4UQ3

Crystal structure of HLA-A0201 in complex with an azobenzene- containing peptide

PDB DOI: https://doi.org/10.2210/pdb4UQ3/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.221
R-Value Work: 0.180
R-Value Observed: 0.182

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Bioorthogonal cleavage and exchange of major histocompatibility complex ligands by employing azobenzene-containing peptides.

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

(2014) Angew Chem Int Ed Engl 53: 13390-13394

PubMed: 25348595 Search on PubMed
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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 89.52 kDa
Atom Count: 6,898
Modelled Residue Count: 762
Deposited Residue Count: 762
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 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
GTEx: ENSG00000206503
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04439
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-2-MICROGLOBULIN	B, D	100	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769 Go to UniProtKB: P61769
GTEx: ENSG00000166710
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P61769
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
AZOBENZENE-CONTAINING PEPTIDE	E, F	6	synthetic construct	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IPA Query on IPA Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain M [auth D] SDF format, chain N [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D]	G [auth A] H [auth A] I [auth A] J [auth B] K [auth C] G [auth A], H [auth A], I [auth A], J [auth B], K [auth C], L [auth C], M [auth D], N [auth D]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.221
R-Value Work: 0.180
R-Value Observed: 0.182
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.79	α = 90
b = 79.58	β = 89.96
c = 83.97	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-09-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-09-17
Type: Initial release
Version 1.1: 2015-03-18
Changes: Atomic model
Version 1.2: 2015-03-25
Changes: Database references
Version 1.3: 2019-01-16
Changes: Data collection, Database references
Version 2.0: 2023-11-15
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations
Version 2.1: 2024-01-10
Changes: Refinement description