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(-) Description

Title :  DYNAMIN (PLECKSTRIN HOMOLOGY DOMAIN) (DYNPH)
 
Authors :  D. E. Timm
Date :  21 Jul 97  (Deposition) - 12 Nov 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (8x)
Keywords :  Motor Protein, Phospholipid Binding, Protein Binding, Signal Transduction (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Timm, K. Salim, I. Gout, L. Guruprasad, M. Waterfield, T. Blundell
Crystal Structure Of The Pleckstrin Homology Domain From Dynamin.
Nat. Struct. Biol. V. 1 782 1994
PubMed-ID: 7634088  |  Reference-DOI: 10.1038/NSB1194-782
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DYNAMIN
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-2T
    Expression System StrainXL1 BLUE
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentPLECKSTRIN HOMOLOGY (PH) DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsEXPRESSED AS GST-FUSION PROTEIN, CLEAVED WITH THROMBIN
    SynonymPH DOMAIN, DYNPH

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (8x)AB

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2DYN)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PH_DOMAINPS50003 PH domain profile.DYN1_HUMAN519-625
 
  2A:11-117
B:11-117
Biological Unit 1 (1, 16)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PH_DOMAINPS50003 PH domain profile.DYN1_HUMAN519-625
 
  16A:11-117
B:11-117

(-) Exons   (4, 8)

Asymmetric Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003729231aENSE00001918226chr9:130965658-130965910253DYN1_HUMAN1-54540--
1.2aENST000003729232aENSE00001674469chr9:130980510-13098058374DYN1_HUMAN54-79260--
1.3ENST000003729233ENSE00001611689chr9:130980861-130981010150DYN1_HUMAN79-129510--
1.4ENST000003729234ENSE00001625483chr9:130981328-130981531204DYN1_HUMAN129-197690--
1.5ENST000003729235ENSE00001739703chr9:130982267-13098236599DYN1_HUMAN197-230340--
1.6ENST000003729236ENSE00001665870chr9:130982460-130982620161DYN1_HUMAN230-283540--
1.7ENST000003729237ENSE00001617368chr9:130984476-130984618143DYN1_HUMAN284-331480--
1.8aENST000003729238aENSE00001622069chr9:130984740-130984875136DYN1_HUMAN331-376460--
1.9aENST000003729239aENSE00001756702chr9:130985072-13098513968DYN1_HUMAN377-399230--
1.10ENST0000037292310ENSE00001586124chr9:130986530-130986668139DYN1_HUMAN399-445470--
1.13bENST0000037292313bENSE00001582932chr9:130996300-13099638687DYN1_HUMAN446-474290--
1.14ENST0000037292314ENSE00001585744chr9:131001724-13100179471DYN1_HUMAN475-498240--
1.15aENST0000037292315aENSE00001582834chr9:131002007-13100205852DYN1_HUMAN498-515180--
1.16ENST0000037292316ENSE00001746307chr9:131002264-13100227512DYN1_HUMAN516-51942A:10-11
B:10-11
2
2
1.18bENST0000037292318bENSE00001708770chr9:131004511-131004624114DYN1_HUMAN520-557382A:12-49
B:12-49
38
38
1.19bENST0000037292319bENSE00001677536chr9:131008673-131008782110DYN1_HUMAN558-594372A:50-86
B:50-86
37
37
1.21bENST0000037292321bENSE00002194146chr9:131009654-131009765112DYN1_HUMAN594-631382A:86-120
B:86-120
35
35
1.22aENST0000037292322aENSE00001686999chr9:131010203-13101021412DYN1_HUMAN632-63540--
1.22cENST0000037292322cENSE00001607425chr9:131010862-131011032171DYN1_HUMAN636-692570--
1.23ENST0000037292323ENSE00001686168chr9:131012394-131012635242DYN1_HUMAN693-773810--
1.24aENST0000037292324aENSE00001728908chr9:131013004-131013219216DYN1_HUMAN773-845730--
1.27cENST0000037292327cENSE00001676343chr9:131016933-131017527595DYN1_HUMAN845-864200--

(-) 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:111
 aligned with DYN1_HUMAN | Q05193 from UniProtKB/Swiss-Prot  Length:864

    Alignment length:111
                                   527       537       547       557       567       577       587       597       607       617       627 
           DYN1_HUMAN   518 ILVIRKGWLTINNIGIMKGGSKEYWFVLTAENLSWYKDDEEKEKKYMLSVDNLKLRDVEKGFMSSKHIFALFNTEQRNVYKDYRQLELACETQEEVDSWKASFLRAGVYPE 628
               SCOP domains d2dyna_ A: Dynamin                                                                                              SCOP domains
               CATH domains 2dynA00 A:10-120 Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee..........eeeeeeee..eeeee.......eeeeee...eeeeee........eeeeeee............eeeee..hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -PH_DOMAIN  PDB: A:11-117 UniProt: 519-625                                                                  --- PROSITE
           Transcript 1 (1) 1.Exon 1.18b  PDB: A:12-49              Exon 1.19b  PDB: A:50-86             ---------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------Exon 1.21b  PDB: A:86-120           Transcript 1 (2)
                 2dyn A  10 ILVIRKGWLTINNIGIMKGGSKEYWFVLTAENLSWYKDDEEKEKKYMLSVDNLKLRDVEKGFMSSKHIFALFNTEQRNVYKDYRQLELACETQEEVDSWKASFLRAGVYPE 120
                                    19        29        39        49        59        69        79        89        99       109       119 

Chain B from PDB  Type:PROTEIN  Length:111
 aligned with DYN1_HUMAN | Q05193 from UniProtKB/Swiss-Prot  Length:864

    Alignment length:111
                                   527       537       547       557       567       577       587       597       607       617       627 
           DYN1_HUMAN   518 ILVIRKGWLTINNIGIMKGGSKEYWFVLTAENLSWYKDDEEKEKKYMLSVDNLKLRDVEKGFMSSKHIFALFNTEQRNVYKDYRQLELACETQEEVDSWKASFLRAGVYPE 628
               SCOP domains d2dynb_ B: Dynamin                                                                                              SCOP domains
               CATH domains 2dynB00 B:10-120 Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee.....hhh....eeeeeee..eeeee.......eeeeee...eeeeee........eeeeeee...........eeeeee..hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -PH_DOMAIN  PDB: B:11-117 UniProt: 519-625                                                                  --- PROSITE
           Transcript 1 (1) 1.Exon 1.18b  PDB: B:12-49              Exon 1.19b  PDB: B:50-86             ---------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------Exon 1.21b  PDB: B:86-120           Transcript 1 (2)
                 2dyn B  10 ILVIRKGWLTINNIGIMKGGSKEYWFVLTAENLSWYKDDEEKEKKYMLSVDNLKLRDVEKGFMSSKHIFALFNTEQRNVYKDYRQLELACETQEEVDSWKASFLRAGVYPE 120
                                    19        29        39        49        59        69        79        89        99       109       119 

   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  (0, 0)

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

(-) Gene Ontology  (38, 38)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DYN1_HUMAN | Q05193)
molecular function
    GO:0031749    D2 dopamine receptor binding    Interacting selectively and non-covalently with a D2 dopamine receptor.
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0050998    nitric-oxide synthase binding    Interacting selectively and non-covalently with the enzyme nitric-oxide synthase.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
    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:0002031    G-protein coupled receptor internalization    The process that results in the uptake of a G-protein coupled receptor into an endocytic vesicle.
    GO:0008344    adult locomotory behavior    Locomotory behavior in a fully developed and mature organism.
    GO:0072583    clathrin-dependent endocytosis    An endocytosis process that begins when material is taken up into clathrin-coated pits, which then pinch off to form clathrin-coated endocytic vesicles.
    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:0007032    endosome organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of endosomes.
    GO:0048013    ephrin receptor signaling pathway    The series of molecular signals generated as a consequence of an ephrin receptor binding to an ephrin.
    GO:1903423    positive regulation of synaptic vesicle recycling    Any process that activates or increases the frequency, rate or extent of synaptic vesicle recycling.
    GO:0051262    protein tetramerization    The formation of a protein tetramer, a macromolecular structure consisting of four noncovalently associated identical or nonidentical subunits.
    GO:0031623    receptor internalization    A receptor-mediated endocytosis process that results in the movement of receptors from the plasma membrane to the inside of the cell. The process begins when cell surface receptors are monoubiquitinated following ligand-induced activation. Receptors are subsequently taken up into endocytic vesicles from where they are either targeted to the lysosome or vacuole for degradation or recycled back to the plasma membrane.
    GO:0006898    receptor-mediated endocytosis    An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles.
    GO:0007605    sensory perception of sound    The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound.
    GO:0051932    synaptic transmission, GABAergic    The vesicular release of gamma-aminobutyric acid (GABA). from a presynapse, across a chemical synapse, the subsequent activation of GABA receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse.
    GO:1901998    toxin transport    The directed movement of a toxin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    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: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:0030117    membrane coat    Any of several different proteinaceous coats that can associate with membranes. Membrane coats include those formed by clathrin plus an adaptor complex, the COPI and COPII complexes, and possibly others. They are found associated with membranes on many vesicles as well as other membrane features such as pits and perhaps tubules.
    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:0043209    myelin sheath    An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system.
    GO:0001917    photoreceptor inner segment    The inner segment of a vertebrate photoreceptor containing mitochondria, ribosomes and membranes where opsin molecules are assembled and passed to be part of the outer segment discs.
    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: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.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        DYN1_HUMAN | Q051931dyn 2x2e 2x2f 3snh 3zyc 3zys 4uud 4uuk 5d3q

(-) Related Entries Specified in the PDB File

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