1FYT	Immune System	date	Oct 03, 2000
title	Crystal Structure Of A Complex Of A Human Alphabeta-T Cell Influenza Ha Antigen Peptide, And Mhc Class II Molecule, Hl
authors	J.Hennecke, A.Carfi, D.C.Wiley
compound		source
Molecule: Hla Class II Histocompatibility Antigen, Dr Alpha Chain: A Fragment: Extracellular Domain Synonym: Hla-Dr1, Dra Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Drosophila Melanogaster Expression_system_common: Fruit Fly Expression_system_taxid: 7227
Molecule: Hla Class II Histocompatibility Antigen, Dr-1 Bet Chain: B Fragment: Extracellular Domain Synonym: Hla-Dr1, Drb1 0101 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Drosophila Melanogaster Expression_system_common: Fruit Fly Expression_system_taxid: 7227
Molecule: Hemagglutinin Ha1 Peptide Chain Chain: C Fragment: Antigen Peptide Engineered: Yes		Organism_scientific: H3n2 Subtype Organism_taxid: 119210 Expression_system: Escherichia Coli Expression_system_taxid: 562
Molecule: T-Cell Receptor Alpha Chain Chain: D Fragment: Extracellular Domain Synonym: Tcr Ha1.7 Alpha Chain Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 562
Molecule: T-Cell Receptor Beta Chain Chain: E Fragment: Extracellular Domain Synonym: Tcr Ha1.7 Beta Chain Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 562
symmetry	Space Group: C 1 2 1	R_factor 0.221 R_Free 0.255
crystal cell	length a length b length c angle alpha angle beta angle gamma 142.902 73.439 122.428 90.00 108.23 90.00
method	X-Ray Diffraction	resolution	2.60 Å
ligand	NAG	enzyme
related structures	by homologous chain: 1AO7, 1BD2, 1BX2, 1ES0, 1HXY, 1R5I
Gene Ontology	Chain Function Process Component C virus-host interaction viral attachment to host cel... viral entry into host cell viral entry into host cell v... viral entry into host cell v... membrane integral to membrane virion viral envelope host cell plasma membrane host cell membrane virion membrane
Primary reference	Structure of a covalently stabilized complex of a human alphabeta T-cell receptor, influenza HA peptide and MHC class II molecule, HLA-DR1., Hennecke J, Carfi A, Wiley DC, EMBO J 2000 Nov 1;19(21):5611-24. PMID:11060013

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (141 Kb) [Save to disk] Biological Unit Coordinates (1fyt.pdb1.gz) 136 Kb LPC: Ligand-Protein Contacts for 1FYT CSU: Contacts of Structural Units for 1FYT Likely Quarternary Molecular Structure file(s) for 1FYT Structure Factors (399 Kb) Retrieve 1FYT in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1FYT from S2C, [Save to disk] Re-refined 1fyt structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1FYT 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 1FYT

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 1FYT, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1fyta2, region A:2-81 [Jmol] [rasmolscript] [script source]     - Domain d1fyta1, region A:82-181 [Jmol] [rasmolscript] [script source]     - Domain d1fytb2, region B:3-92 [Jmol] [rasmolscript] [script source]     - Domain d1fytb1, region B:93-190 [Jmol] [rasmolscript] [script source]     - Domain d1fytd1, region D:1-117 [Jmol] [rasmolscript] [script source]     - Domain d1fytd2, region D:118-203 [Jmol] [rasmolscript] [script source]     - Domain d1fyte2, region E:119-246 [Jmol] [rasmolscript] [script source]     - Domain d1fyte1, region E:3-118 [Jmol] [rasmolscript] [script source] Fold representative 1fyt from FSSP and Dali (Families of Structurally Similar Proteins) Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH Summaries and structural analyses of PDB data files from PDBSum Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1fyt_A] [1fyt_B] [1fyt_C] [1fyt_D] [1fyt_E] SWISS-PROT database: [P04229] [P01903] [P03437] [P01850] Domain organization of [2B11_HUMAN] [DRA_HUMAN] [HEMA_I68A0] [TCB_HUMAN] by SWISSPFAM Domains found in 1FYT: [IG] [IG_like] [IGc1] [MHC_II_alpha] [MHC_II_beta ] by SMART Alignments of the sequence of 1FYT with the sequences similar proteins can be viewed for 1FYT's classification [2B11_HUMAN] [DRA_HUMAN] [HEMA_I68A0] [TCB_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] [HEMA_I68A0] [TCB_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 1FYT

Community annotation for 1FYT 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

---