4UQ2

Crystal structure of HLA-A1101 in complex with an azobenzene- containing peptide

• PDB DOI: https://doi.org/10.2210/pdb4UQ2/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-06-19 Released: 2014-09-17 
• Deposition Author(s): Thong, S.Y., Yap, J.W., Lim, P.Y., Verhelst, S.H., Lescar, J., Meijers, R., Grotenbreg, G.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.43 Å
• R-Value Free: 0.251 
• R-Value Work: 0.187 
• R-Value Observed: 0.190 

Literature

Bioorthogonal Cleavage and Exchange of Major Histocompatibility Complex Ligands by Employing Azobenzene-Containing Peptides.

Choo, J.A.L., Thong, S.Y., Yap, J., Van Esch, W.J.E., Raida, M., Meijers, R., Lescar, J., Verhelst, S.H.L., Grotenbreg, G.M.

(2014) Angew Chem Int Ed Engl 53: 13390

• PubMed: 25348595 
• DOI: https://doi.org/10.1002/anie.201406295
• Primary Citation of Related Structures:  
  4UQ2, 4UQ3


• PubMed Abstract: 
  

  Bioorthogonal cleavable linkers are attractive building blocks for compounds that can be manipulated to study biological and cellular processes. Sodium dithionite sensitive azobenzene-containing (Abc) peptides were applied for the temporary stabilization of recombinant MHC complexes, which can then be employed to generate libraries of MHC tetramers after exchange with a novel epitope. This technology represents an important tool for high-throughput studies of disease-specific T cell responses.

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Organizational Affiliation: 

Department of Microbiology and Immunology Programme, National University of Singapore (NUS), Life Sciences Institute, #03-05, 28 Medical Drive, 117456 (Singapore).

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 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 89.19 kDa 
• Atom Count: 6,761 
• Modelled Residue Count: 762 
• Deposited Residue Count: 762 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-11 ALPHA CHAIN	A, C	275	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P04439 (Homo sapiens) Explore P04439  Go to UniProtKB:  P04439
PHAROS:  P04439 GTEx:  ENSG00000206503

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-2-MICROGLOBULIN	B, D	99	Homo sapiens	Mutation(s): 0
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
AZOBENZENE-CONTAINING PEPTIDE	E, F [auth G]	7	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.43 Å
• R-Value Free: 0.251 
• R-Value Work: 0.187 
• R-Value Observed: 0.190 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.14	α = 106.74
b = 71.46	β = 96.74
c = 75.43	γ = 105.28

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-17 
Deposition Author(s): Thong, S.Y., Yap, J.W., Lim, P.Y., Verhelst, S.H., Lescar, J., Meijers, R., Grotenbreg, G.M.

Revision History  

• Version 1.0: 2014-09-17
  Type: Initial release
  
• Version 1.1: 2015-03-25
  Changes: Database references
• Version 2.0: 2023-11-15
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description
• Version 2.1: 2024-01-10
  Changes: Refinement description