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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN RAB25 IN COMPLEX WITH GDP
 
Authors :  H. Zhu, J. Wang, Y. Shen, W. Tempel, R. Landry, C. H. Arrowsmith, A. M. Edwards, M. Sundstrom, J. Weigelt, A. Bochkarev, H. Park, Structural Genomics Consortium (Sgc)
Date :  11 Jan 07  (Deposition) - 23 Jan 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  G-Protein, Rab, Gdp, Structural Genomics, Structural Genomics Consortium, Sgc, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Zhu, J. Wang, Y. Shen, W. Tempel, R. Landry, C. H. Arrowsmith, A. M. Edwards, M. Sundstrom, J. Weigelt, A. Bochkarev, H. Park
Crystal Structure Of Human Rab25 In Complex With Gdp
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RAS-RELATED PROTEIN RAB-25
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidP28A-THROMBIN-LIC
    Expression System StrainBL21-CODONPLUS (DE-3)-RIL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneRAB25, CATX8
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCATX-8

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3UNX1Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (0, 0)

(no "Site" information available for 2OIL)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2OIL)

(-) Exons   (5, 5)

Asymmetric/Biological Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003610841aENSE00001842111chr1:156030951-156031234284RAB25_HUMAN1-15151A:7-159
1.2aENST000003610842aENSE00000855863chr1:156035702-156035897196RAB25_HUMAN15-80661A:15-8066
1.3bENST000003610843bENSE00000788616chr1:156038061-156038254194RAB25_HUMAN80-145661A:80-14566
1.4aENST000003610844aENSE00000788617chr1:156039462-15603954281RAB25_HUMAN145-172281A:145-17228
1.5bENST000003610845bENSE00001862439chr1:156039951-156040295345RAB25_HUMAN172-213421A:172-1809

(-) 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:174
 aligned with RAB25_HUMAN | P57735 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:174
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176    
          RAB25_HUMAN     7 EDYNFVFKVVLIGESGVGKTNLLSRFTRNEFSHDSRTTIGVEFSTRTVMLGTAAVKAQIWDTAGLERYRAITSAYYRGAVGALLVFDLTKHQTYAVVERWLKELYDHAEATIVVMLVGNKSDLSQAREVPTEEARMFAENNGLLFLETSALDSTNVELAFETVLKEIFAKVSKQ 180
               SCOP domains d2oila_ A: automated matches                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -------Ras-2oilA01 A:14-175                                                                                                                                              ----- Pfam domains
         Sec.struct. author ....eeeeeeee.....hhhhhhhhhhhh...........eeeeeeeeee..eeeeeeeeee........hhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhh......eeeeeee.hhhhhhh..hhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.1a----------------------------------------------------------------Exon 1.3b  PDB: A:80-145 UniProt: 80-145                          --------------------------Exon 1.5b Transcript 1 (1)
           Transcript 1 (2) --------Exon 1.2a  PDB: A:15-80 UniProt: 15-80                            ----------------------------------------------------------------Exon 1.4a  PDB: A:145-172   -------- Transcript 1 (2)
                 2oil A   7 EDYNFVFKVVLIGESGVGKTNLLSRFTRNEFSHDSRTTIGVEFSTRTVMLGTAAVKAQIWDTAGLERYRAITSAYYRGAVGALLVFDLTKHQTYAVVERWLKELYDHAEATIVVMLVGNKSDLSQAREVPTEEARMFAENNGLLFLETSALDSTNVELAFETVLKEIFAKVSKQ 180
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176    

   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 2OIL)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Family: Ras (176)

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RAB25_HUMAN | P57735)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    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: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:0003382    epithelial cell morphogenesis    The change in form that occurs when an epithelial cell progresses from its initial formation to its mature state.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0010634    positive regulation of epithelial cell migration    Any process that activates or increases the frequency, rate or extent of epithelial cell migration.
    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:0031268    pseudopodium organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a pseudopodium, a temporary protrusion or retractile process of a cell, associated with cellular movement.
    GO:0060627    regulation of vesicle-mediated transport    Any process that modulates the rate, frequency, or extent of vesicle-mediated transport, the directed movement of substances, either within a vesicle or in the vesicle membrane, into, out of or within a cell.
    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:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0031410    cytoplasmic vesicle    A vesicle found 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: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:0031143    pseudopodium    A temporary protrusion or retractile process of a cell, associated with flowing movements of the protoplasm, and serving for locomotion and feeding.
    GO:0031260    pseudopodium membrane    The portion of the plasma membrane surrounding a pseudopodium.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RAB25_HUMAN | P577353tso

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