2VDP	Cell Adhesion Immune System	date	Oct 10, 2007
title	Integrin Alphaiibbeta3 Headpiece Bound To Fibrinogen Gamma Chain Peptide,Lggakqagdv
authors	T.A.Springer, J.Zhu, T.Xiao
compound		source
Molecule: Integrin Alpha-Iib Chain: A Fragment: Headpiece, Residues 32-483 Synonym: Platelet Membrane Glycoprotein Iib, Gpalpha Iib, G Integrin Alpha-Iib Heavy Chain; Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Cricetulus Griseus Expression_system_taxid: 10029 Expression_system_cell_line: Lec 3.2.8.1 Expression_system_vector_type: Plasmid
Molecule: Integrin Beta-3 Chain: B Fragment: Headpiece, Residues 27-487 Synonym: Platelet Membrane Glycoprotein Iiia, Gpiiia, Cd61 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Cricetulus Griseus Expression_system_taxid: 10029 Expression_system_cell_line: Lec 3.2.8.1 Expression_system_vector_type: Plasmid
Molecule: Monoclonal Antibody 10e5 Heavy Chain Chain: H		Organism_scientific: Mus Musculus Organism_common: Mouse Organism_taxid: 10090 Strain: Balbc Cell_line: 10e5 Hybridoma
Molecule: Monoclonal Antibody 10e5 Light Chain Chain: L		Organism_scientific: Mus Musculus Organism_common: Mouse Organism_taxid: 10090 Strain: Balbc Cell_line: 10e5 Hybridoma
Molecule: Fibrinogen Chain: C Fragment: Gamma Chain C-Terminal Peptide, Residues 428-437		Synthetic: Yes Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606
symmetry	Space Group: P 32 2 1	R_factor 0.156 R_Free 0.204
crystal cell	length a length b length c angle alpha angle beta angle gamma 148.429 148.429 177.160 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.80 Å
ligand	CA, GOL, MAN, MG, NAG	enzyme
Gene Ontology	Chain Function Process Component A protein binding identical protein binding metal ion binding extracellular matrix binding... platelet degranulation cell adhesion cell-matrix adhesion integrin-mediated signaling ... axon guidance blood coagulation platelet activation plasma membrane integral to plasma membrane focal adhesion external side of plasma memb... membrane integral to membrane platelet alpha granule membr... B protein disulfide isomerase ... platelet-derived growth fact... protein binding identical protein binding vascular endothelial growth ... cell adhesion molecule bindi... positive regulation of prote... positive regulation of endot... platelet degranulation protein folding cell adhesion integrin-mediated signaling ... axon guidance blood coagulation positive regulation of endot... negative regulation of macro... negative regulation of lipid... smooth muscle cell migration... virus-host interaction platelet activation extracellular matrix organiz... positive regulation of vascu... activation of protein kinase... negative regulation of lipid... tube development wound healing regulation of bone resorptio... negative regulation of low-d... positive regulation of pepti... negative regulation of lipop... leukocyte migration angiogenesis involved in wou... platelet aggregation nucleus plasma membrane integral to plasma membrane focal adhesion integrin complex membrane integral to membrane cell junction platelet alpha granule membr... lamellipodium membrane melanosome cell projection alphav-beta3 integrin-vitron... C eukaryotic cell surface bind... metal ion binding platelet degranulation blood coagulation hemostasis platelet activation response to calcium ion extracellular region fibrinogen complex extracellular space plasma membrane cell cortex external side of plasma memb... platelet alpha granule platelet alpha granule lumen... blood microparticle
Primary reference	Structural basis for distinctive recognition of fibrinogen gammaC peptide by the platelet integrin alphaIIbbeta3., Springer TA, Zhu J, Xiao T, J Cell Biol. 2008 Aug 25;182(4):791-800. Epub 2008 Aug 18. PMID:18710925

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (244 Kb) [Save to disk] Biological Unit Coordinates (2vdp.pdb1.gz) 230 Kb LPC: Ligand-Protein Contacts for 2VDP CSU: Contacts of Structural Units for 2VDP Likely Quarternary Molecular Structure file(s) for 2VDP Structure Factors (734 Kb) Retrieve 2VDP in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2VDP from S2C, [Save to disk] Re-refined 2vdp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2VDP 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 2VDP

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

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2vdp_A] [2vdp_B] [2vdp_C] [2vdp_H] [2vdp_L] SWISS-PROT database: [P02679] [P01837] [P08514] [P05106] Domain organization of [FIBG_HUMAN] [IGKC_MOUSE] [ITA2B_HUMAN] [ITB3_HUMAN] by SWISSPFAM Domains found in 2VDP: [IG_like] [IGv] [INB] [Int_alpha] [PSI] [VWA ] by SMART Alignments of the sequence of 2VDP with the sequences similar proteins can be viewed for 2VDP's classification [FIBG_HUMAN] [IGKC_MOUSE] [ITA2B_HUMAN] [ITB3_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 [FIBG_HUMAN] [IGKC_MOUSE] [ITA2B_HUMAN] [ITB3_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 2VDP

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

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