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
View more details

wwPDB Validation 3D Report Full Report

This is version 2.2 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
PHAROS: P04439 GTEx: ENSG00000206503
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04439
Sequence Annotations Expand
Reference Sequence

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(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
PHAROS: 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 I [auth A] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain M [auth D] SDF format, chain N [auth D] MOL2 format, chain I [auth A] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] mmCIF format, chain I [auth A] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth D] mmCIF 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

View Full Validation Report

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
Version 2.2: 2024-11-20
Changes: Structure summary