ISDA

Deposition Date 2010-02-02

Release Date 2010-03-02

Last Version Date 2023-12-20

Entry Detail

PDB ID:

2X4N

Keywords:

IMMUNE SYSTEM

Title:

Crystal structure of MHC CLass I HLA-A2.1 bound to residual fragments of a photocleavable peptide that is cleaved upon UV-light treatment

Biological Source:

Source Organism:

HOMO SAPIENS (Taxon ID: 9606)
INFLUENZA A VIRUS (Taxon ID: 11320)

Host Organism:

ESCHERICHIA COLI

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.34 Å

R-Value Free:

0.27

R-Value Work:

0.19

R-Value Observed:

0.20

Space Group:

P 1 21 1

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
Chain IDs:A, D
Chain Length:275
Number of Molecules:2
Biological Source:HOMO SAPIENS

UniProt ID:P04439 Pfam ID:PF00129, PF07654

Protein Blast

Polymer Type:polypeptide(L)
Molecule:BETA-2-MICROGLOBULIN
Gene (Uniprot):B2M
Chain IDs:B, E
Chain Length:100
Number of Molecules:2
Biological Source:HOMO SAPIENS

UniProt ID:P61769 Pfam ID:PF07654

Polymer Type:polypeptide(L)
Molecule:HLA-A2.1-RESTRICTED INFLUENZA A MATRIX EPITOPE
Chain IDs:C, F
Chain Length:9
Number of Molecules:2
Biological Source:INFLUENZA A VIRUS

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details	2D Image
PRV	C	GLY	(2R)-AMINO(2-NITROPHENYL)ETHANOIC ACID

Ligand Molecules

GOL

MES

Primary Citation

Uv-Induced Ligand Exchange in Mhc Class I Protein Crystals.

Celie, P.H.N, Toebes, M, Rodenko, B, Ovaa, H, Perrakis, A, Schumacher, T.N.M.Show

J.Am.Chem.Soc. 131 12298 ? (2009)

PMID: 19655750 DOI: 10.1021/JA9037559

Abstact

High-throughput structure determination of protein-ligand complexes is central in drug development and structural proteomics. To facilitate such high-throughput structure determination we designed an induced replacement strategy. Crystals of a protein complex bound to a photosensitive ligand are exposed to UV light, inducing the departure of the bound ligand, allowing a new ligand to soak in. We exemplify the approach for a class of protein complexes that is especially recalcitrant to high-throughput strategies: the MHC class I proteins. We developed a UV-sensitive, "conditional", peptide ligand whose UV-induced cleavage in the crystals leads to the exchange of the low-affinity lytic fragments for full-length peptides introduced in the crystallant solution. This "in crystallo" exchange is monitored by the loss of seleno-methionine anomalous diffraction signal of the conditional peptide compared to the signal of labeled MHC beta2m subunit. This method has the potential to facilitate high-throughput crystallography in various protein families.

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Primary Citation of related structures