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(-) Description

Title :  MONA SH3C IN COMPLEX
 
Authors :  M. Harkiolaki, S. M. Feller
Date :  13 Oct 08  (Deposition) - 19 May 09  (Release) - 23 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Alternative Splicing, Tpr Repeat, Sh2 Domain, Sh3 Domain, Coiled Coil, Protein Phosphatase, Cytoplasmic Vesicle, Phosphoprotein, Signal Tranduction, Sh3 Domain/Complex, Sh3, Gads, Mona, Dimer, Hd-Ptp, Hydrolase, Cytoplasm (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Harkiolaki, T. Tsirka, M. Lewitzky, P. C. Simister, D. Joshi, L. E. Bird, E. Y. Jones, N. O'Reilly, S. M. Feller
Distinct Binding Modes Of Two Epitopes In Gab2 That Interact With The Sh3C Domain Of Grb2.
Structure V. 17 809 2009
PubMed-ID: 19523899  |  Reference-DOI: 10.1016/J.STR.2009.03.017

(-) Compounds

Molecule 1 - GRB2-RELATED ADAPTOR PROTEIN 2
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentSH3 2, RESIDUES 265-322
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymMONA SH3C, GADS PROTEIN, GROWTH FACTOR RECEPTOR BINDING PROTEIN, GRB-2-LIKE PROTEIN, GRB2L, HEMATOPOIETIC CELL-ASSOCIATED ADAPTOR PROTEIN GRPL, GRB-2-RELATED MONOCYTIC ADAPTER PROTEIN, MONOCYTIC ADAPTER, MONA, ADAPTER PROTEIN GRID
 
Molecule 2 - TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 23
    ChainsC, D
    EC Number3.1.3.48
    FragmentSH3 BINDING REGION, RESIDUES 719-730
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymHD-PTP
    SyntheticYES

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:6 , TRP A:7 , PRO B:1 , LEU B:2 , ARG B:6 , HOH B:2063 , HOH B:2064BINDING SITE FOR RESIDUE PO4 B1063
2AC2SOFTWARELEU A:2 , GLY A:3 , SER A:4 , ARG A:9 , ARG B:9BINDING SITE FOR RESIDUE PO4 A1062

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2W10)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2W10)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2W10)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.GRAP2_MOUSE1-56
263-322
 
  2-
A:5-61
B:5-62
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.GRAP2_MOUSE1-56
263-322
 
  1-
A:5-61
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.GRAP2_MOUSE1-56
263-322
 
  1-
-
B:5-62

(-) Exons   (0, 0)

(no "Exon" information available for 2W10)

(-) 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 GRAP2_MOUSE | O89100 from UniProtKB/Swiss-Prot  Length:322

    Alignment length:82
                                   249       259       269       279       289       299       309       319  
          GRAP2_MOUSE   240 LGSEVNATLMHRRHTDPVQLQAAGRVRWARALYDFEALEEDELGFRSGEVVEVLDSSNPSWWTGRLHNKLGLFPANYVAPMM 321
               SCOP domains d2w                      10a_ A: automated matches                                 SCOP domains
               CATH domains 2w1                      0A00 A:2-61 SH3 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: A:5-61 UniProt: 263-322                           PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 2w10 A   2 LGS----------------------VRWARALYDFEALEEDELGFRSGEVVEVLDSSNPSWWTGRLHNKLGLFPANYVAPMM  61
                              |      -         -     |   9        19        29        39        49        59  
                              4                      5                                                        

Chain B from PDB  Type:PROTEIN  Length:62
 aligned with GRAP2_MOUSE | O89100 from UniProtKB/Swiss-Prot  Length:322

    Alignment length:133
                                   199       209       219       229       239       249       259       269       279       289       299       309       319   
          GRAP2_MOUSE   190 PLGPQQFHPHQQPSPQFTPGPQPPQQQRYLQHFHQDRRGGSLDINDGHCGLGSEVNATLMHRRHTDPVQLQAAGRVRWARALYDFEALEEDELGFRSGEVVEVLDSSNPSWWTGRLHNKLGLFPANYVAPMMR 322
               SCOP domains d2w                                                                       10b_ B: automated matches                                   SCOP domains
               CATH domains 2w1                                                                       0B00 B:1-62 SH3 Domains                                     CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------SH3_1-2w10B01 B:9-54                          -------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------SH3_1-2w10B02 B:9-54                          -------- Pfam domains (2)
         Sec.struct. author ...-----------------------------------------------------------------------...eeee..................eeeeee.....eeeeee..eeeeee...eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------SH3  PDB: B:5-62 UniProt: 263-322                            PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w10 B   1 PLG-----------------------------------------------------------------------SVRWARALYDFEALEEDELGFRSGEVVEVLDSSNPSWWTGRLHNKLGLFPANYVAPMMR  62
                              |      -         -         -         -         -         -         -    |    9        19        29        39        49        59   
                              3                                                                       4                                                          

Chain C from PDB  Type:PROTEIN  Length:10
 aligned with PTN23_MOUSE | Q6PB44 from UniProtKB/Swiss-Prot  Length:1692

    Alignment length:10
                                   728
          PTN23_MOUSE   719 PPPRPTAPKP 728
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 2w10 C   3 PPPRPTAPKP  12
                                    12

Chain D from PDB  Type:PROTEIN  Length:12
 aligned with PTN23_MOUSE | Q6PB44 from UniProtKB/Swiss-Prot  Length:1692

    Alignment length:12
                                   728  
          PTN23_MOUSE   719 PPPRPTAPKPLL 730
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author ............ Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 2w10 D   3 PPPRPTAPKPLL  14
                                    12  

   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  (1, 2)

Asymmetric Unit
(-)
Clan: SH3 (175)

(-) Gene Ontology  (30, 34)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (GRAP2_MOUSE | O89100)
molecular function
    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).
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Chain C,D   (PTN23_MOUSE | Q6PB44)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016791    phosphatase activity    Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
    GO:0004721    phosphoprotein phosphatase activity    Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity.
    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.
    GO:0004725    protein tyrosine phosphatase activity    Catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
biological process
    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: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:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0010633    negative regulation of epithelial cell migration    Any process that stops, prevents, or reduces the frequency, rate or extent of epithelial cell migration.
    GO:0035335    peptidyl-tyrosine dephosphorylation    The removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine.
    GO:1903393    positive regulation of adherens junction organization    Any process that activates or increases the frequency, rate or extent of adherens junction organization.
    GO:2000643    positive regulation of early endosome to late endosome transport    Any process that activates or increases the frequency, rate or extent of early endosome to late endosome transport.
    GO:1903387    positive regulation of homophilic cell adhesion    Any process that activates or increases the frequency, rate or extent of homophilic cell adhesion.
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0030334    regulation of cell migration    Any process that modulates the frequency, rate or extent of cell migration.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
    GO:0043162    ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway    The chemical reactions and pathways resulting in the breakdown of a protein or peptide covalently tagged with ubiquitin, via the multivesicular body (MVB) sorting pathway; ubiquitin-tagged proteins are sorted into MVBs, and delivered to a lysosome/vacuole for degradation.
cellular component
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0036064    ciliary basal body    A membrane-tethered, short cylindrical array of microtubules and associated proteins found at the base of a eukaryotic cilium (also called flagellum) that is similar in structure to a centriole and derives from it. The cilium basal body is the site of assembly and remodelling of the cilium and serves as a nucleation site for axoneme growth. As well as anchoring the cilium, it is thought to provide a selective gateway regulating the entry of ciliary proteins and vesicles by intraflagellar transport.
    GO:0005929    cilium    A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    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:0005769    early endosome    A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    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:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GRAP2_MOUSE | O891001h3h 1oeb 1r1p 1r1q 1r1s 1uti 2d0n

(-) Related Entries Specified in the PDB File

1h3h STRUCTURAL BASIS FOR SPECIFIC RECOGNITION OF AN RXXK-CONTAINING SLP-76 PEPTIDE BY THE GADS C-TERMINAL SH3 DOMAIN
1oeb MONA/GADS SH3C DOMAIN
1r1p STRUCTURAL BASIS FOR DIFFERENTIAL RECOGNITION OF TYROSINEPHOSPHORYLATED SITES IN THE LINKER FOR ACTIVATION OF TCELLS (LAT) BY THE ADAPTOR PROTEIN GADS
1r1q STRUCTURAL BASIS FOR DIFFERENTIAL RECOGNITION OF TYROSINEPHOSPHORYLATED SITES IN THE LINKER FOR ACTIVATION OF TCELLS (LAT) BY THE ADAPTOR PROTEIN GADS
1r1s STRUCTURAL BASIS FOR DIFFERENTIAL RECOGNITION OF TYROSINEPHOSPHORYLATED SITES IN THE LINKER FOR ACTIVATION OF TCELLS (LAT) BY THE ADAPTOR PROTEIN GADS
1uti MONA/GADS SH3C IN COMPLEX WITH HPK DERIVED PEPTIDE
2d0n CRYSTAL STRUCTURE OF THE GADS-CSH3 DOMAIN IN COMPLEX WITHSLP-76 MOTIF PEPTIDE REVEALS A NOVEL DIMERIZATION MODEWITHIN THE SH3 PROTEIN DOMAINS