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(-) Description

Authors :  B. Hong, J. Wang, L. Shen, W. Tempel, R. Landry, C. H. Arrowsmith, A. M. Edwards, M. Sundstrom, J. Weigelt, A. Bochkarev, H. Park, Structural Genomics Consortium (Sgc)
Date :  21 Mar 06  (Deposition) - 02 May 06  (Release) - 24 Feb 09  (Revision)
Resolution :  1.53
Chains :  Asym./Biol. Unit :  A
Keywords :  G-Protein, Rab, Structural Genomics, Structural Genomics Consortium, Sgc, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  B. Hong, J. Wang, L. Shen, W. Tempel, R. Landry, C. H. Arrowsmith, A. M. Edwards, M. Sundstrom, J. Weigelt, A. Bochkarev, H. Park
Crystal Structure Of Human Rab3D In Complex With Gdp
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

    Expression SystemESCHERICHIA COLI
    Expression System PlasmidP28A-LIC
    Expression System StrainBL21-CODONPLUS(DE-3)-RIL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 20-189
    GeneRAB3D, GOV, RAB16
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
1AC1SOFTWARETHR A:36 , GDP A:501 , HOH A:1017 , HOH A:1030 , HOH A:1054 , HOH A:1056BINDING SITE FOR RESIDUE MG A 201
4AC4SOFTWARESER A:32 , VAL A:33 , GLY A:34 , LYS A:35 , THR A:36 , SER A:37 , PHE A:47 , ASN A:135 , LYS A:136 , ASP A:138 , LEU A:139 , GLU A:148 , SER A:165 , ALA A:166 , LYS A:167 , MG A:201 , HOH A:1005 , HOH A:1007 , HOH A:1012 , HOH A:1017 , HOH A:1035 , HOH A:1041 , HOH A:1047 , HOH A:1054 , HOH A:1055 , HOH A:1056 , HOH A:1065BINDING SITE FOR RESIDUE GDP A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2GF9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2GF9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
1RABPS51419 small GTPase Rab1 family profile.RAB3D_HUMAN18-219  1A:20-189

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2ENST000002221202ENSE00001061192chr19:11448136-11447848289RAB3D_HUMAN1-76761A:14-76 (gaps)76

(-) 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:176
 aligned with RAB3D_HUMAN | O95716 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:189
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180         
               SCOP domains d2gf9a             _ A: automated matches                                                                                                                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......-------------.eeeeeeee.....hhhhhhhhhhhh............eeeeeeeee..eeeeeeeee.........hhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhh..hhhhhhhhhhhhh.eeee.......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------I----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------RAB  PDB: A:20-189 UniProt: 18-219                                                                                                                                           PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:14-76 (gaps) UniProt: 1-76                                 Exon 1.3  PDB: A:77-116 UniProt: 77-116 -----------------------------------------Exon 1.5  PDB: A:158-189         Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------------------Exon 1.4  PDB: A:116-158 UniProt: 116-158  ------------------------------- Transcript 1 (2)
                                 |   -        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180         
                                19            20                                                                                                                                                                         

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2GF9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GF9)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RAB3D_HUMAN | O95716)
molecular function
    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:0051020    GTPase binding    Interacting selectively and non-covalently with a GTPase, any enzyme that catalyzes the hydrolysis of GTP.
    GO:0031489    myosin V binding    Interacting selectively and non-covalently with a class V myosin; myosin V is a dimeric molecule involved in intracellular transport.
    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.
biological process
    GO:0045453    bone resorption    The process in which specialized cells known as osteoclasts degrade the organic and inorganic portions of bone, and endocytose and transport the degradation products.
    GO:0006887    exocytosis    A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell.
    GO:0018125    peptidyl-cysteine methylation    The methylation of peptidyl-cysteine to form peptidyl-S-methyl-L-cysteine.
    GO:1903307    positive regulation of regulated secretory pathway    Any process that activates or increases the frequency, rate or extent of regulated secretory pathway.
    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:0017157    regulation of exocytosis    Any process that modulates the frequency, rate or extent of exocytosis.
    GO:0007264    small GTPase mediated signal transduction    Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals.
    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.
cellular component
    GO:0005881    cytoplasmic microtubule    Any microtubule in the cytoplasm of a cell.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    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:0099503    secretory vesicle    A cytoplasmic, membrane bound vesicle that is capable of fusing to the plasma membrane to release its contents into the extracellular space.
    GO:0030133    transport vesicle    Any of the vesicles of the constitutive secretory pathway, which carry cargo from the endoplasmic reticulum to the Golgi, between Golgi cisternae, from the Golgi to the ER (retrograde transport) or to destinations within or outside the cell.
    GO:0042588    zymogen granule    A membrane-bounded, cytoplasmic secretory granule found in enzyme-secreting cells and visible by light microscopy. Contain zymogen, an inactive enzyme precursor, often of a digestive enzyme.


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