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(-) Description

Title :  CRYSTAL STRUCTURE OF THE C-TERMINAL CALPONIN HOMOLOGY DOMAIN OF ALPHA PARVIN
 
Authors :  S. Lorenz, I. Vakonakis, E. D. Lowe, I. D. Campbell, M. E. M. Noble, M. K. Hoellerer
Date :  31 Jul 08  (Deposition) - 28 Oct 08  (Release) - 28 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.05
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Membrane, Cytoplasm, Cytoskeleton, Cell Junction, Alternative Splicing, Calponin Homology Domain, Actin-Binding, Cell Membrane, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Lorenz, I. Vakonakis, E. D. Lowe, I. D. Campbell, M. E. M. Noble, M. K. Hoellerer
Structural Analysis Of The Interactions Between Paxillin Ld Motifs And Alpha-Parvin
Structure V. 16 1521 2008
PubMed-ID: 18940607  |  Reference-DOI: 10.1016/J.STR.2008.08.007

(-) Compounds

Molecule 1 - ALPHA-PARVIN
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-6P1
    Expression System StrainBL21
    Expression System Taxid511693
    FragmentC-TERMINAL CALPONIN HOMOLOGY DOMAIN, RESIDUES 242-372
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCALPONIN-LIKE INTEGRIN-LINKED KINASE-BINDING PROTEIN, CH-ILKBP, MATRIX-REMODELING-ASSOCIATED PROTEIN 2, ACTOPAXIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 4)

Asymmetric Unit (4, 4)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3MRD1Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
4TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MPD-1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3MRD-1Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
4TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3MRD1Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
4TRS-1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:347 , HOH A:2104 , SER B:312 , PHE B:314 , LEU B:325 , HOH B:2062 , HOH B:2139BINDING SITE FOR RESIDUE MRD B1373
2AC2SOFTWARESER A:312 , HOH A:2050 , ARG B:345 , GLU B:347 , HOH B:2110 , HOH B:2140BINDING SITE FOR RESIDUE MPD B1374
3AC3SOFTWAREASP A:255 , HIS A:256 , ASP A:318 , GLN A:322 , HOH A:2057 , HOH A:2138 , HOH A:2139 , GLU B:321BINDING SITE FOR RESIDUE TRS A1373
4AC4SOFTWAREGLN A:289 , ASP A:292 , TYR A:295 , HOH A:2036 , HOH A:2040BINDING SITE FOR RESIDUE GOL A1374

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VZC)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHPS50021 Calponin homology domain profile.PARVA_HUMAN95-201
262-369
 
  2-
A:262-369
B:262-369
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHPS50021 Calponin homology domain profile.PARVA_HUMAN95-201
262-369
 
  1-
A:262-369
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHPS50021 Calponin homology domain profile.PARVA_HUMAN95-201
262-369
 
  1-
-
B:262-369

(-) Exons   (0, 0)

(no "Exon" information available for 2VZC)

(-) 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:127
 aligned with PARVA_HUMAN | Q9NVD7 from UniProtKB/Swiss-Prot  Length:372

    Alignment length:127
                                   255       265       275       285       295       305       315       325       335       345       355       365       
          PARVA_HUMAN   246 ERDAFDTLFDHAPDKLNVVKKTLITFVNKHLNKLNLEVTELETQFADGVYLVLLMGLLEGYFVPLHSFFLTPDSFEQKVLNVSFAFELMQDGGLEKPKPRPEDIVNCDLKSTLRVLYNLFTKYRNVE 372
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhh.......hhhhhhh.hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------CH  PDB: A:262-369 UniProt: 262-369                                                                         --- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vzc A 246 ERDAFDTLFDHAPDKLNVVKKTLITFVNKHLNKLNLEVTELETQFADGVYLVLLMGLLEGYFVPLHSFFLTPDSFEQKVLNVSFAFELMQDGGLEKPKPRPEDIVNCDLKSTLRVLYNLFTKYRNVE 372
                                   255       265       275       285       295       305       315       325       335       345       355       365       

Chain B from PDB  Type:PROTEIN  Length:126
 aligned with PARVA_HUMAN | Q9NVD7 from UniProtKB/Swiss-Prot  Length:372

    Alignment length:126
                                   256       266       276       286       296       306       316       326       336       346       356       366      
          PARVA_HUMAN   247 RDAFDTLFDHAPDKLNVVKKTLITFVNKHLNKLNLEVTELETQFADGVYLVLLMGLLEGYFVPLHSFFLTPDSFEQKVLNVSFAFELMQDGGLEKPKPRPEDIVNCDLKSTLRVLYNLFTKYRNVE 372
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhh...hhhhh.....hhhhhhhhhhhhhhhhhhh.......hhhhhhh.hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------CH  PDB: B:262-369 UniProt: 262-369                                                                         --- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2vzc B 247 RDAFDTLFDHAPDKLNVVKKTLITFVNKHLNKLNLEVTELETQFADGVYLVLLMGLLEGYFVPLHSFFLTPDSFEQKVLNVSFAFELMQDGGLEKPKPRPEDIVNCDLKSTLRVLYNLFTKYRNVE 372
                                   256       266       276       286       296       306       316       326       336       346       356       366      

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (0, 0)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2VZC)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (24, 24)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PARVA_HUMAN | Q9NVD7)
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).
biological process
    GO:0031532    actin cytoskeleton reorganization    A process that is carried out at the cellular level which results in dynamic structural changes to the arrangement of constituent parts of cytoskeletal structures comprising actin filaments and their associated proteins.
    GO:0070252    actin-mediated cell contraction    The actin filament-based process in which cytoplasmic actin filaments slide past one another resulting in contraction of all or part of the cell body.
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    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:0030030    cell projection organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0006935    chemotaxis    The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    GO:0060271    cilium assembly    The assembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole.
    GO:0007163    establishment or maintenance of cell polarity    Any cellular process that results in the specification, formation or maintenance of anisotropic intracellular organization or cell growth patterns.
    GO:0034113    heterotypic cell-cell adhesion    The attachment of a cell to a cell of a different type via adhesion molecules.
    GO:0003148    outflow tract septum morphogenesis    The process in which the anatomical structures of the outflow tract septum are generated and organized. The outflow tract septum is a partition in the outflow tract.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    GO:0071670    smooth muscle cell chemotaxis    The directed movement of a smooth muscle cell in response to an external stimulus.
    GO:0002040    sprouting angiogenesis    The extension of new blood vessels from existing capillaries into avascular tissues resulting from the proliferation of blood vessel endothelial cells.
    GO:0034446    substrate adhesion-dependent cell spreading    The morphogenetic process that results in flattening of a cell as a consequence of its adhesion to a substrate.
cellular component
    GO:0030018    Z disc    Platelike region of a muscle sarcomere to which the plus ends of actin filaments are attached.
    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: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: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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PARVA_HUMAN | Q9NVD72k2r 2vzd 2vzg 2vzi 3kmu 3kmw 3rep

(-) Related Entries Specified in the PDB File

2vzd CRYSTAL STRUCTURE OF THE C-TERMINAL CALPONIN HOMOLOGY DOMAIN OF ALPHA PARVIN IN COMPLEX WITH PAXILLIN LD1 MOTIF
2vzg CRYSTAL STRUCTURE OF THE C-TERMINAL CALPONIN HOMOLOGY DOMAIN OF ALPHA-PARVIN IN COMPLEX WITH PAXILLIN LD2 MOTIF
2vzi CRYSTAL STRUCTURE OF THE C-TERMINAL CALPONIN HOMOLOGY DOMAIN OF ALPHA-PARVIN IN COMPLEX WITH PAXILLIN LD4 MOTIF