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(-) Description

Title :  GPPNHP-BOUND RAB3A AT 2.0 A RESOLUTION
 
Authors :  J. J. Dumas, Z. Zhu, J. L. Connolly, D. G. Lambright
Date :  16 Nov 98  (Deposition) - 16 Apr 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  G Protein, Vesicular Trafficking, Gtp Hydrolysis, Rab Protein, Neurotransmitter Release, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. J. Dumas, Z. Zhu, J. L. Connolly, D. G. Lambright
Structural Basis Of Activation And Gtp Hydrolysis In Rab Proteins.
Structure Fold. Des. V. 7 413 1999
PubMed-ID: 10196122  |  Reference-DOI: 10.1016/S0969-2126(99)80054-9
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (RAB3A)
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPGEX
    Expression System StrainBL21/DE3
    Expression System Taxid469008
    FragmentGTPASE DOMAIN
    OrganBRAIN
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:36 , THR A:54 , GNP A:200 , HOH A:301 , HOH A:318BINDING SITE FOR RESIDUE MG A 201
2AC2SOFTWARESER A:31 , SER A:32 , VAL A:33 , GLY A:34 , LYS A:35 , THR A:36 , SER A:37 , PHE A:47 , THR A:48 , PRO A:49 , ALA A:50 , PHE A:51 , SER A:53 , THR A:54 , GLY A:80 , ASN A:135 , LYS A:136 , ASP A:138 , MET A:139 , SER A:165 , ALA A:166 , LYS A:167 , MG A:201 , HOH A:302 , HOH A:318 , HOH A:566BINDING SITE FOR RESIDUE GNP A 200

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RABPS51419 small GTPase Rab1 family profile.RAB3A_RAT18-220  1A:18-186

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000263911ENSRNOE00000426276chr16:19193874-19193767108RAB3A_RAT-00--
1.2bENSRNOT000000263912bENSRNOE00000188693chr16:19192725-19192498228RAB3A_RAT1-76761A:18-7659
1.5ENSRNOT000000263915ENSRNOE00000291604chr16:19192016-19191898119RAB3A_RAT77-116401A:77-11640
1.6ENSRNOT000000263916ENSRNOE00000188854chr16:19191277-19191153125RAB3A_RAT116-158431A:116-15843
1.8ENSRNOT000000263918ENSRNOE00000238253chr16:19190563-19189768796RAB3A_RAT158-220631A:158-18629

(-) 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:169
 aligned with RAB3A_RAT | P63012 from UniProtKB/Swiss-Prot  Length:220

    Alignment length:169
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177         
            RAB3A_RAT    18 NFDYMFKILIIGNSSVGKTSFLFRYADDSFTPAFVSTVGIDFKVKTIYRNDKRIKLQIWDTAGQERYRTITTAYYRGAMGFILMYDITNEESFNAVQDWSTQIKTYSWDNAQVLLVGNKCDMEDERVVSSERGRQLADHLGFEFFEASAKDNINVKQTFERLVDVICEK 186
               SCOP domains d3raba_ A: Rab3a                                                                                                                                                          SCOP domains
               CATH domains 3rabA00 A:18-186 P-loop containing nucleotide triphosphate hydrolases                                                                                                     CATH domains
               Pfam domains ------Ras-3rabA01 A:24-185                                                                                                                                              - Pfam domains
         Sec.struct. author ...eeeeeeeee.....hhhhhhhhhh............eeeeeeeeee..eeeeeeeeee...hhhhhhhhhh.....eeeeeee...hhhhh.hhhhhhhhhhh.....eeeeeee...........hhhhhhhhhhh..eeee........hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE RAB  PDB: A:18-186 UniProt: 18-220                                                                                                                                        PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: A:18-76 UniProt: 1-76 [INCOMPLETE]         Exon 1.5  PDB: A:77-116 UniProt: 77-116 -----------------------------------------Exon 1.8  PDB: A:158-186      Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------------Exon 1.6  PDB: A:116-158 UniProt: 116-158  ---------------------------- Transcript 1 (2)
                 3rab A  18 NFDYMFKILIIGNSSVGKTSFLFRYADDSFTPAFVSTVGIDFKVKTIYRNDKRIKLQIWDTAGQERYRTITTAYYRGAMGFILMYDITNEESFNAVQDWSTQIKTYSWDNAQVLLVGNKCDMEDERVVSSERGRQLADHLGFEFFEASAKDNINVKQTFERLVDVICEK 186
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177         

   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (43, 43)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RAB3A_RAT | P63012)
molecular function
    GO:0001671    ATPase activator activity    Binds to and increases the ATP hydrolysis activity of an ATPase.
    GO:0051117    ATPase binding    Interacting selectively and non-covalently with an ATPase, any enzyme that catalyzes the hydrolysis of ATP.
    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.
    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).
biological process
    GO:0032482    Rab protein signal transduction    A series of molecular signals within the cell that are mediated by a member of the Rab family of proteins switching to a GTP-bound active state.
    GO:0007409    axonogenesis    De novo generation of a long process of a neuron, that carries efferent (outgoing) action potentials from the cell body towards target cells. Refers to the morphogenesis or creation of shape or form of the developing axon.
    GO:0061670    evoked neurotransmitter secretion    Neurotransmitter secretion that occurs in the presence of the action of a secretagogue or a presynaptic action potential.
    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:0030324    lung development    The process whose specific outcome is the progression of the lung over time, from its formation to the mature structure. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax.
    GO:0048790    maintenance of presynaptic active zone structure    A process which maintains the organization and the arrangement of proteins at the active zone to ensure the fusion and docking of vesicles and the release of neurotransmitters.
    GO:0007005    mitochondrion organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrion; includes mitochondrial morphogenesis and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components.
    GO:0007274    neuromuscular synaptic transmission    The process of synaptic transmission from a neuron to a muscle, across a synapse.
    GO:0032781    positive regulation of ATPase activity    Any process that activates or increases the rate of ATP hydrolysis by an ATPase.
    GO:1903307    positive regulation of regulated secretory pathway    Any process that activates or increases the frequency, rate or extent of regulated secretory pathway.
    GO:0009791    post-embryonic development    The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development.
    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:0048172    regulation of short-term neuronal synaptic plasticity    A process that modulates short-term neuronal synaptic plasticity, the ability of neuronal synapses to change in the short-term as circumstances require. Short-term neuronal synaptic plasticity generally involves increasing or decreasing synaptic sensitivity.
    GO:0031630    regulation of synaptic vesicle fusion to presynaptic active zone membrane    Any process that modulates the frequency, rate or extent of synaptic vesicle fusion to the presynaptic membrane.
    GO:0003016    respiratory system process    A system process carried out by the organs and tissues of the respiratory system. The respiratory system is an organ system responsible for respiratory gaseous exchange.
    GO:0051602    response to electrical stimulus    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an electrical stimulus.
    GO:0050975    sensory perception of touch    The series of events required for an organism to receive a touch stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. The perception of touch in animals is mediated by mechanoreceptors in the skin and mucous membranes and is the sense by which contact with objects gives evidence as to certain of their qualities. Different types of touch can be perceived (for example, light, coarse, pressure and tickling) and the stimulus may be external or internal (e.g. the feeling of a full stomach).
    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:0016079    synaptic vesicle exocytosis    Fusion of intracellular membrane-bounded vesicles with the pre-synaptic membrane of the neuronal cell resulting in release of neurotransmitter into the synaptic cleft.
    GO:0016188    synaptic vesicle maturation    Steps required to form an initiated synaptic vesicle into a fully formed and transmissible synaptic vesicle.
    GO:0036465    synaptic vesicle recycling    The trafficking of synaptic vesicles from the pre-synaptic membrane so the vesicle can dock and prime for another round of exocytosis and neurotransmitter release. Recycling occurs after synaptic vesicle exocytosis, and is necessary to replenish presynaptic vesicle pools, sustain transmitter release and preserve the structural integrity of the presynaptic membrane. Recycling can occur following transient fusion with the presynaptic membrane (kiss and run), or via endocytosis of presynaptic membrane.
    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:0001669    acrosomal vesicle    A structure in the head of a spermatozoon that contains acid hydrolases, and is concerned with the breakdown of the outer membrane of the ovum during fertilization. It lies just beneath the plasma membrane and is derived from the lysosome.
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:1903561    extracellular vesicle    Any vesicle that is part of the extracellular region.
    GO:0043229    intracellular organelle    Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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: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:0043195    terminal bouton    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 bouton is a specialized region of it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RAB3A_RAT | P630121zbd

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3RAB)