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(-) Description

Title :  GPPNHP-BOUND RAB6 GTPASE
 
Authors :  S. Eathiraj, X. Pan, C. Ritacco, D. G. Lambright
Date :  28 Feb 05  (Deposition) - 26 Jul 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.78
Chains :  Asym./Biol. Unit :  A
Keywords :  Rab Gtpase, Rab6, Vesicular Trafficking, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Eathiraj, X. Pan, C. Ritacco, D. G. Lambright
Structural Basis Of Family-Wide Rab Gtpase Recognition By Rabenosyn-5.
Nature V. 436 415 2005
PubMed-ID: 16034420  |  Reference-DOI: 10.1038/NATURE03798
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SMALL GTP BINDING PROTEIN RAB6 ISOFORM
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX4T1
    Expression System Strain: BL21 (DE3) CODON PLUS-RIL CELLS
    Expression System Taxid: 562
    Expression System Vector Type: GST FUSION, PGEX
    Gene: RAB6
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 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:27 , THR A:45 , GNP A:900 , HOH A:933BINDING SITE FOR RESIDUE MG A 901
2AC2SOFTWAREGLN A:22 , SER A:23 , VAL A:24 , GLY A:25 , LYS A:26 , THR A:27 , SER A:28 , PHE A:38 , ASP A:39 , ASN A:40 , TYR A:42 , THR A:45 , GLY A:71 , ASN A:126 , LYS A:127 , ASP A:129 , LEU A:130 , SER A:156 , ALA A:157 , LYS A:158 , MG A:901 , HOH A:933 , HOH A:934 , HOH A:942BINDING SITE FOR RESIDUE GNP A 900

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1YZQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1YZQ)

(-) Exons   (7, 7)

Asymmetric/Biological Unit (7, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003360831bENSE00001358766chr11:73471749-73471611139RAB6A_HUMAN1-24241A:14-2411
1.2ENST000003360832ENSE00001184551chr11:73441868-7344181059RAB6A_HUMAN24-43201A:24-4320
1.3ENST000003360833ENSE00001759909chr11:73431944-7343189154RAB6A_HUMAN44-61181A:44-6118
1.5ENST000003360835ENSE00001184543chr11:73429763-73429658106RAB6A_HUMAN62-97361A:62-9736
1.6ENST000003360836ENSE00001753791chr11:73427407-73427296112RAB6A_HUMAN97-134381A:97-13438
1.7ENST000003360837ENSE00001358756chr11:73418558-7341846594RAB6A_HUMAN134-165321A:134-16532
1.8ENST000003360838ENSE00001358753chr11:73390765-7339069967RAB6A_HUMAN166-188231A:166-17712
1.9aENST000003360839aENSE00001515886chr11:73389007-733869392069RAB6A_HUMAN188-208210--

(-) 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:164
 aligned with RAB6A_HUMAN | P20340 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:164
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173    
          RAB6A_HUMAN    14 FKLVFLGEQSVGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNVNSFQQTTKWIDDVRTERGSDVIIMLVGNKTDLADKRQVSIEEGERKAKELNVMFIETSAKAGYNVKQLFRRVAAALPGM 177
               SCOP domains d1yzqa1 A:14-177 Rab6                                                                                                                                                SCOP domains
               CATH domains 1yzqA00 A:14-177 P-loop containing nucleotide triphosphate hydrolases                                                                                                CATH domains
               Pfam domains -Ras-1yzqA01 A:15-175                                                                                                                                             -- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhh...........eeeeeeeee....eeeeeeeee..hhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhhh...eeeeeee...hhhhh..hhhhhhhhhhhh..eeee.......hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1b  -------------------Exon 1.3          Exon 1.5  PDB: A:62-97              ------------------------------------Exon 1.7  PDB: A:134-165        Exon 1.8     Transcript 1 (1)
           Transcript 1 (2) ----------Exon 1.2            -----------------------------------------------------Exon 1.6  PDB: A:97-134               ------------------------------------------- Transcript 1 (2)
                 1yzq A  14 FKLVFLGEQSVGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTIRLQLWDTAGQERFRSLIPSYIRDSAAAVVVYDITNVNSFQQTTKWIDDVRTERGSDVIIMLVGNKTDLADKRQVSIEEGERKAKELNVMFIETSAKAGYNVKQLFRRVAAALPGM 177
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173    

   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
(-)
Family: Ras (176)

(-) Gene Ontology  (28, 28)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RAB6A_HUMAN | P20340)
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: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).
    GO:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
biological process
    GO:0019882    antigen processing and presentation    The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex.
    GO:0034498    early endosome to Golgi transport    The directed movement of substances from early endosomes to the Golgi.
    GO:0072385    minus-end-directed organelle transport along microtubule    The directed movement of an organelle towards the minus end of a microtubule, mediated by motor proteins. This process begins with the attachment of an organelle to a microtubule, and ends when the organelle reaches its final destination.
    GO:0018125    peptidyl-cysteine methylation    The methylation of peptidyl-cysteine to form peptidyl-S-methyl-L-cysteine.
    GO:0034067    protein localization to Golgi apparatus    A process in which a protein is transported to, or maintained in, a location within the Golgi apparatus.
    GO:0000042    protein targeting to Golgi    The process of directing proteins towards the Golgi; usually uses signals contained within the protein.
    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:0006890    retrograde vesicle-mediated transport, Golgi to ER    The directed movement of substances from the Golgi back to the endoplasmic reticulum, mediated by vesicles bearing specific protein coats such as COPI or COG.
    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.
    GO:0016192    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.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
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:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0070381    endosome to plasma membrane transport vesicle    A transport vesicle that mediates transport from the endosome to the plasma membrane, and fuses with the plasma membrane to deliver lipids and membrane proteins to the plasma membrane and to release various cargo molecules, such as proteins or hormones, by exocytosis.
    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:0005802    trans-Golgi network    The network of interconnected tubular and cisternal structures located within the Golgi apparatus on the side distal to the endoplasmic reticulum, from which secretory vesicles emerge. The trans-Golgi network is important in the later stages of protein secretion where it is thought to play a key role in the sorting and targeting of secreted proteins to the correct destination.
    GO:0032588    trans-Golgi network membrane    The lipid bilayer surrounding any of the compartments that make up the trans-Golgi network.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RAB6A_HUMAN | P20340: 2gil 3bbp 3cwz 4dkx

(-) Related Entries Specified in the PDB File

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