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(-) Description

Title :  CRYSTAL STRUCTURE OF YPT31 IN COMPLEX WITH YEAST RAB-GDI
 
Authors :  S. Kravchenko, A. Ignatev, R. S. Goody, A. Rak, O. Pylypenko
Date :  31 Mar 08  (Deposition) - 06 May 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  B,G
Keywords :  Rab Gtpase, Prenylation, Vesicular Transport, Acetylation, Golgi Apparatus, Gtp-Binding, Lipoprotein, Membrane, Nucleotide-Binding, Protein Transport, Cytoplasm, Gtpase Activation, Phosphoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Ignatev, S. Kravchenko, A. Rak, R. S. Goody, O. Pylypenko
A Structural Model Of The Gdp Dissociation Inhibitor Rab Membrane Extraction Mechanism.
J. Biol. Chem. V. 283 18377 2008
PubMed-ID: 18426803  |  Reference-DOI: 10.1074/JBC.M709718200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RAB GDP-DISSOCIATION INHIBITOR
    ChainsG
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET19
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymRAB GDI, SECRETORY PATHWAY GDP DISSOCIATION INHIBITOR
 
Molecule 2 - GTP-BINDING PROTEIN YPT31/YPT8
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET19
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    MutationYES
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymRAB GTPASE YPT31

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit BG

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
3MG1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER B:27BINDING SITE FOR RESIDUE MG B 1208
2AC2SOFTWAREARG G:147 , GLY G:186 , THR G:189BINDING SITE FOR RESIDUE CL G 2001
3AC3SOFTWARELEU G:89 , MET G:90 , PHE G:421BINDING SITE FOR RESIDUE CL G 2002
4AC4SOFTWAREASP B:21 , SER B:22 , GLY B:23 , GLY B:25 , LYS B:26 , SER B:27 , ASN B:28 , PHE B:38 , ASN B:39 , MET B:40 , ASN B:126 , LYS B:127 , ASP B:129 , LEU B:130 , SER B:156 , ALA B:157 , LEU B:158BINDING SITE FOR RESIDUE GDP B 1207

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3CPJ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3CPJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3CPJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3CPJ)

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YER136W1YER136W.1V:439612-4409671356GDI1_YEAST1-4514511G:6-443438

(-) 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 B from PDB  Type:PROTEIN  Length:164
 aligned with YPT31_YEAST | P38555 from UniProtKB/Swiss-Prot  Length:223

    Alignment length:198
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199        
          YPT31_YEAST    10 YDLLFKIVLIGDSGVGKSNLLSRFTKNEFNMDSKSTIGVEFATRTLEIDGKRIKAQIWDTAGQERYRAITSAYYRGAVGALIVYDISKSSSYENCNHWLSELRENADDNVAVGLIGNKSDLAHLRAVPTEESKTFAQENQLLFTETSALNSENVDKAFEELINTIYQKVSKHQMDLGDSSANGNANGASAPNGPTISL 207
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeee.....hhhhhhhhhhhh....------...eeeeeeee..eeeeeeee...........hhhhh....eeeeee.-.hhhhhhhhhhhhhhhhhhh.--.eeeeee.hhhhhhhh..hhhhhhhhhhhh..eeee....-..hhhhhhhhhhhhhh...------------------------..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3cpj B  10 YDLLFKIVLIGDSGVGKSNLLSRFTKNEFNM------GVEFATRTLEIEGKRIKAQIWDTAGQERYRAITSAYYRGAVGALIVYD-SKSSSYENCNHWLSELRENAD--VAVGLIGNKSDLAHLRAVPTEESKTFAQENQLLFTETSAL-SENVDKAFEELINTIYQKV------------------------PTISL 207
                                    19        29        39|      |49        59        69        79        89    | | 99       109      |119       129       139       149        |-|      169        |-         -         -   |    
                                                         40     47                                             94 |                 116  |                                    158 |               178                      203    
                                                                                                                 96                    119                                      160                                               

Chain G from PDB  Type:PROTEIN  Length:438
 aligned with GDI1_YEAST | P39958 from UniProtKB/Swiss-Prot  Length:451

    Alignment length:438
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435        
           GDI1_YEAST     6 IDTDYDVIVLGTGITECILSGLLSVDGKKVLHIDKQDHYGGEAASVTLSQLYEKFKQNPISKEERESKFGKDRDWNVDLIPKFLMANGELTNILIHTDVTRYVDFKQVSGSYVFKQGKIYKVPANEIEAISSPLMGIFEKRRMKKFLEWISSYKEDDLSTHQGLDLDKNTMDEVYYKFGLGNSTKEFIGHAMALWTNDDYLQQPARPSFERILLYCQSVARYGKSPYLYPMYGLGELPQGFARLSAIYGGTYMLDTPIDEVLYKKDTGKFEGVKTKLGTFKAPLVIADPTYFPEKCKSTGQRVIRAICILNHPVPNTSNADSLQIIIPQSQLGRKSDIYVAIVSDAHNVCSKGHYLAIISTIIETDKPHIELEPAFKLLGPIEEKFMGIAELFEPREDGSKDNIYLSRSYDASSHFESMTDDVKDIYFRVTGHPLVLK 443
               SCOP domains d3cpjg1 G:6-301 automated matches                                                                                                                                                                                                                                                                       d3cpjg3 G:302-399 automated matches                                                               d3cpjg2 G:400-443 automated matches          SCOP domains
               CATH domains 3cpjG01 G:6-61,G:232-305,G:398-443                      3cpjG02 G:62-126,G:306-397                                       3cpjG03 G:127-231 Guanine Nucleotide Dissociation Inhibitor, domain 1                                    3cpjG01 G:6-61,G:232-305,G:398-443  [code=3.50.50.60, no name defined]    3cpjG02 G:62-126,G:306-397 Guanine Nucleotide Dissociation Inhibitor, domain 2              3cpjG01 G:6-61,G:232-305,G:398-443             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeee..hhhhhhhhhhhhhh...eeee......hhhh.eehhhhhhhhhh....hhhhhhhhhhhhhhh.ee.....ee..hhhhhhhhhhhhhhh..eee...eeeee..eeee...hhhhhhhh...hhhhhhhhhhhhhhhhhh...hhhhh........hhhhhhhhh..hhhhhhhhhhhh.....hhhhhh.hhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhh..eee......eeee......eeeeee..eeee...eee.hhhhhh.eeeeeeeeeeeeeee............eeeeehhhhh.....eeeeeee.hhh......eeeeeeee....hhhhhhhhhhh......eeeeeeeeeeee........eee.........hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: G:6-443 UniProt: 1-451 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                     Transcript 1
                 3cpj G   6 IDTDYDVIVLGTGITECILSGLLSVDGKKVLHIDKQDHYGGEAASVTLSQLYEKFKQNPISKEERESKFGKDRDWNVDLIPKFLMANGELTNILIHTDVTRYVDFKQVSGSYVFKQGKIYKVPANEIEAISSPLMGIFEKRRMKKFLEWISSYKEDDLSTHQGLDLDKNTMDEVYYKFGLGNSTKEFIGHAMALWTNDDYLQQPARPSFERILLYCQSVARYGKSPYLYPMYGLGELPQGFARLSAIYGGTYMLDTPIDEVLYKKDTGKFEGVKTKLGTFKAPLVIADPTYFPEKCKSTGQRVIRAICILNHPVPNTSNADSLQIIIPQSQLGRKSDIYVAIVSDAHNVCSKGHYLAIISTIIETDKPHIELEPAFKLLGPIEEKFMGIAELFEPREDGSKDNIYLSRSYDASSHFESMTDDVKDIYFRVTGHPLVLK 443
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435        

   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  (3, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (3, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3CPJ)

(-) Gene Ontology  (27, 32)

Asymmetric/Biological Unit(hide GO term definitions)
Chain B   (YPT31_YEAST | P38555)
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: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:0034498    early endosome to Golgi transport    The directed movement of substances from early endosomes to the Golgi.
    GO:0006887    exocytosis    A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell.
    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: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.
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: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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0055037    recycling endosome    An organelle consisting of a network of tubules that functions in targeting molecules, such as receptors transporters and lipids, to the plasma membrane.
    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.

Chain G   (GDI1_YEAST | P39958)
molecular function
    GO:0005092    GDP-dissociation inhibitor activity    Prevents the dissociation of GDP from a GTPase, thereby preventing GTP from binding.
    GO:0005096    GTPase activator activity    Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
    GO:0005093    Rab GDP-dissociation inhibitor activity    Prevents the dissociation of GDP from the small GTPase Rab, thereby preventing GTP from binding.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    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:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    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:0050790    regulation of catalytic activity    Any process that modulates the activity of an enzyme.
    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.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GDI1_YEAST | P399581ukv 2bcg 3cph 3cpi

(-) Related Entries Specified in the PDB File

3cph 3cpi