J.P.

Revision History 

• Version 1.0: 2017-03-01
  Type: Initial release
• Version 1.1: 2017-04-19
  Type: Database references
• Version 1.2: 2017-08-09
  Type: Data collection, Structure summary