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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SH3 DOMAIN FROM RAT AMPHIPHYSIN 2
 
Authors :  D. J. Owen, H. T. Mcmahon, P. R. Evans
Date :  29 Apr 98  (Deposition) - 17 Jun 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Transferase, Sh3 Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. J. Owen, P. Wigge, Y. Vallis, J. D. Moore, P. R. Evans, H. T. Mcmahon
Crystal Structure Of The Amphiphysin-2 Sh3 Domain And Its Role In The Prevention Of Dynamin Ring Formation.
Embo J. V. 17 5273 1998
PubMed-ID: 9736607  |  Reference-DOI: 10.1093/EMBOJ/17.18.5273
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AMPHIPHYSIN 2
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPET15B
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentSH3 DOMAIN
    OrganBRAIN
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1BB9)

(-) Sites  (0, 0)

(no "Site" information available for 1BB9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1BB9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1BB9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1BB9)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.BIN1_RAT515-588  1A:21-94
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.BIN1_RAT515-588  2A:21-94

(-) Exons   (0, 0)

(no "Exon" information available for 1BB9)

(-) 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:83
 aligned with BIN1_RAT | O08839 from UniProtKB/Swiss-Prot  Length:588

    Alignment length:83
                                   515       525       535       545       555       565       575       585   
             BIN1_RAT   506 TTGRLDLPPGFMFKVQAQHDYTATDTDELQLKAGDVVLVIPFQNPEEQDEGWLMGVKESDWNQHKELEKCRGVFPENFTERVQ 588
               SCOP domains d1bb9a_ A: Amphiphysin 2                                                            SCOP domains
               CATH domains 1bb9A00 A:12-94 SH3 Domains                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeee..................eeeee....hhh....eeeeeehhhhh....hhhh.eeeehhheeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------SH3  PDB: A:21-94 UniProt: 515-588                                         PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                 1bb9 A  12 TTGRLDLPPGFMFKVQAQHDYTATDTDELQLKAGDVVLVIPFQNPEEQDEGWLMGVKESDWNQHKELEKCRGVFPENFTERVQ  94
                                    21        31        41        51        61        71        81        91   

   Legend:   → Mismatch (orange background)
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  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, 1)

Asymmetric Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1BB9)

(-) Gene Ontology  (29, 29)

Asymmetric Unit(hide GO term definitions)
Chain A   (BIN1_RAT | O08839)
molecular function
    GO:0051020    GTPase binding    Interacting selectively and non-covalently with a GTPase, any enzyme that catalyzes the hydrolysis of GTP.
    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:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    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:0060988    lipid tube assembly    The aggregation, arrangement and bonding together of a set of macromolecules to form a macromolecular complex that contains a tube of lipid surrounded by a protein coat involved in membrane shaping of vesicle membranes as they fuse or undergo fission.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    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:0048711    positive regulation of astrocyte differentiation    Any process that activates or increases the frequency, rate or extent of astrocyte differentiation.
    GO:0045807    positive regulation of endocytosis    Any process that activates or increases the frequency, rate or extent of endocytosis.
    GO:0071156    regulation of cell cycle arrest    Any process that modulates the rate, frequency, or extent of cell cycle arrest, the process in which the cell cycle is halted during one of the normal phases.
    GO:0030100    regulation of endocytosis    Any process that modulates the frequency, rate or extent of endocytosis.
    GO:0045664    regulation of neuron differentiation    Any process that modulates the frequency, rate or extent of neuron differentiation.
cellular component
    GO:0031674    I band    A region of a sarcomere that appears as a light band on each side of the Z disc, comprising a region of the sarcomere where thin (actin) filaments are not overlapped by thick (myosin) filaments; contains actin, troponin, and tropomyosin; each sarcomere includes half of an I band at each end.
    GO:0030315    T-tubule    Invagination of the plasma membrane of a muscle cell that extends inward from the cell surface around each myofibril. The ends of T-tubules make contact with the sarcoplasmic reticulum membrane.
    GO:0030018    Z disc    Platelike region of a muscle sarcomere to which the plus ends of actin filaments are attached.
    GO:0030424    axon    The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
    GO:0043194    axon initial segment    Portion of the axon proximal to the neuronal cell body, at the level of the axon hillock. The action potentials that propagate along the axon are generated at the level of this initial segment.
    GO:0043679    axon terminus    Terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters. The axon terminus is considered to be the whole region of thickening and the terminal button is a specialized region of it.
    GO:0044300    cerebellar mossy fiber    An axon arising from cerebellar projecting cells in the cochlea, vestibular nuclei, spinal cord, reticular formation, cerebellar nuclei and basilar pontine nuclei. Mossy fibers enter through all three cerebellar peduncles and send collaterals to the deep cerebellar nuclei, then branch in the white matter and terminate in the granule cell layer. Through this branching, a given mossy fiber can innervate several folia. Mossy fibers synapse on granule cells. The synaptic contacts are made at enlargements along the length of the mossy fiber called mossy fiber rosettes. The enlargements of the rosettes give the axons as "mossy" appearance in Golgi stained preparations.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0060987    lipid tube    A macromolecular complex that contains a tube of lipid surrounded by a protein coat.
    GO:0005874    microtubule    Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.
    GO:0033268    node of Ranvier    An axon part that is a gap in the myelin where voltage-gated sodium channels cluster and saltatory conduction is executed.
    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.
    GO:0008021    synaptic vesicle    A secretory organelle, typically 50 nm in diameter, of presynaptic nerve terminals; accumulates in high concentrations of neurotransmitters and secretes these into the synaptic cleft by fusion with the 'active zone' of the presynaptic plasma membrane.
    GO:0043196    varicosity    Non-terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters.

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