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(-) Description

Title :  SOLUTION STRUCTURE OF DOMAIN B FROM HUMAN CIN85 PROTEIN
 
Authors :  A. Ababou, M. Pfuhl, I. Dikic, J. E. Ladbury
Date :  30 Nov 06  (Deposition) - 13 Nov 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (27x)
Keywords :  Sh3, Cin85, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Ababou, M. Pfuhl, I. Dikic, J. E. Ladbury
Investigation Of Domain B From Human Cin85 Protein: Structure, Dynamics And Proline-Rich Motif Binding
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SH3-DOMAIN KINASE-BINDING PROTEIN 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET21B
    Expression System StrainBL21*
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentCIN85_B
    GeneSH3KBP1, CIN85
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSH3-DOMAIN B, CBL-INTERACTING PROTEIN OF 85 KDA, HUMAN SRC-FAMILY KINASE-BINDING PROTEIN 1, HSB-1, CD2- BINDING PROTEIN 3, CD2BP3

 Structural Features

(-) Chains, Units

  
NMR Structure (27x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2O2O)

(-) Sites  (0, 0)

(no "Site" information available for 2O2O)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2O2O)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2O2O)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2O2O)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.SH3K1_HUMAN1-58
98-157
267-328
  1-
A:98-157
-

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003978211aENSE00002155133X:19905719-19905425295SH3K1_HUMAN1-220--
1.2ENST000003978212ENSE00001789519X:19854400-19854243158SH3K1_HUMAN2-54530--
1.5aENST000003978215aENSE00001709790X:19764559-19764436124SH3K1_HUMAN55-96421A:92-965
1.8ENST000003978218ENSE00001200119X:19725102-19724999104SH3K1_HUMAN96-130351A:96-13035
1.9aENST000003978219aENSE00001200111X:19713859-19713730130SH3K1_HUMAN131-174441A:131-16636
1.12bENST0000039782112bENSE00002170582X:19702146-19701941206SH3K1_HUMAN174-242690--
1.15bENST0000039782115bENSE00001752859X:19663593-1966351876SH3K1_HUMAN243-268260--
1.16ENST0000039782116ENSE00001789134X:19650076-1964998295SH3K1_HUMAN268-299320--
1.17ENST0000039782117ENSE00001667936X:19626163-19626056108SH3K1_HUMAN300-335360--
1.19ENST0000039782119ENSE00001798573X:19613118-1961306752SH3K1_HUMAN336-353180--
1.20bENST0000039782120bENSE00001780198X:19610265-1961018581SH3K1_HUMAN353-380280--
1.21bENST0000039782121bENSE00001781910X:19606920-19606761160SH3K1_HUMAN380-433540--
1.22ENST0000039782122ENSE00001696322X:19587306-1958722186SH3K1_HUMAN433-462300--
1.23ENST0000039782123ENSE00001670343X:19568201-19568092110SH3K1_HUMAN462-498370--
1.24ENST0000039782124ENSE00001757635X:19564168-19564040129SH3K1_HUMAN499-541430--
1.25ENST0000039782125ENSE00001659172X:19560311-19560043269SH3K1_HUMAN542-631900--
1.26ENST0000039782126ENSE00001632685X:19555898-1955583564SH3K1_HUMAN631-652220--
1.27eENST0000039782127eENSE00001938509X:19554576-195520932484SH3K1_HUMAN653-665130--

(-) Sequences/Alignments

NMR Structure
   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:75
 aligned with SH3K1_HUMAN | Q96B97 from UniProtKB/Swiss-Prot  Length:665

    Alignment length:75
                                   101       111       121       131       141       151       161     
          SH3K1_HUMAN    92 TNKRGERRRRRCQVAFSYLPQNDDELELKVGDIIEVVGEVEEGWWEGVLNGKTGMFPSNFIKELSGESDELGISQ 166
               SCOP domains --------------------------------------------------------------------------- SCOP domains
               CATH domains 2o2oA00 A:92-166 SH3 Domains                                                CATH domains
               Pfam domains ----------SH3_2-2o2oA01 A:102-155                               ----------- Pfam domains
         Sec.struct. author ..........eeee..................eee..hhhhh.....ee..ee.......ee............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------SH3  PDB: A:98-157 UniProt: 98-157                          --------- PROSITE
           Transcript 1 (1) 1.5a ----------------------------------Exon 1.9a  PDB: A:131-166            Transcript 1 (1)
           Transcript 1 (2) ----Exon 1.8  PDB: A:96-130            ------------------------------------ Transcript 1 (2)
                 2o2o A  92 TNKRGERRRRRCQVAFSYLPQNDDELELKVGDIIEVVGEVEEGWWEGVLNGKTGMFPSNFIKELSGESDELGISQ 166
                                   101       111       121       131       141       151       161     

   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 2O2O)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: SH3 (175)

(-) Gene Ontology  (22, 22)

NMR Structure(hide GO term definitions)
Chain A   (SH3K1_HUMAN | Q96B97)
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: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:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    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:0007267    cell-cell signaling    Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
    GO:0007010    cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures.
    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:0042059    negative regulation of epidermal growth factor receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of epidermal growth factor receptor signaling pathway activity.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
cellular component
    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: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:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0030659    cytoplasmic vesicle membrane    The lipid bilayer surrounding a cytoplasmic vesicle.
    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: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: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:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    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:0045202    synapse    The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.

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 Related Entries

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

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        SH3K1_HUMAN | Q96B972bz8 2k6d 2k9g 2n64 2ydl 5abs

(-) Related Entries Specified in the PDB File

6855