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(-) Description

Title :  HUMAN VINCULIN HEAD DOMAIN (VH1, RESIDUES 1-258) IN COMPLEX WITH THE VINCULIN BINDING SITE OF THE SURFACE CELL ANTIGEN 4 (SCA4-VBS-C; RESIDUES 812-835) FROM RICKETTSIA RICKETTSII
 
Authors :  H. Park, J. H. Lee, E. Gouin, P. Cossart, T. Izard
Date :  23 Aug 11  (Deposition) - 07 Sep 11  (Release) - 01 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.76
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (3x)
Keywords :  Cytoskeleton, Epidemic Typhus, Sca4, Spotted Fever, Alpha-Helix Bundle Domain, Protein-Protein Interactions, Cell Adhesion, Cytosol, Focal Adhesion, Protein Binding-Toxin Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Park, J. H. Lee, E. Gouin, P. Cossart, T. Izard
The Rickettsia Surface Cell Antigen 4 Applies Mimicry To Bind To And Activate Vinculin.
J. Biol. Chem. V. 286 35096 2011
PubMed-ID: 21841197  |  Reference-DOI: 10.1074/JBC.M111.263855

(-) Compounds

Molecule 1 - VINCULIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneVCL
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMETAVINCULIN
 
Molecule 2 - ANTIGENIC HEAT-STABLE 120 KDA PROTEIN
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 812-834
    GeneRRIOWA_0797
    Organism ScientificRICKETTSIA RICKETTSII
    Organism Taxid452659
    StrainIOWA
    Synonym120 KDA ANTIGEN, PROTEIN PS 120, PS120

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)AB
Biological Unit 2 (3x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3TJ6)

(-) Sites  (0, 0)

(no "Site" information available for 3TJ6)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3TJ6)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asn A:217 -Ser A:218
2Ser A:218 -Lys A:219
3Gln A:221 -Gly A:222
4Glu A:255 -Asp A:256

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_037667V234LVINC_HUMANPolymorphism17853882AV234L

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_037667V234LVINC_HUMANPolymorphism17853882AV234L

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_037667V234LVINC_HUMANPolymorphism17853882AV234L

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VINCULIN_1PS00663 Vinculin family talin-binding region signature.VINC_HUMAN162-182  1A:162-182
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VINCULIN_1PS00663 Vinculin family talin-binding region signature.VINC_HUMAN162-182  1A:162-182
Biological Unit 2 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VINCULIN_1PS00663 Vinculin family talin-binding region signature.VINC_HUMAN162-182  3A:162-182

(-) Exons   (6, 6)

Asymmetric Unit (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002119981aENSE00002146319chr10:75757872-75758133262VINC_HUMAN1-56561A:1-56 (gaps)56
1.2aENST000002119982aENSE00001607712chr10:75802841-7580291171VINC_HUMAN57-80241A:57-8024
1.4ENST000002119984ENSE00001024254chr10:75830428-75830578151VINC_HUMAN80-130511A:80-13051
1.5ENST000002119985ENSE00001024245chr10:75830733-75830841109VINC_HUMAN131-167371A:131-16737
1.6ENST000002119986ENSE00001024249chr10:75832488-75832610123VINC_HUMAN167-208421A:167-20842
1.7aENST000002119987aENSE00001024263chr10:75834501-75834661161VINC_HUMAN208-261541A:208-25750
1.8ENST000002119988ENSE00001024248chr10:75842212-7584230291VINC_HUMAN262-292310--
1.9aENST000002119989aENSE00000986356chr10:75843124-75843271148VINC_HUMAN292-341500--
1.10ENST0000021199810ENSE00000986357chr10:75848954-75849107154VINC_HUMAN341-392520--
1.11ENST0000021199811ENSE00000986358chr10:75849781-75849956176VINC_HUMAN393-451590--
1.12ENST0000021199812ENSE00001024262chr10:75854029-75854219191VINC_HUMAN451-515650--
1.13ENST0000021199813ENSE00000986360chr10:75855414-75855613200VINC_HUMAN515-581670--
1.14ENST0000021199814ENSE00000986361chr10:75856962-75857090129VINC_HUMAN582-624430--
1.15aENST0000021199815aENSE00000986362chr10:75860706-75860855150VINC_HUMAN625-674500--
1.16ENST0000021199816ENSE00000986363chr10:75863578-75863686109VINC_HUMAN675-711370--
1.17cENST0000021199817cENSE00000986364chr10:75864809-75865111303VINC_HUMAN711-8121020--
1.18ENST0000021199818ENSE00000986365chr10:75866988-75867112125VINC_HUMAN812-853420--
1.19bENST0000021199819bENSE00000834577chr10:75868729-75868914186VINC_HUMAN854-915620--
1.20ENST0000021199820ENSE00000709651chr10:75871667-75871870204VINC_HUMAN916-983680--
1.21ENST0000021199821ENSE00000709670chr10:75873942-75874145204VINC_HUMAN984-1051680--
1.22ENST0000021199822ENSE00000986366chr10:75874553-75874657105VINC_HUMAN1052-1086350--
1.23aENST0000021199823aENSE00001373600chr10:75877781-758799102130VINC_HUMAN1087-1134480--

(-) Sequences/Alignments

Asymmetric 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:253
 aligned with VINC_HUMAN | P18206 from UniProtKB/Swiss-Prot  Length:1134

    Alignment length:257
                                    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 MPVFHTRTIESILEPVAQQISHLVIMHEEGEVDGKAIPDLTAPVAAVQAAVSNLVRVGKETVQTTEDQILKRDMPPAFIKVENACTKLVQAAQMLQSDPYSVPARDYLIDGSRGILSGTSDLLLTFDEAEVRKIIRVCKGILEYLTVAEVVETMEDLVTYTKNLGPGMTKMAKMIDERQQELTHQEHRVMLVNSMNTVKELLPVLISAMKIFVTTKNSKNQGIEEALKNRNFTVEKMSAEINEIIRVLQLTSWDEDA 257
               SCOP domains d3tj6a1 A:1-128 Vinculin                                                                                                        d3tj6a2 A:129-257 Vinculin                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhh...----......hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L----------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------VINCULIN_1           --------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:1-56 (gaps) UniProt: 1-56             Exon 1.2a  PDB: A:57-80 --------------------------------------------------Exon 1.5  PDB: A:131-167             ----------------------------------------Exon 1.7a  PDB: A:208-257 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)
                 3tj6 A   1 MPVFHTRTIESILEPVAQQISHLVIMHEE----GKAIPDLTAPVAAVQAAVSNLVRVGKETVQTTEDQILKRDMPPAFIKVENACTKLVQAAQMLQSDPYSVPARDYLIDGSRGILSGTSDLLLTFDEAEVRKIIRVCKGILEYLTVAEVVETMEDLVTYTKNLGPGMTKMAKMIDERQQELTHQEHRVMLVNSMNTVKELLPVLISAMKIFVTTKNSKNQGIEEALKNRNFTVEKMSAEINEIIRVLQLTSWDEDA 257
                                    10        20        |-   |    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       
                                                       29   34                                                                                                                                                                                                                               

Chain B from PDB  Type:PROTEIN  Length:23
 aligned with B0BXR4_RICRO | B0BXR4 from UniProtKB/TrEMBL  Length:1024

    Alignment length:23
                                   821       831   
         B0BXR4_RICRO   812 DDIYNKAREVINAVNPVIEALEK 834
               SCOP domains ----------------------- SCOP domains
               CATH domains ----------------------- CATH domains
               Pfam domains ----------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------- SAPs(SNPs)
                    PROSITE ----------------------- PROSITE
                 Transcript ----------------------- Transcript
                 3tj6 B 812 DDIYNKAREVINAVNPVIEALEK 834
                                   821       831   

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TJ6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TJ6)

(-) Gene Ontology  (48, 48)

Asymmetric 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   (B0BXR4_RICRO | B0BXR4)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        VINC_HUMAN | P182061rkc 1rke 1syq 1tr2 1ydi 2gww 2hsq 2ibf 3h2u 3h2v 3jbk 3myi 3rf3 3s90 3tj5 3vf0 4dj9 4ehp 4ln2 4lnp 4pr9 5l0c 5l0d 5l0f 5l0g 5l0h 5l0i 5l0j
UniProtKB/TrEMBL
        B0BXR4_RICRO | B0BXR43tj5 4lq8

(-) Related Entries Specified in the PDB File

1rkc HUMAN VINCULIN HEAD (1-258) IN COMPLEX WITH TALIN'S VINCULIN BINDING SITE 3 (RESIDUES 1944-1969)
2gww HUMAN VINCULIN (HEAD DOMAIN, VH1, RESIDUES 1-258) IN COMPLEX WITH SHIGELLA'S IPAA VINCULIN BINDING SITE (RESIDUES 602-633)
2hsq HUMAN VINCULIN (HEAD DOMAIN, VH1, RESIDUES 1-258) IN COMPLEX WITH SHIGELLA'S IPAA VINCULIN BINDING SITE 2 (RESIDUES 565-587)
2ibf HUMAN VINCULIN'S HEAD DOMAIN (VH1, RESIDUES 1-258) IN COMPLEX WITH TWO VINCULIN BINDING SITES OF SHIGELLA FLEXNERI'S IPAA (RESIDUES 565-587)
3rf3 SHIGELLA IPAA-VBS3 IN COMPLEX WITH HUMAN VINCULIN
3s90 HUMAN VINCULIN HEAD DOMAIN VH1 (RESIDUES 1-252) IN COMPLEX WITH MURINE TALIN (VBS33; RESIDUES 1512-1546)
3tj5