An Information Portal to 109093 Biological Macromolecular Structures

Biology and Chemistry Report
  •   Structure Details   Hide

    Structure Keywords

    Text GTPase-GDP-metal-GEF complex, vps9 domain, Ras super family, guanine nucleotide exchange factor, small GTPase, GDP/GTP binding, divalent metal binding, geranylgeranylation, TRANSPORT PROTEIN

    Polymeric Molecules

    Chain A
    Description Vacuolar protein sorting-associated protein 9A 
    Fragment VPS9 domain, UNP residues 1-265 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 30168.5 
    Source Method genetically manipulated  
    Entity Name VPS9a, AtVSP9a 
    Chain B
    Description Ras-related protein RABF2b 
    Fragment small GTPase, UNP residues 1-179 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 19887.6 
    Source Method genetically manipulated  
    Entity Name ARA7, AtRABF2b, Ras-related protein Ara-7, Ras-related protein Rab5B, AtRab5B 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    CA  CALCIUM ION  Ca   40.08  View 
    GDP  GUANOSINE-5'-DIPHOSPHATE  C10 H15 N5 O11 P2   443.20  View 
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A VPS9A_ARATH Q9LT31     
    B RAF2B_ARATH Q9SN68     

    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain B
    GO ID   Ontology GO Term Definition
    6886   Intracellular Protein Transport  The Directed Movement of Proteins in a Cell Including the Movement of Proteins Between Specific Compartments or Structures Within a Cell Such As Organelles of a Eukaryotic Cell. 
    6897   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. 
    6913   Nucleocytoplasmic Transport  The Directed Movement of Molecules Between the Nucleus and the Cytoplasm. 
    7165   Signal Transduction  The Cellular Process in Which a Signal Is Conveyed to Trigger a Change in the Activity or State of a Cell. Signal Transduction Begins with Reception of a Signal (e.g. a Ligand Binding to a Receptor or Receptor Activation by a Stimulus Such As Light) or For Signal Transduction in the Absence of Ligand Signal Withdrawal or the Activity of a Constitutively Active Receptor. Signal Transduction Ends with Regulation of a Downstream Cellular Process E.g. Regulation of Transcription or Regulation of a Metabolic Process. Signal Transduction Covers Signaling From Receptors Located On the Surface of the Cell and Signaling Via Molecules Located Within the Cell. For Signaling Between Cells Signal Transduction Is Restricted to Events At and Within the Receiving Cell. 
    7264   Small Gtpase Mediated Signal Transduction  Any Series of Molecular Signals in Which a Small Monomeric Gtpase Relays One or More of the Signals. 
    8152   Metabolic Process  The Chemical Reactions and Pathways Including Anabolism and Catabolism by Which Living Organisms Transform Chemical Substances. Metabolic Processes Typically Transform Small Molecules But Also Include Macromolecular Processes Such As DNA Repair and Replication and Protein Synthesis and Degradation. 
    10200   Response to Chitin  A 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 a Chitin Stimulus. 
    15031   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. 
    16192   Vesicle Mediated Transport  A Cellular Transport Process in Which Transported Substances Are Moved in Membrane Bounded Vesicles; Transported Substances Are Enclosed in the Vesicle Lumen or Located in the Vesicle Membrane. the Process Begins with a Step That Directs a Substance to the Forming Vesicle and Includes Vesicle Budding and Coating. Vesicles Are Then Targeted to and Fuse with an Acceptor Membrane. 
    32482   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. 
    48193   Golgi Vesicle Transport  The Directed Movement of Substances Into Out of or Within the Golgi Apparatus Mediated by Vesicles. 
    61025   Membrane Fusion  The Membrane Organization Process That Joins Two Lipid Bilayers to Form a Single Membrane. 
    5622   Intracellular  The Living Contents of a Cell; the Matter Contained Within (but Not Including) the Plasma Membrane Usually Taken to Exclude Large Vacuoles and Masses of Secretory or Ingested Material. in Eukaryotes It Includes the Nucleus and Cytoplasm. 
    5768   Endosome  A Membrane Bounded Organelle to Which Materials Ingested by Endocytosis Are Delivered. 
    5769   Early Endosome  A Membrane Bounded Organelle That Receives Incoming Material From Primary Endocytic Vesicles That Have Been Generated by Clathrin Dependent and Clathrin Independent Endocytosis; Vesicles Fuse with the Early Endosome to Deliver Cargo For Sorting Into Recycling or Degradation Pathways. 
    5773   Vacuole  A Closed Structure Found Only in Eukaryotic Cells That Is Completely Surrounded by Unit Membrane and Contains Liquid Material. Cells Contain One or Several Vacuoles That May Have Different Functions From Each Other. Vacuoles Have a Diverse Array of Functions. They Can Act As a Storage Organelle For Nutrients or Waste Products As a Degradative Compartment As a Cost Effective Way of Increasing Cell Size and As a Homeostatic Regulator Controlling Both Turgor Pressure and Ph of the Cytosol. 
    5774   Vacuolar Membrane  The Lipid Bilayer Surrounding the Vacuole and Separating Its Contents From the Cytoplasm of the Cell. 
    5783   Endoplasmic Reticulum  The Irregular Network of Unit Membranes Visible Only by Electron Microscopy That Occurs in the Cytoplasm of Many Eukaryotic Cells. the Membranes Form a Complex Meshwork of Tubular Channels Which Are Often Expanded Into Slitlike Cavities Called Cisternae. the Er Takes Two Forms Rough (or Granular) with Ribosomes Adhering to the Outer Surface and Smooth (with No Ribosomes Attached). 
    5886   Plasma Membrane  The Membrane Surrounding a Cell That Separates the Cell From Its External Environment. It Consists of a Phospholipid Bilayer and Associated Proteins. 
    10008   Endosome Membrane  The Lipid Bilayer Surrounding an Endosome. 
    16020   Membrane  A Lipid Bilayer Along with All the Proteins and Protein Complexes Embedded in It an Attached to It. 
    30139   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. 
    31901   Early Endosome Membrane  The Lipid Bilayer Surrounding an Early Endosome. 
    166   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. 
    3924   Gtpase Activity  Catalysis of the Reaction: GTP + H2o = GDP + Phosphate. 
    5515   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). 
    5525   GTP Binding  Interacting Selectively and Non Covalently with GTP Guanosine Triphosphate. 

  •   Gene Details   Hide

    Genetic Source

    Chain B
    Common Name Mouse Ear Cress
    Scientific Name Arabidopsis thaliana  
    Gene ara-7
    Host Scientific Name Escherichia coli  

    Chain A
    Common Name Mouse Ear Cress
    Scientific Name Arabidopsis thaliana  
    Gene vps9a
    Host Scientific Name Escherichia coli  

    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    3 - 821514     guanine nucleotide exchange factor VPS9a VPS9A    
    4 - 827706     Rab5 GTPase-like protein Ara7 ARA7