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(-) Description

Title :  GDP-BOUND RAB7
 
Authors :  A. Rak, O. Pylypenko, A. Niculae, K. Pyatkov, R. S. Goody, K. Alexandrov
Date :  22 Apr 04  (Deposition) - 20 Jul 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Gtp-Binding Protein, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Rak, O. Pylypenko, A. Niculae, K. Pyatkov, R. S. Goody, K. Alexandrov
Structure Of The Rab7:Rep-1 Complex: Insights Into The Mechanism Of Rab Prenylation And Choroideremia Disease
Cell(Cambridge, Mass. ) V. 117 749 2004
PubMed-ID: 15186776  |  Reference-DOI: 10.1016/J.CELL.2004.05.017
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RAS-RELATED PROTEIN RAB-7
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET19
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: GTPASE DOMAIN
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: RAS-RELATED PROTEIN P23, RAS-RELATED PROTEIN BRL- RAS

 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
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:22 , HOH A:1085 , HOH A:1087 , HOH A:1088 , HOH A:1153 , GDP A:1557BINDING SITE FOR RESIDUE MG A 3000
2AC2SOFTWAREGLY A:18 , VAL A:19 , GLY A:20 , LYS A:21 , THR A:22 , SER A:23 , PHE A:33 , ASN A:125 , LYS A:126 , ASP A:128 , LEU A:129 , SER A:155 , ALA A:156 , LYS A:157 , HOH A:1033 , HOH A:1048 , HOH A:1085 , HOH A:1087 , HOH A:1088 , HOH A:1091 , MG A:3000BINDING SITE FOR RESIDUE GDP A 1557

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VG1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VG1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VG1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VG1)

(-) Exons   (5, 5)

Asymmetric/Biological Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000164321ENSRNOE00000116420chr4:122220655-12222058868RAB7A_RAT1-18181A:5-1814
1.2ENSRNOT000000164322ENSRNOE00000116592chr4:122217534-122217408127RAB7A_RAT18-60431A:18-60 (gaps)43
1.3ENSRNOT000000164323ENSRNOE00000116782chr4:122208992-122208774219RAB7A_RAT61-133731A:61-133 (gaps)73
1.4ENSRNOT000000164324ENSRNOE00000116963chr4:122208105-122207977129RAB7A_RAT134-176431A:134-17643
1.5ENSRNOT000000164325ENSRNOE00000117137chr4:122204075-1222026971379RAB7A_RAT177-207311A:177-1859

(-) 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:166
 aligned with RAB7A_RAT | P09527 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:181
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184 
            RAB7A_RAT     5 KKVLLKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVMVDDRLVTMQIWDTAGQERFQSLGVAFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPRDPENFPFVVLGNKIDLENRQVATKRAQAWCYSKNNIPYFETSAKEAINVEQAFQTIARNALKQETEVELYNE 185
               SCOP domains d1vg1a_ A: Rab7                                                                                                                                                                       SCOP domains
               CATH domains 1vg1A00 A:5-185 P-loop contain        ing nucleotide triphos       phate hydrolases                                                                                                   CATH domains
               Pfam domains -----Ras-1vg1A01 A:10-175                                                                                                                                                  ---------- Pfam domains
         Sec.struct. author ...eeeeeee.....hhhhhhhhhhhh...--------.eeeeeeeee..eeeeeeeee.-------..hhhhhhh..eeeeeee..hhhhhhhhhhhhhhhhhhhh........eeeeee.........hhhhhhhhhhh.....eeee......hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1      ------------------------------------------Exon 1.3  PDB: A:61-133 (gaps) UniProt: 61-133                           Exon 1.4  PDB: A:134-176 UniProt: 134-176  Exon 1.5  Transcript 1 (1)
           Transcript 1 (2) -------------Exon 1.2  PDB: A:18-60 (gaps)              ----------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1vg1 A   5 KKVLLKVIILGDSGVGKTSLMNQYVNKKFS--------ADFLTKEVMVDDRLVTMQIWDT-------SLGVAFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPRDPENFPFVVLGNKIDLENRQVATKRAQAWCYSKNNIPYFETSAKEAINVEQAFQTIARNALKQETEVELYNE 185
                                    14        24        34        44        54        64       |74        84        94       104       114       124       134       144       154       164       174       184 
                                                        34       43                   64      72
   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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: P-loop_NTPase (1112)

(-) Gene Ontology  (50, 50)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RAB7A_RAT | P09527)
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:0048365    Rac GTPase binding    Interacting selectively and non-covalently with Rac protein, any member of the Rac subfamily of the Ras superfamily of monomeric GTPases.
    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:0006914    autophagy    The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
    GO:0045453    bone resorption    The process in which specialized cells known as osteoclasts degrade the organic and inorganic portions of bone, and endocytose and transport the degradation products.
    GO:0045022    early endosome to late endosome transport    The directed movement of substances, in membrane-bounded vesicles, from the early sorting endosomes to the late sorting endosomes; transport occurs along microtubules and can be experimentally blocked with microtubule-depolymerizing drugs.
    GO:0008333    endosome to lysosome transport    The directed movement of substances from endosomes to lysosomes.
    GO:0007174    epidermal growth factor catabolic process    The chemical reactions and pathways resulting in the breakdown of epidermal growth factor (EGF), following internalization of the receptor-bound ligand into the signal-receiving cell. Full breakdown of epidermal growth factor results in a ligand that is unable to bind and activate its receptor.
    GO:0016042    lipid catabolic process    The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0061724    lipophagy    The autophagic process in which lipid droplets are delivered to the vacuole and degraded in response to changing cellular conditions.
    GO:0090383    phagosome acidification    Any process that reduces the pH of the phagosome, measured by the concentration of the hydrogen ion.
    GO:0090385    phagosome-lysosome fusion    The creation of a phagolysosome from a phagosome and a lysosome.
    GO:1903543    positive regulation of exosomal secretion    Any process that activates or increases the frequency, rate or extent of exosomal secretion.
    GO:0045732    positive regulation of protein catabolic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
    GO:0048524    positive regulation of viral process    Any process that activates or increases the frequency, rate or extent of a multi-organism process in which a virus is a participant.
    GO:0006622    protein targeting to lysosome    The process of directing proteins towards the lysosome using signals contained within the protein.
    GO:0022615    protein to membrane docking    The initial attachment of a protein to a target membrane, mediated by a proteins protruding from the target membrane. Docking requires only that the proteins come close enough to interact and adhere.
    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:2000785    regulation of autophagosome assembly    Any process that modulates the frequency, rate or extent of autophagosome assembly.
    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.
    GO:0019076    viral release from host cell    The dissemination of mature viral particles from the host cell, e.g. by cell lysis or the budding of virus particles from the cell membrane.
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:0097208    alveolar lamellar body    A specialized secretory organelle found in type II pneumocytes and involved in the synthesis, secretion, and reutilization of pulmonary surfactant.
    GO:0000421    autophagosome membrane    The lipid bilayer surrounding an autophagosome, a double-membrane-bounded vesicle in which endogenous cellular material is sequestered.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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: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:0032419    extrinsic component of lysosome membrane    The component of an lysosome membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    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:0031902    late endosome membrane    The lipid bilayer surrounding a late endosome.
    GO:0005811    lipid droplet    An intracellular non-membrane-bounded organelle comprising a matrix of coalesced lipids surrounded by a phospholipid monolayer. May include associated proteins.
    GO:0005765    lysosomal membrane    The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm.
    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:0033162    melanosome membrane    The lipid bilayer surrounding a melanosome.
    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:0034045    pre-autophagosomal structure membrane    A cellular membrane associated with the pre-autophagosomal structure.
    GO:0030904    retromer complex    A conserved hetero-pentameric membrane-associated complex involved in retrograde transport from endosomes to the Golgi apparatus. The budding yeast retromer comprises Vps35p, Vps29p, Vps26p, Vps5p, and Vps17p. The mammalian complex shows slight variation in composition compared to yeast, and comprises SNX1 or SNX2, SNX5 or SNX6, VPS26A or VPS26B, VPS29, and VPS35.
    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.
    GO:0005774    vacuolar membrane    The lipid bilayer surrounding the vacuole and separating its contents from the cytoplasm of the cell.

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  RAB7A_RAT | P09527
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 Related Entries

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

UniProtKB/Swiss-Prot
        RAB7A_RAT | P09527: 1vg0 1vg8 1vg9

(-) Related Entries Specified in the PDB File

1vg0 THE REP-1 PROTEIN IN COMPLEX WITH MONOPRENYLATED RAB7 PROTEIN
1vg8 GPPNHP-BOUND RAB7
1vg9 THE REP-1 PROTEIN IN COMPLEX WITH C-TERMINALLY TRUNCATED RAB7 PROTEIN