2X4P	Immune System	date	Feb 02, 2010
title	Crystal Structure Of Mhc Class I Hla-A2.1 Bound To A Photocleavable Peptide
authors	P.H.N.Celie, M.Toebes, B.Rodenko, H.Ovaa, A.Perrakis, T.N.M.Schumacher
compound		source
Molecule: Hla Class I Histocompatibility Antigen, A-2.1 Chain: A, D Fragment: Residues 25-299 Synonym: Hla Class I Histocompatibility Antigen, A-2 Alpha Chain; Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid
Molecule: Beta-2-Microglobulin Chain: B, E Synonym: Beta-2-Microglobulin Form Pi 5.3 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Xli Blue Expression_system_vector_type: Plasmid
Molecule: Hla-A2.1-Restricted Influenza A Matrix Epitope Chain: C, F Fragment: Fragment Residues 58-66 Other_details: Modified At P5 (Residue62) And P8 (Residue 65).(2-Nitro)Phenyl-Propionic Acid At P5 And 3-Amino-3-(2- Nitro)Phenyl-Propionic Acid At P8		Synthetic: Yes Organism_scientific: Influenza A Virus Organism_taxid: 11320
symmetry	Space Group: P 1 21 1	R_factor 0.1580 R_Free 0.2222
crystal cell	length a length b length c angle alpha angle beta angle gamma 62.201 86.496 80.783 90.00 90.04 90.00
method	X-Ray Diffraction	resolution	2.30 Å
ligand	GOL, MES, MSE, PRQ, PRV	enzyme
Gene Ontology	Chain Function Process Component E, B protein binding positive regulation of T cel... response to molecule of bact... antigen processing and prese... antigen processing and prese... antigen processing and prese... antigen processing and prese... immune response viral reproduction cytokine-mediated signaling ... T cell differentiation in th... protein refolding response to drug antigen processing and prese... innate immune response response to cadmium ion regulation of defense respon... regulation of immune respons... interferon-gamma-mediated si... Golgi membrane extracellular region extracellular space endoplasmic reticulum lumen plasma membrane external side of plasma memb... ER to Golgi transport vesicl... phagocytic vesicle membrane early endosome membrane early endosome lumen MHC class I protein complex
Primary reference	Class I major histocompatibility complexes loaded by a periodate trigger., Rodenko B, Toebes M, Celie PH, Perrakis A, Schumacher TN, Ovaa H, J Am Chem Soc. 2009 Sep 2;131(34):12305-13. PMID:19655751

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (287 Kb) [Save to disk] Biological Unit Coordinates (2x4p.pdb1.gz) 138 Kb Biological Unit Coordinates (2x4p.pdb2.gz) 140 Kb LPC: Ligand-Protein Contacts for 2X4P CSU: Contacts of Structural Units for 2X4P Structure Factors (575 Kb) Retrieve 2X4P in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2X4P from S2C, [Save to disk] Re-refined 2x4p structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2X4P in 3D

Proteopedia, because life has more than 2D. On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure. On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 2X4P

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Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute Crystal Contacts, from CryCo at Weizmann Institute 3D motif for 2X4P, from MSDmotif at EBI Fold representative 2x4p from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2x4p_A] [2x4p_B] [2x4p_C] [2x4p_D] [2x4p_E] [2x4p_F] SWISS-PROT database: Domain organization of by SWISSPFAM Alignments of the sequence of 2X4P with the sequences similar proteins can be viewed for 2X4P's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list. A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.

Other resources with information on 2X4P

Community annotation for 2X4P at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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