3FQR	Immune System	date	Jan 07, 2009
title	Phosphorylation Of Self-Peptides Alters Human Leukocyte Anti I-Restricted Antigen Presentation And Generates Tumor Speci Epitopes
authors	J.Petersen, J.Rossjohn
compound		source
Molecule: Hla Class I Histocompatibility Antigen, A-2 Alpha Chain: A Fragment: Extracellular Domains Alpha1, Alpha2, Alpha3, Unp 25-299; Synonym: Mhc Class I Antigen A2 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Hla-A, Hlaa Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet 30
Molecule: Beta-2-Microglobulin Chain: B Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: B2m Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet 30
Molecule: Phospho-Peptide 30-39 From Beta-Catenin: Yld(Sep) Chain: C Engineered: Yes		Synthetic: Yes Other_details: Synthetic Peptide
symmetry	Space Group: P 21 21 21	R_factor 0.169 R_Free 0.189
crystal cell	length a length b length c angle alpha angle beta angle gamma 59.678 79.706 111.558 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	1.70 Å
ligand	CD, GOL, MG, SEP	enzyme
Gene Ontology	Chain Function Process Component 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	Phosphorylated self-peptides alter human leukocyte antigen class I-restricted antigen presentation and generate tumor-specific epitopes., Petersen J, Wurzbacher SJ, Williamson NA, Ramarathinam SH, Reid HH, Nair AK, Zhao AY, Nastovska R, Rudge G, Rossjohn J, Purcell AW, Proc Natl Acad Sci U S A. 2009 Feb 24;106(8):2776-81. Epub 2009 Feb 5. PMID:19196958

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (154 Kb) [Save to disk] Biological Unit Coordinates (3fqr.pdb1.gz) 147 Kb LPC: Ligand-Protein Contacts for 3FQR CSU: Contacts of Structural Units for 3FQR Likely Quarternary Molecular Structure file(s) for 3FQR Structure Factors (1447 Kb) Retrieve 3FQR in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3FQR from S2C, [Save to disk] Re-refined 3fqr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3FQR 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 3FQR

Cartoon representation from PDB Cartoon Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala Dipole moment, from Dipole Server at Weizmann Institute Crystal Contacts, from CryCo at Weizmann Institute 3D motif for 3FQR, from MSDmotif at EBI Fold representative 3fqr from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3fqr_A] [3fqr_B] [3fqr_C] SWISS-PROT database: [P01892] [P61769] [P35222] Domain organization of [1A02_HUMAN] [B2MG_HUMAN] [CTNB1_HUMAN] by SWISSPFAM Domain found in 3FQR: [IGc1 ] by SMART Alignments of the sequence of 3FQR with the sequences similar proteins can be viewed for 3FQR's classification [1A02_HUMAN] [B2MG_HUMAN] [CTNB1_HUMAN] 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 [1A02_HUMAN] [B2MG_HUMAN] [CTNB1_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 3FQR

Community annotation for 3FQR at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

You may enter another PDB ID code

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]

---

OCA© by Jaime Prilusky, 1996-2010 Bioinformatics Unit Weizmann Institute of Science

---