2IAM	Immune System	date	Sep 08, 2006
title	Structural Basis For Recognition Of Mutant Self By A Tumor- Specific, Mhc Class II-Restricted Tcr
authors	L.Deng, R.J.Langley, R.A.Mariuzza
compound		source
Molecule: Hla Class II Histocompatibility Antigen, Dr Alpha Chain; Chain: A Fragment: Residues 1-182 (26-207) Synonym: Mhc Class II Antigen Dra, Major Histocompatibility Complex Class II Hla-Dr1 Alpha Chain; Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Hla-Dra Expression_system: Escherichia Coli Bl21 Expression_system_taxid: 511693 Expression_system_strain: Bl21 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pt7-7
Molecule: Hla Class II Histocompatibility Antigen, Drb1-1 Beta Chain; Chain: B Fragment: Residues 1-190 (30-219) Synonym: Mhc Class I Antigen Drb11, Dr-1, Dr1, Major Histocompatibility Complex Class II Hla-Dr1 Beta Chain; Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Hla-Drb1 Expression_system: Escherichia Coli Bl21 Expression_system_taxid: 511693 Expression_system_strain: Bl21 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pt7-7
Molecule: 15-Mer Peptide From Triosephosphate Isomerase Chain: P Fragment: Residues 23-37 (22-36) Ec: 5.3.1.1 Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Tpi1, Tpi Expression_system: Escherichia Coli Bl21 Expression_system_taxid: 511693 Expression_system_strain: Bl21 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pt7-7
Molecule: Cd4+ T Cell Receptor E8 Alpha Chain Chain: C Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Bl21 Expression_system_taxid: 511693 Expression_system_strain: Bl21 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pt7-7
Molecule: Cd4+ T Cell Receptor E8 Beta Chain Chain: D Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Bl21 Expression_system_taxid: 511693 Expression_system_strain: Bl21 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pt7-7
symmetry	Space Group: C 2 2 2	R_factor 0.207 R_Free 0.279
crystal cell	length a length b length c angle alpha angle beta angle gamma 86.391 270.542 97.396 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.80 Å
ligand		enzyme	Isomerase E.C.5.3.1.1 BRENDA
Primary reference	Structural basis for the recognition of mutant self by a tumor-specific, MHC class II-restricted T cell receptor., Deng L, Langley RJ, Brown PH, Xu G, Teng L, Wang Q, Gonzales MI, Callender GG, Nishimura MI, Topalian SL, Mariuzza RA, Nat Immunol. 2007 Apr;8(4):398-408. Epub 2007 Mar 4. PMID:17334368

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (139 Kb) [Save to disk] Biological Unit Coordinates (2iam.pdb1.gz) 133 Kb CSU: Contacts of Structural Units for 2IAM Likely Quarternary Molecular Structure file(s) for 2IAM Structure Factors (525 Kb) Retrieve 2IAM in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2IAM from S2C, [Save to disk] Re-refined 2iam structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2IAM 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 2IAM

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 2IAM, from MSDmotif at EBI Fold representative 2iam from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2iam_A] [2iam_B] [2iam_C] [2iam_D] [2iam_P] SWISS-PROT database: [P04229] [P01903] [P01848] [P01850] [P60174] Domain organization of [2B11_HUMAN] [DRA_HUMAN] [TCA_HUMAN] [TCB_HUMAN] [TPIS_HUMAN] by SWISSPFAM Domains found in 2IAM: [IG] [IG_like] [IGc1] [MHC_II_alpha] [MHC_II_beta ] by SMART Alignments of the sequence of 2IAM with the sequences similar proteins can be viewed for 2IAM's classification [2B11_HUMAN] [DRA_HUMAN] [TCA_HUMAN] [TCB_HUMAN] [TPIS_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 [2B11_HUMAN] [DRA_HUMAN] [TCA_HUMAN] [TCB_HUMAN] [TPIS_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 2IAM

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

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