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(-) Description

Title :  HIGH RESOLUTION CRYSTAL STRUCTURE OF HUMAN RAB9 GTPASE: A NOVEL ANTIVIRAL DRUG TARGET
 
Authors :  L. Chen, E. Digiammarino, X. E. Zhou, Y. Wang, D. Toh, T. W. Hodge, E. J. Meehan
Date :  16 Jul 04  (Deposition) - 14 Sep 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.25
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Gtpase, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Chen, E. Digiammarino, X. E. Zhou, Y. Wang, D. Toh, T. W. Hodge, E. J. Meehan
High Resolution Crystal Structure Of Human Rab9 Gtpase: A Novel Antiviral Drug Target
J. Biol. Chem. V. 279 40204 2004
PubMed-ID: 15263003  |  Reference-DOI: 10.1074/JBC.M407114200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RAS-RELATED PROTEIN RAB-9A
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28-RAB9(1-177)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL TRUNCATED
    Gene: RAB9
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: RAB-9, RAB9

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:17 , VAL A:18 , GLY A:19 , LYS A:20 , SER A:21 , SER A:22 , PHE A:32 , THR A:34 , ASN A:124 , LYS A:125 , ASP A:127 , SER A:154 , ALA A:155 , LYS A:156 , HOH A:1004 , HOH A:1017 , HOH A:1029 , HOH A:1031 , HOH A:1042 , HOH A:1081 , HOH A:1094 , HOH A:1146 , HOH A:1239 , ARG B:78 , ASP B:110 , HOH B:1106BINDING SITE FOR RESIDUE GDP A 1001
2AC2SOFTWAREGLY B:17 , VAL B:18 , GLY B:19 , LYS B:20 , SER B:21 , SER B:22 , PHE B:32 , THR B:34 , ASN B:124 , LYS B:125 , ASP B:127 , ILE B:128 , SER B:154 , ALA B:155 , LYS B:156 , HOH B:1025 , HOH B:1048 , HOH B:1084 , HOH B:1137 , HOH B:1138 , HOH B:1161 , HOH B:1226BINDING SITE FOR RESIDUE GDP B 1002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WMS)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ser B:5 -Ser B:6

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WMS)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RABPS51419 small GTPase Rab1 family profile.RAB9A_HUMAN3-201  1A:3-175
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RABPS51419 small GTPase Rab1 family profile.RAB9A_HUMAN3-201  1A:3-175
Biological Unit 2 (, 0)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RABPS51419 small GTPase Rab1 family profile.RAB9A_HUMAN3-201  0-

(-) Exons   (0, 0)

(no "Exon" information available for 1WMS)

(-) 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:170
 aligned with RAB9A_HUMAN | P51151 from UniProtKB/Swiss-Prot  Length:201

    Alignment length:174
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171    
          RAB9A_HUMAN     2 AGKSSLFKVILLGDGGVGKSSLMNRYVTNKFDTQLFHTIGVEFLNKDLEVDGHFVTMQIWDTAGQERFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFIYYADVKEPESFPFVILGNKIDISERQVSTEEAQAWCRDNGDYPYFETSAKDATNVAAAFEEAVRRVLAT 175
               SCOP domains d1wmsa_ A: Rab9a                                                                                                                                                               SCOP domains
               CATH domains 1wmsA00 A:2-175 P-loop containing     nucleotide triphosphate hydrolases                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeee.....hhhhhhhhhhhh....----...eeeeeeeeee..eeeeeeeee...hhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhhh........eeeeee.........hhhhhhhhhhhh....eee.......hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -RAB  PDB: A:3-175 UniProt: 3-201                                                                                                                                              PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1wms A   2 AGKSSLFKVILLGDGGVGKSSLMNRYVTNKFDT----TIGVEFLNKDLEVDGHFVTMQIWDTAGQERFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFIYYADVKEPESFPFVILGNKIDISERQVSTEEAQAWCRDNGDYPYFETSAKDATNVAAAFEEAVRRVLAT 175
                                    11        21        31  |    |41        51        61        71        81        91       101       111       121       131       141       151       161       171    
                                                           34   39                                                                                                                                        

Chain B from PDB  Type:PROTEIN  Length:163
 aligned with RAB9A_HUMAN | P51151 from UniProtKB/Swiss-Prot  Length:201

    Alignment length:171
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174 
          RAB9A_HUMAN     5 SSLFKVILLGDGGVGKSSLMNRYVTNKFDTQLFHTIGVEFLNKDLEVDGHFVTMQIWDTAGQERFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFIYYADVKEPESFPFVILGNKIDISERQVSTEEAQAWCRDNGDYPYFETSAKDATNVAAAFEEAVRRVLAT 175
               SCOP domains d1wmsb_ B: Rab9a                                                                                                                                                            SCOP domains
               CATH domains 1wmsB00 B:5-175 P-loop contain    ing nucleotide triphosphate hydrolases                                                                                                    CATH domains
           Pfam domains (1) ----Ras-1wmsB01 B:9-174                                                                                                                                                   - Pfam domains (1)
           Pfam domains (2) ----Ras-1wmsB02 B:9-174                                                                                                                                                   - Pfam domains (2)
         Sec.struct. author ..eeeeeee.....hhhhhhhhhhhh....----...eeeeeeeeee..eeeeeeeee...hhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh.----....eeeeee.........hhhhhhhhhhhh....eee.......hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE RAB  PDB: - UniProt: 3-201                                                                                                                                                  PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wms B   5 SSLFKVILLGDGGVGKSSLMNRYVTNKFDT----TIGVEFLNKDLEVDGHFVTMQIWDTAGQERFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFIYYAD----ESFPFVILGNKIDISERQVSTEEAQAWCRDNGDYPYFETSAKDATNVAAAFEEAVRRVLAT 175
                                    14        24        34    |   44        54        64        74        84        94       104     |   -|      124       134       144       154       164       174 
                                                        34   39                                                                    110  115                                                            

   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: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Family: Ras (176)
1aRas-1wmsB01B:9-174
1bRas-1wmsB02B:9-174

(-) Gene Ontology  (28, 28)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (RAB9A_HUMAN | P51151)
molecular function
    GO:0019003    GDP binding    Interacting selectively and non-covalently with GDP, guanosine 5'-diphosphate.
    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: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:0052405    negative regulation by host of symbiont molecular function    Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of the functional activity of symbiont proteins. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction.
    GO:0045921    positive regulation of exocytosis    Any process that activates or increases the frequency, rate or extent of exocytosis.
    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:0032880    regulation of protein localization    Any process that modulates the frequency, rate or extent of any process in which a protein is transported to, or maintained in, a specific location.
    GO:0042147    retrograde transport, endosome to Golgi    The directed movement of membrane-bounded vesicles from endosomes back to the trans-Golgi network where they are recycled for further rounds of transport.
    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: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:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    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:0005783    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).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    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:0005770    late endosome    A prelysosomal endocytic organelle differentiated from early endosomes by lower lumenal pH and different protein composition. Late endosomes are more spherical than early endosomes and are mostly juxtanuclear, being concentrated near the microtubule organizing center.
    GO:0005764    lysosome    A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0045335    phagocytic vesicle    A membrane-bounded intracellular vesicle that arises from the ingestion of particulate material by phagocytosis.
    GO:0030670    phagocytic vesicle membrane    The lipid bilayer surrounding a phagocytic vesicle.
    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:0032588    trans-Golgi network membrane    The lipid bilayer surrounding any of the compartments that make up the trans-Golgi network.
    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.

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