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(-) Description

Title :  ATOMIC STRUCTURE OF THE N-TERMINAL SH3 DOMAIN OF MOUSE BETA PIX,P21-ACTIVATED KINASE (PAK)-INTERACTING EXCHANGE FACTOR
 
Authors :  Z. Rao
Date :  27 Oct 05  (Deposition) - 11 Apr 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Beta Barrel, Sh3 Domain, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Li, X. Liu, F. Sun, J. Gao, H. Zhou, G. F. Gao, M. Bartlam, Z. Rao
Crystal Structure Of The N-Terminal Sh3 Domain Of Mouse Betapix, P21-Activated Kinase-Interacting Exchange Factor
Biochem. Biophys. Res. Commun. V. 339 407 2006
PubMed-ID: 16307729  |  Reference-DOI: 10.1016/J.BBRC.2005.10.212
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 7
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX6P-1
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentSH3 DOMAIN
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymPAK-INTERACTING EXCHANGE FACTOR BETA, BETA-PIX, P85SPR

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric Unit (2, 9)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2HG6Ligand/IonMERCURY (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2HG-1Ligand/IonMERCURY (II) ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2HG-1Ligand/IonMERCURY (II) ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2HG-1Ligand/IonMERCURY (II) ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:20 , HIS A:46 , ARG A:49 , CL A:1008BINDING SITE FOR RESIDUE HG A 1001
2AC2SOFTWARETRP A:41 , THR B:18 , ASN B:19BINDING SITE FOR RESIDUE HG A 1003
3AC3SOFTWARETHR A:18 , ASN A:19 , HIS A:46 , CL A:1009 , GLY B:40 , CL B:1007BINDING SITE FOR RESIDUE HG A 1004
4AC4SOFTWAREGLU A:20 , ASP A:29 , HG A:1001 , HOH A:1011BINDING SITE FOR RESIDUE CL A 1008
5AC5SOFTWARETHR A:18 , ASP A:29 , HIS A:46 , HG A:1004 , HOH A:1011BINDING SITE FOR RESIDUE CL A 1009
6AC6SOFTWARETHR A:18 , ASN A:19 , TRP B:41BINDING SITE FOR RESIDUE HG B 1002
7AC7SOFTWAREHIS B:46BINDING SITE FOR RESIDUE HG B 1005
8AC8SOFTWAREHIS B:46BINDING SITE FOR RESIDUE HG B 1006
9AC9SOFTWARETHR A:18 , HG A:1004 , GLY B:40 , PRO B:54 , SER B:55 , ASN B:56BINDING SITE FOR RESIDUE CL B 1007

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.ARHG7_MOUSE163-222  1A:5-61
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.ARHG7_MOUSE163-222  1A:5-61
Biological Unit 2 (, 0)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.ARHG7_MOUSE163-222  0-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.ARHG7_MOUSE163-222  1A:5-61

(-) Exons   (0, 0)

(no "Exon" information available for 2ESW)

(-) 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:60
 aligned with ARHG7_MOUSE | Q9ES28 from UniProtKB/Swiss-Prot  Length:862

    Alignment length:96
                                   134       144       154       164       174       184       194       204       214      
          ARHG7_MOUSE   125 PSSHRIKSFDSLGSQSSHSRTSKLLQSQYRSLDMTDNTNSQLVVRAKFNFQQTNEDELSFSKGDVIHVTRVEEGGWWEGTHNGRTGWFPSNYVREI 220
               SCOP domains d          2e                          swa_ A: automated matches                                 SCOP domains
               CATH domains 2          es                          wA00 A:2-61 SH3 Domains                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .----------..--------------------------...eeee..................eeeeeee....eeeeee..eeeeee...eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------SH3  PDB: A:5-61 UniProt: 163-222                          PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 2esw A   2 P----------LG--------------------------SQLVVRAKFNFQQTNEDELSFSKGDVIHVTRVEEGGWWEGTHNGRTGWFPSNYVREI  61
                            |        - ||      -         -         5        15        25        35        45        55      
                            |          3|                          5                                                        
                            2           4                                                                                   

Chain B from PDB  Type:PROTEIN  Length:57
 aligned with ARHG7_MOUSE | Q9ES28 from UniProtKB/Swiss-Prot  Length:862

    Alignment length:57
                                   173       183       193       203       213       
          ARHG7_MOUSE   164 SQLVVRAKFNFQQTNEDELSFSKGDVIHVTRVEEGGWWEGTHNGRTGWFPSNYVREI 220
               SCOP domains d2eswb_ B: automated matches                              SCOP domains
               CATH domains 2eswB00 B:5-61 SH3 Domains                                CATH domains
               Pfam domains --------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..................eeeeeee....eeeeee..eeeeee...eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                    PROSITE SH3  PDB: - UniProt: 163-222                              PROSITE
                 Transcript --------------------------------------------------------- Transcript
                 2esw B   5 SQLVVRAKFNFQQTNEDELSFSKGDVIHVTRVEEGGWWEGTHNGRTGWFPSNYVREI  61
                                    14        24        34        44        54       

   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  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (32, 32)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ARHG7_MOUSE | Q9ES28)
molecular function
    GO:0005089    Rho guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Rho family. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    GO:0005085    guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    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:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
biological process
    GO:0007030    Golgi organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the Golgi apparatus.
    GO:0048041    focal adhesion assembly    The aggregation and bonding together of a set of components to form a focal adhesion, a complex of intracellular signaling and structural proteins that provides a structural link between the internal actin cytoskeleton and the ECM, and also function as a locus of signal transduction activity.
    GO:0002244    hematopoietic progenitor cell differentiation    The process in which precursor cell type acquires the specialized features of a hematopoietic progenitor cell, a class of cell types including myeloid progenitor cells and lymphoid progenitor cells.
    GO:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    GO:0030032    lamellipodium assembly    Formation of a lamellipodium, a thin sheetlike extension of the surface of a migrating cell.
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0010763    positive regulation of fibroblast migration    Any process that increases the rate, frequency or extent of fibroblast cell migration. Fibroblast cell migration is accomplished by extension and retraction of a pseudopodium.
    GO:0060124    positive regulation of growth hormone secretion    Any process that increases the frequency, rate or extent of the regulated release of growth hormone from a cell.
    GO:2000394    positive regulation of lamellipodium morphogenesis    Any process that activates or increases the frequency, rate or extent of lamellipodium morphogenesis.
    GO:0032092    positive regulation of protein binding    Any process that activates or increases the frequency, rate or extent of protein binding.
    GO:1900026    positive regulation of substrate adhesion-dependent cell spreading    Any process that activates or increases the frequency, rate or extent of substrate adhesion-dependent cell spreading.
    GO:1904424    regulation of GTP binding    Any process that modulates the frequency, rate or extent of GTP binding.
    GO:0035023    regulation of Rho protein signal transduction    Any process that modulates the frequency, rate or extent of Rho protein signal transduction.
cellular component
    GO:0005938    cell cortex    The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.
    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:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0030027    lamellipodium    A thin sheetlike process extended by the leading edge of a migrating cell or extending cell process; contains a dense meshwork of actin filaments.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    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:0001726    ruffle    Projection at the leading edge of a crawling cell; the protrusions are supported by a microfilament meshwork.
    GO:0000322    storage vacuole    A vacuole that functions primarily in the storage of materials, including nutrients, pigments, waste products, and small molecules.

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