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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SH3 DOMAIN OF BETAPIX IN COMPLEX WITH A HIGH AFFINITY PEPTIDE FROM PAK2
 
Authors :  A. Hoelz
Date :  25 Feb 06  (Deposition) - 11 Apr 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Sh3 Domain, Peptide Interaction, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Hoelz, J. M. Janz, S. D. Lawrie, B. Corwin, A. Lee, T. P. Sakmar
Crystal Structure Of The Sh3 Domain Of Betapix In Complex With A High Affinity Peptide From Pak2
J. Mol. Biol. V. 358 509 2006
PubMed-ID: 16527308  |  Reference-DOI: 10.1016/J.JMB.2006.02.027
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 7
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPGEX-6P1
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentSH3 DOMAIN(RESIDUES 10-63)
    GeneARHGEF7, PAK3BP, PIXB
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymPAK-INTERACTING EXCHANGE FACTOR BETA, BETA-PIX
 
Molecule 2 - 18-MER FROM PAK2
    ChainsC, D
    EC Number2.7.1.37
    EngineeredYES
    FragmentRESIDUES 180-197
    Other DetailsTHE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN HUMAN, RAT.
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A C 
Biological Unit 2 (1x) B D

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2DF6)

(-) Sites  (0, 0)

(no "Site" information available for 2DF6)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DF6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DF6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DF6)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.ARHG7_RAT6-65
 
  2A:9-63
B:9-63
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.ARHG7_RAT6-65
 
  1A:9-63
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.ARHG7_RAT6-65
 
  1-
B:9-63

(-) Exons   (2, 4)

Asymmetric Unit (2, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000179471ENSRNOE00000277809chr16:82635476-82635312165ARHG7_RAT1-55552A:5-55 (gaps)
B:5-55 (gaps)
53
53
1.2bENSRNOT000000179472bENSRNOE00000350383chr16:82603278-8260319287ARHG7_RAT56-84292A:56-63
B:56-63
8
8
1.3ENSRNOT000000179473ENSRNOE00000342668chr16:82581873-8258178985ARHG7_RAT85-113290--
1.4ENSRNOT000000179474ENSRNOE00000338153chr16:82580441-82580311131ARHG7_RAT113-156440--
1.5ENSRNOT000000179475ENSRNOE00000299788chr16:82577209-82577008202ARHG7_RAT157-224680--
1.6ENSRNOT000000179476ENSRNOE00000123133chr16:82567614-8256752689ARHG7_RAT224-253300--
1.7ENSRNOT000000179477ENSRNOE00000128814chr16:82560132-8256003895ARHG7_RAT254-285320--
1.8ENSRNOT000000179478ENSRNOE00000123260chr16:82559813-8255971896ARHG7_RAT285-317330--
1.9ENSRNOT000000179479ENSRNOE00000123318chr16:82554748-82554626123ARHG7_RAT317-358420--
1.10ENSRNOT0000001794710ENSRNOE00000123372chr16:82550615-82550477139ARHG7_RAT358-404470--
1.11ENSRNOT0000001794711ENSRNOE00000123438chr16:82549894-8254983560ARHG7_RAT405-424200--
1.12ENSRNOT0000001794712ENSRNOE00000129046chr16:82549272-82549126147ARHG7_RAT425-473490--
1.13ENSRNOT0000001794713ENSRNOE00000123551chr16:82546857-8254677187ARHG7_RAT474-502290--
1.14ENSRNOT0000001794714ENSRNOE00000123615chr16:82541663-8254158579ARHG7_RAT503-529270--
1.15ENSRNOT0000001794715ENSRNOE00000123672chr16:82541425-82541286140ARHG7_RAT529-575470--
1.16ENSRNOT0000001794716ENSRNOE00000127997chr16:82538706-82538482225ARHG7_RAT576-650750--
1.17ENSRNOT0000001794717ENSRNOE00000123730chr16:82536831-8253673894ARHG7_RAT651-682320--
1.18aENSRNOT0000001794718aENSRNOE00000123790chr16:82534037-8253394890ARHG7_RAT682-712310--
1.21ENSRNOT0000001794721ENSRNOE00000123923chr16:82524702-82524603100ARHG7_RAT712-745340--
1.22ENSRNOT0000001794722ENSRNOE00000124026chr16:82524361-8252430755ARHG7_RAT745-763190--
1.23ENSRNOT0000001794723ENSRNOE00000389941chr16:82523402-825212262177ARHG7_RAT764-803400--

(-) 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:59
 aligned with ARHG7_RAT | O55043 from UniProtKB/Swiss-Prot  Length:646

    Alignment length:61
                                    12        22        32        42        52        62 
            ARHG7_RAT     3 DNANSQLVVRAKFNFQQTNEDELSFSKGDVIHVTRVEEGGWWEGTHNGRTGWFPSNYVREI  63
               SCOP domains ------------------------------------------------------------- SCOP domains
               CATH 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:9-63 UniProt: 6-65                             PROSITE
               Transcript 1 Exon 1.1  PDB: A:5-55 (gaps) UniProt: 1-55           1.2b     Transcript 1
                 2df6 A   5 GPLGS--VVRAKFNFQQTNEDELSFSKGDVIHVTRVEEGGWWEGTHNGRTGWFPSNYVREI  63
                                |  |12        22        32        42        52        62 
                                9 10                                                     

Chain B from PDB  Type:PROTEIN  Length:59
 aligned with ARHG7_RAT | O55043 from UniProtKB/Swiss-Prot  Length:646

    Alignment length:61
                                    12        22        32        42        52        62 
            ARHG7_RAT     3 DNANSQLVVRAKFNFQQTNEDELSFSKGDVIHVTRVEEGGWWEGTHNGRTGWFPSNYVREI  63
               SCOP domains ------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author .....--eeee..................eeeeee.....eeeeee..eeeeee...eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---SH3  PDB: B:9-63 UniProt: 6-65                             PROSITE
               Transcript 1 Exon 1.1  PDB: B:5-55 (gaps) UniProt: 1-55           1.2b     Transcript 1
                 2df6 B   5 GPLGS--VVRAKFNFQQTNEDELSFSKGDVIHVTRVEEGGWWEGTHNGRTGWFPSNYVREI  63
                                |  |12        22        32        42        52        62 
                                9 10                                                     

Chain C from PDB  Type:PROTEIN  Length:18
                                                  
               SCOP domains ------------------ SCOP domains
               CATH domains ------------------ CATH domains
               Pfam domains ------------------ Pfam domains
         Sec.struct. author .......hhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------ SAPs(SNPs)
                    PROSITE ------------------ PROSITE
                 Transcript ------------------ Transcript
                 2df6 C 180 PPVIAPRPEHTKSIYTRS 197
                                   189        

Chain D from PDB  Type:PROTEIN  Length:12
                                            
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author .......hhhhh Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 2df6 D 180 PPVIAPRPEHTK 191
                                   189  

   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  (0, 0)

(no "SCOP Domain" information available for 2DF6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2DF6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DF6)

(-) Gene Ontology  (20, 20)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ARHG7_RAT | O55043)
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:0043615    astrocyte cell migration    The orderly movement of an astrocyte, a class of large neuroglial (macroglial) cells in the central nervous system, the largest and most numerous neuroglial cells in the brain and spinal cord.
    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:0035023    regulation of Rho protein signal transduction    Any process that modulates the frequency, rate or extent of Rho protein signal transduction.
    GO:0007264    small GTPase mediated signal transduction    Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals.
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: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:0030426    growth cone    The migrating motile tip of a growing nerve cell axon or dendrite.
    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:0001726    ruffle    Projection at the leading edge of a crawling cell; the protrusions are supported by a microfilament meshwork.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ARHG7_RAT | O550432ak5 2g6f 2p4r 2w6b 3l4f 3qjn

(-) Related Entries Specified in the PDB File

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