Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

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

Macromolecule Content

• Total Structure Weight: 90123.45 
• Atom Count: 6334 
• Residue Count: 768 
• Unique protein chains: 3

2X4S

Crystal structure of MHC CLass I HLA-A2.1 bound to a peptide representing the epitope of the H5N1 (Avian Flu) Nucleoprotein

• DOI: 10.2210/pdb2X4S/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Influenza A virus, Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Escherichia coli


• Deposited: 2010-02-02 Released: 2010-03-02 
• Deposition Author(s): Celie, P.H.N., Toebes, M., Rodenko, B., Ovaa, H., Perrakis, A., Schumacher, T.N.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.247 
• R-Value Work: 0.178 

Literature

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.

(2009) J.Am.Chem.Soc. 131: 12298

• PubMed: 19655750 
• DOI: 10.1021/ja9037559
• Primary Citation of Related Structures:  
  2X70, 2X4U, 2X4R, 2X4N, 2X4O
• Also Cited By: 2X4T, 2X4Q, 2X4P


• PubMed Abstract: 
  

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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Organizational Affiliation: 

Division of Biochemistry, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2.1	A, D	275	Homo sapiens	Mutation(s): 0  Gene Names: HLA-A (HLAA)
Find proteins for P01892 (Homo sapiens) Go to Gene View: HLA-A Go to UniProtKB:  P01892

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
BETA-2-MICROGLOBULIN	B, E	100	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
H5N1 INFLUENZA A NUCLEOPROTEIN	C, F	9	Influenza A virus	Mutation(s): 0  Gene Names: NP
Find proteins for Q33CG5 (Influenza A virus) Go to UniProtKB:  Q33CG5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GOL	B	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MES	B, E	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	B, E	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.247 
• R-Value Work: 0.178 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 62.377	α = 90.00
b = 84.112	β = 90.97
c = 80.035	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-02-02 
• Released Date: 2010-03-02 
• Deposition Author(s): Celie, P.H.N., Toebes, M., Rodenko, B., Ovaa, H., Perrakis, A., Schumacher, T.N.M.

Revision History 

• Version 1.0: 2010-03-02
  Type: Initial release
• Version 1.1: 2011-05-07
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance