2IBF - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   HUMAN VINCULIN'S HEAD DOMAIN (VH1, RESIDUES 1-258) IN COMPLEX WITH TWO VINCULIN BINDING SITES OF SHIGELLA FLEXNERI'S IPAA (RESIDUES 565-587)

Authors :   T. Izard

Date :   11 Sep 06 (Deposition) - 18 Sep 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.20

Chains :   Asym./Biol. Unit : A,B,D

Keywords :   Cell Adhesion, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. T. Nhieu, T. Izard
Vinculin Binding In Its Closed Conformation By A Helix Addition Mechanism.
Embo J. V. 26 4588 2007
PubMed-ID: 17932491 | Reference-DOI: 10.1038/SJ.EMBOJ.7601863
(for further references see the PDB file header)

Molecule 1 - VINCULIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	VCL
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	METAVINCULIN

Molecule 2 - INVASIN IPAA
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	IPAA
	Organism Scientific	:	SHIGELLA FLEXNERI
	Organism Taxid	:	623
	Synonym	:	70 KDA ANTIGEN

		1	2	3
Asymmetric/Biological Unit	:	A	B	D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2IBF)

(no "Site" information available for 2IBF)

(no "SS Bond" information available for 2IBF)

(no "Cis Peptide Bond" information available for 2IBF)

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_037667	V	234	L	VINC_HUMAN	Polymorphism	17853882	A	V	234	L

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	VINCULIN_1	PS00663	Vinculin family talin-binding region signature.	VINC_HUMAN	162-182	1	A:162-182

Asymmetric/Biological Unit (6, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000211998	1a	ENSE00002146319	chr10:75757872-75758133	262	VINC_HUMAN	1-56	56	1	A:1-56	56
1.2a	ENST00000211998	2a	ENSE00001607712	chr10:75802841-75802911	71	VINC_HUMAN	57-80	24	1	A:57-80	24
1.4	ENST00000211998	4	ENSE00001024254	chr10:75830428-75830578	151	VINC_HUMAN	80-130	51	1	A:80-130	51
1.5	ENST00000211998	5	ENSE00001024245	chr10:75830733-75830841	109	VINC_HUMAN	131-167	37	1	A:131-167	37
1.6	ENST00000211998	6	ENSE00001024249	chr10:75832488-75832610	123	VINC_HUMAN	167-208	42	1	A:167-208	42
1.7a	ENST00000211998	7a	ENSE00001024263	chr10:75834501-75834661	161	VINC_HUMAN	208-261	54	1	A:208-258	51
1.8	ENST00000211998	8	ENSE00001024248	chr10:75842212-75842302	91	VINC_HUMAN	262-292	31	0	-	-
1.9a	ENST00000211998	9a	ENSE00000986356	chr10:75843124-75843271	148	VINC_HUMAN	292-341	50	0	-	-
1.10	ENST00000211998	10	ENSE00000986357	chr10:75848954-75849107	154	VINC_HUMAN	341-392	52	0	-	-
1.11	ENST00000211998	11	ENSE00000986358	chr10:75849781-75849956	176	VINC_HUMAN	393-451	59	0	-	-
1.12	ENST00000211998	12	ENSE00001024262	chr10:75854029-75854219	191	VINC_HUMAN	451-515	65	0	-	-
1.13	ENST00000211998	13	ENSE00000986360	chr10:75855414-75855613	200	VINC_HUMAN	515-581	67	0	-	-
1.14	ENST00000211998	14	ENSE00000986361	chr10:75856962-75857090	129	VINC_HUMAN	582-624	43	0	-	-
1.15a	ENST00000211998	15a	ENSE00000986362	chr10:75860706-75860855	150	VINC_HUMAN	625-674	50	0	-	-
1.16	ENST00000211998	16	ENSE00000986363	chr10:75863578-75863686	109	VINC_HUMAN	675-711	37	0	-	-
1.17c	ENST00000211998	17c	ENSE00000986364	chr10:75864809-75865111	303	VINC_HUMAN	711-812	102	0	-	-
1.18	ENST00000211998	18	ENSE00000986365	chr10:75866988-75867112	125	VINC_HUMAN	812-853	42	0	-	-
1.19b	ENST00000211998	19b	ENSE00000834577	chr10:75868729-75868914	186	VINC_HUMAN	854-915	62	0	-	-
1.20	ENST00000211998	20	ENSE00000709651	chr10:75871667-75871870	204	VINC_HUMAN	916-983	68	0	-	-
1.21	ENST00000211998	21	ENSE00000709670	chr10:75873942-75874145	204	VINC_HUMAN	984-1051	68	0	-	-
1.22	ENST00000211998	22	ENSE00000986366	chr10:75874553-75874657	105	VINC_HUMAN	1052-1086	35	0	-	-
1.23a	ENST00000211998	23a	ENSE00001373600	chr10:75877781-75879910	2130	VINC_HUMAN	1087-1134	48	0	-	-

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:258
 aligned with VINC_HUMAN | P18206 from UniProtKB/Swiss-Prot  Length:1134

    Alignment length:258
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250        
           VINC_HUMAN     1 MPVFHTRTIESILEPVAQQISHLVIMHEEGEVDGKAIPDLTAPVAAVQAAVSNLVRVGKETVQTTEDQILKRDMPPAFIKVENACTKLVQAAQMLQSDPYSVPARDYLIDGSRGILSGTSDLLLTFDEAEVRKIIRVCKGILEYLTVAEVVETMEDLVTYTKNLGPGMTKMAKMIDERQQELTHQEHRVMLVNSMNTVKELLPVLISAMKIFVTTKNSKNQGIEEALKNRNFTVEKMSAEINEIIRVLQLTSWDEDAW 258
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2ibfA01 A:1-129 vbs2 fragment of talin                                                                                           2ibfA02 A:130-258  [code=1.20.120.230, no name defined]                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------VINCULIN_1           ---------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:1-56 UniProt: 1-56                    Exon 1.2a  PDB: A:57-80 --------------------------------------------------Exon 1.5  PDB: A:131-167             ----------------------------------------Exon 1.7a  PDB: A:208-258 UniProt: 208-261          Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------Exon 1.4  PDB: A:80-130 UniProt: 80-130            ------------------------------------Exon 1.6  PDB: A:167-208 UniProt: 167-208 -------------------------------------------------- Transcript 1 (2)
                 2ibf A   1 MPVFHTRTIESILEPVAQQISHLVIMHEEGEVDGKAIPDLTAPVAAVQAAVSNLVRVGKETVQTTEDQILKRDMPPAFIKVENACTKLVQAAQMLQSDPYSVPARDYLIDGSRGILSGTSDLLLTFDEAEVRKIIRVCKGILEYLTVAEVVETMEDLVTYTKNLGPGMTKMAKMIDERQQELTHQEHRVMLVNSMNTVKELLPVLISAMKIFVTTKNSKNQGIEEALKNRNFTVEKMSAEINEIIRVLQLTSWDEDAW 258
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250

Chain B from PDB  Type:PROTEIN  Length:25
 aligned with IPAA_SHIFL | P18010 from UniProtKB/Swiss-Prot  Length:633

    Alignment length:25
                                   572       582     
           IPAA_SHIFL   563 NHAIYEKAKEVSSALSKVLSKIDDT 587
               SCOP domains ------------------------- SCOP domains
               CATH domains ------------------------- CATH domains
               Pfam domains ------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------- SAPs(SNPs)
                    PROSITE ------------------------- PROSITE
                 Transcript ------------------------- Transcript
                 2ibf B 563 NHAIYEKAKEVSSALSKVLSKIDDT 587
                                   572       582

Chain D from PDB  Type:PROTEIN  Length:19
 aligned with IPAA_SHIFL | P18010 from UniProtKB/Swiss-Prot  Length:633

    Alignment length:19
                                   576         
           IPAA_SHIFL   567 YEKAKEVSSALSKVLSKID 585
               SCOP domains ------------------- SCOP domains
               CATH domains ------------------- CATH domains
               Pfam domains ------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------- SAPs(SNPs)
                    PROSITE ------------------- PROSITE
                 Transcript ------------------- Transcript
                 2ibf D 567 YEKAKEVSSALSKVLSKID 585
                                   576

Legend:		→ Mismatch	(orange background)
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		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 2IBF)

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Four Helix Bundle (Hemerythrin (Met), subunit A) (300)

Homologous Superfamily: [code=1.20.120.230, no name defined] (23)

Human (Homo sapiens) (11)

2ibfA02

A:130-258

Topology: vbs2 fragment of talin (15)

Homologous Superfamily: vbs2 fragment of talin (15)

Human (Homo sapiens) (7)

2ibfA01

A:1-129

(no "Pfam Domain" information available for 2IBF)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (VINC_HUMAN | P18206)

molecular function
	GO:0003779	actin binding	Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
	GO:0045294	alpha-catenin binding	Interacting selectively and non-covalently with the alpha subunit of the catenin complex.
	GO:0008013	beta-catenin binding	Interacting selectively and non-covalently with the beta subunit of the catenin complex.
	GO:0045296	cadherin binding	Interacting selectively and non-covalently with cadherin, a type I membrane protein involved in cell adhesion.
	GO:0002162	dystroglycan binding	Interacting selectively and non-covalently with dystroglycan. Dystroglycan is glycoprotein found in non-muscle tissues as well as in muscle tissues, often in association with dystrophin. The native dystroglycan cleaved into two non-covalently associated subunits, alpha (N-terminal) and beta (C-terminal).
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0005198	structural molecule activity	The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
	GO:0031625	ubiquitin protein ligase binding	Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
	GO:0034333	adherens junction assembly	The aggregation, arrangement and bonding together of a set of components to form an adherens junction. An adherens junction is a cell junction at which the cytoplasmic face of the plasma membrane is attached to actin filaments.
	GO:0043297	apical junction assembly	The formation of an apical junction, a functional unit located near the cell apex at the points of contact between epithelial cells composed of the tight junction, the zonula adherens junction and the desmosomes, by the aggregation, arrangement and bonding together of its constituents.
	GO:0048675	axon extension	Long distance growth of a single axon process involved in cellular development.
	GO:0007155	cell adhesion	The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
	GO:0007160	cell-matrix adhesion	The binding of a cell to the extracellular matrix via adhesion molecules.
	GO:0090136	epithelial cell-cell adhesion	The attachment of an epithelial cell to another epithelial cell via adhesion molecules.
	GO:0030032	lamellipodium assembly	Formation of a lamellipodium, a thin sheetlike extension of the surface of a migrating cell.
	GO:0002009	morphogenesis of an epithelium	The process in which the anatomical structures of epithelia are generated and organized. An epithelium consists of closely packed cells arranged in one or more layers, that covers the outer surfaces of the body or lines any internal cavity or tube.
	GO:0006928	movement of cell or subcellular component	The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore.
	GO:0006936	muscle contraction	A process in which force is generated within muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis.
	GO:0030336	negative regulation of cell migration	Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration.
	GO:0070527	platelet aggregation	The adhesion of one platelet to one or more other platelets via adhesion molecules.
	GO:0002576	platelet degranulation	The regulated exocytosis of secretory granules containing preformed mediators such as histamine and serotonin by a platelet.
	GO:0034394	protein localization to cell surface	A process in which a protein is transported to, or maintained in, a location within the external part of the cell wall and/or plasma membrane.
	GO:0030334	regulation of cell migration	Any process that modulates the frequency, rate or extent of cell migration.
cellular component
	GO:0015629	actin cytoskeleton	The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
	GO:0005912	adherens junction	A cell junction at which anchoring proteins (cadherins or integrins) extend through the plasma membrane and are attached to actin filaments.
	GO:0005903	brush border	The dense covering of microvilli on the apical surface of a epithelial cells in tissues such as the intestine, kidney, and choroid plexus; the microvilli aid absorption by increasing the surface area of the cell.
	GO:0005623	cell	The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
	GO:0030054	cell junction	A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
	GO:0005913	cell-cell adherens junction	An adherens junction which connects a cell to another cell.
	GO:0005911	cell-cell junction	A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
	GO:0030055	cell-substrate junction	A cell junction that forms a connection between a cell and the extracellular matrix.
	GO:0043034	costamere	Regular periodic sub membranous arrays of vinculin in skeletal and cardiac muscle cells, these arrays link Z-discs to the sarcolemma and are associated with links to extracellular matrix.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005856	cytoskeleton	Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:1903561	extracellular vesicle	Any vesicle that is part of the extracellular region.
	GO:0005916	fascia adherens	A cell-cell adherens junction that contains the transmembrane protein N-cadherin, which interacts with identical molecules from neighboring cells to form a tight mechanical intercellular link; forms a large portion of the intercalated disc, the structure at which myofibrils terminate in cardiomyocytes.
	GO:0005925	focal adhesion	Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
	GO:0090637	inner dense plaque of desmosome	The desmosomal part containing the C-termini of desmoplakins which interact with the keratin intermediate filaments, serving to tether the intermediate filaments to the plasma membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0045121	membrane raft	Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
	GO:0090636	outer dense plaque of desmosome	The desmosomal part containing plakoglobins, plakophilins, the N-termini of desmoplakins, as well as the cytoplasmic tails of the desmosomal cadherins, which together attach the plaque to the plasma membrane.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
	GO:0043234	protein complex	A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
	GO:1990357	terminal web	An actin-rich cytoskeletal network located beneath the microvilli of the apical plasma membrane of polarized epithelial cells. In addition to actin filaments, the terminal web may contain actin-binding proteins, myosin motor proteins, and intermediate filaments. The terminal web can function as a contractile structure that influences the spatial distribution of microvilli as well as the development and morphogenesis of tissues containing polarized epithelial cells.
	GO:0005915	zonula adherens	A cell-cell adherens junction which forms a continuous belt near the apex of epithelial cells.

Chain B,D (IPAA_SHIFL | P18010)

molecular function
	GO:0003779	actin binding	Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0017166	vinculin binding	Interacting selectively and non-covalently with vinculin, a protein found in muscle, fibroblasts, and epithelial cells that binds actin and appears to mediate attachment of actin filaments to integral proteins of the plasma membrane.
biological process
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
	GO:0030836	positive regulation of actin filament depolymerization	Any process that activates or increases the frequency, rate or extent of actin depolymerization.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Asymmetric/Biological Unit
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