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(-) Description

Title :  ATOMIC RESOLUTION CRYSTAL STRUCTURE OF THE 2ND SH3 DOMAIN FROM HUMAN CD2AP (CMS) IN COMPLEX WITH A PROLINE-RICH PEPTIDE FROM HUMAN RIN3
 
Authors :  P. C. Simister, E. Rouka, M. Janning, J. R. C. Muniz, K. H. Kirsch, S. Knap Delft, P. Filippakopoulos, C. H. Arrowsmith, T. Krojer, A. M. Edwards J. Weigelt, C. Bountra, S. M. Feller, Structural Genomics Consorti
Date :  30 Sep 11  (Deposition) - 28 Dec 11  (Release) - 09 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.11
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Structural Genomics Consortium, Sgc, Beta- Barrel, Adaptor Protein, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Rouka, P. C. Simister, M. Janning, J. Kumbrink, T. Konstantinou, J. R. Muniz, D. Joshi, N. O'Reilly, R. Volkmer, B. Ritter, S. Knapp, F. Von Delft, K. H. Kirsch, S. M. Feller
Differential Recognition Preferences Of The Three Src Homology 3 (Sh3) Domains From The Adaptor Cd2-Associated Protein (Cd2Ap) And Direct Association With Ras And Rab Interactor 3 (Rin3).
J. Biol. Chem. V. 290 25275 2015
PubMed-ID: 26296892  |  Reference-DOI: 10.1074/JBC.M115.637207

(-) Compounds

Molecule 1 - CD2-ASSOCIATED PROTEIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 109-168
    GeneCD2AP
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymADAPTER PROTEIN CMS, CAS LIGAND WITH MULTIPLE SH3 DOMAINS
 
Molecule 2 - RAS AND RAB INTERACTOR 3
    ChainsB
    EngineeredYES
    FragmentUNP RESIDUES 452-467
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsSYNTHESISED PEPTIDE
    SynonymRAS INTERACTION/INTERFERENCE PROTEIN 3
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2NH21Mod. Amino AcidAMINO GROUP

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:72 , HOH A:99 , ILE A:137 , VAL A:162BINDING SITE FOR RESIDUE EDO A 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3U23)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3U23)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3U23)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3U23)

(-) Exons   (2, 2)

Asymmetric/Biological Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003593141ENSE00001516297chr6:47445525-47445984460CD2AP_HUMAN1-220--
1.2ENST000003593142ENSE00000755720chr6:47471016-47471176161CD2AP_HUMAN2-55540--
1.3aENST000003593143aENSE00000619362chr6:47501338-47501491154CD2AP_HUMAN56-107520--
1.4aENST000003593144aENSE00001139103chr6:47512342-47512442101CD2AP_HUMAN107-140341A:111-14030
1.5ENST000003593145ENSE00001139093chr6:47522382-47522502121CD2AP_HUMAN141-181411A:141-16626
1.6ENST000003593146ENSE00001139085chr6:47541800-47541987188CD2AP_HUMAN181-243630--
1.7bENST000003593147bENSE00001139077chr6:47544260-4754433879CD2AP_HUMAN244-270270--
1.8ENST000003593148ENSE00002190760chr6:47544745-4754483995CD2AP_HUMAN270-301320--
1.9aENST000003593149aENSE00001139061chr6:47547121-47547225105CD2AP_HUMAN302-336350--
1.10ENST0000035931410ENSE00002145560chr6:47548600-4754863637CD2AP_HUMAN337-349130--
1.11aENST0000035931411aENSE00001139049chr6:47549739-4754980163CD2AP_HUMAN349-370220--
1.12ENST0000035931412ENSE00001139043chr6:47563597-47563762166CD2AP_HUMAN370-425560--
1.13ENST0000035931413ENSE00001139036chr6:47567037-47567179143CD2AP_HUMAN425-473490--
1.14ENST0000035931414ENSE00001139029chr6:47573901-47574013113CD2AP_HUMAN473-510380--
1.15bENST0000035931415bENSE00001139023chr6:47575663-47575764102CD2AP_HUMAN511-544340--
1.16aENST0000035931416aENSE00001139019chr6:47576859-47577040182CD2AP_HUMAN545-605610--
1.17ENST0000035931417ENSE00001176400chr6:47580209-4758027264CD2AP_HUMAN605-626220--
1.18ENST0000035931418ENSE00001454693chr6:47591922-475949993078CD2AP_HUMAN627-639130--

(-) Sequences/Alignments

Asymmetric/Biological 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:56
 aligned with CD2AP_HUMAN | Q9Y5K6 from UniProtKB/Swiss-Prot  Length:639

    Alignment length:56
                                   120       130       140       150       160      
          CD2AP_HUMAN   111 RQCKVLFEYIPQNEDELELKVGDIIDINEEVEEGWWSGTLNNKLGLFPSNFVKELE 166
               SCOP domains -------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..................eeeeeeeee..eeeeee..eeeeee...eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.4a  PDB: A:111-140     Exon 1.5  PDB: A:141-166   Transcript 1
                 3u23 A 111 RQCKVLFEYIPQNEDELELKVGDIIDINEEVEEGWWSGTLNNKLGLFPSNFVKELE 166
                                   120       130       140       150       160      

Chain B from PDB  Type:PROTEIN  Length:14
 aligned with RIN3_HUMAN | Q8TB24 from UniProtKB/Swiss-Prot  Length:985

    Alignment length:14
                                   464    
           RIN3_HUMAN   455 QPPVPPPRKKRISR 468
               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
                 3u23 B 455 QPPVPPPRKKRISx 468
                                   464   |
                                       468-NH2

   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 3U23)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3U23)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3U23)

(-) Gene Ontology  (43, 46)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CD2AP_HUMAN | Q9Y5K6)
molecular function
    GO:0017124    SH3 domain binding    Interacting selectively and non-covalently with a SH3 domain (Src homology 3) of a protein, small protein modules containing approximately 50 amino acid residues found in a great variety of intracellular or membrane-associated proteins.
    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:0008022    protein C-terminus binding    Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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:0032403    protein complex binding    Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0005200    structural constituent of cytoskeleton    The action of a molecule that contributes to the structural integrity of a cytoskeletal structure.
    GO:0005172    vascular endothelial growth factor receptor binding    Interacting selectively and non-covalently with any vascular endothelial growth factor receptor.
biological process
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0016477    cell migration    The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
    GO:0032911    negative regulation of transforming growth factor beta1 production    Any process that stops, prevents, or reduces the frequency, rate, or extent of production of transforming growth factor-beta1.
    GO:1900182    positive regulation of protein localization to nucleus    Any process that activates or increases the frequency, rate or extent of protein localization to nucleus.
    GO:0043161    proteasome-mediated ubiquitin-dependent protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
    GO:0006461    protein complex assembly    The aggregation, arrangement and bonding together of a set of components to form a protein complex.
    GO:2000249    regulation of actin cytoskeleton reorganization    Any process that modulates the frequency, rate or extent of actin cytoskeleton reorganization.
    GO:0048259    regulation of receptor-mediated endocytosis    Any process that modulates the frequency, rate or extent of receptor mediated endocytosis, the uptake of external materials by cells, utilizing receptors to ensure specificity of transport.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0016337    single organismal cell-cell adhesion    The attachment of one cell to another cell via adhesion molecules, where both cells are part of the same organism.
    GO:0006930    substrate-dependent cell migration, cell extension    The formation of a cell surface protrusion, such as a lamellipodium or filopodium, at the leading edge of a migrating cell.
    GO:0016050    vesicle organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vesicle.
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:0031252    cell leading edge    The area of a motile cell closest to the direction of movement.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    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: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:0030139    endocytic vesicle    A membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance. Endocytic vesicles fuse with early endosomes to deliver the cargo for further sorting.
    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:0031941    filamentous actin    A two-stranded helical polymer of the protein actin.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    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.

Chain B   (RIN3_HUMAN | Q8TB24)
molecular function
    GO:0005096    GTPase activator activity    Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
    GO:0017137    Rab GTPase binding    Interacting selectively and non-covalently with Rab protein, any member of the Rab subfamily of the Ras superfamily of monomeric GTPases.
    GO:0017112    Rab guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Rab 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: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:0006897    endocytosis    A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CD2AP_HUMAN | Q9Y5K62fei 2j6f 2j6k 2j6o 2j7i 3aa6 3lk4 4wci 4x1v
        RIN3_HUMAN | Q8TB244wci

(-) Related Entries Specified in the PDB File

2fei 2krn 4wci