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(-) Description

Title :  NON-MYRISTOYLATED RAT ADP-RIBOSYLATION FACTOR-1 COMPLEXED WITH GDP, DIMERIC CRYSTAL FORM
 
Authors :  S. E. Greasley, H. Jhoti, B. Bax
Date :  16 Dec 95  (Deposition) - 20 Jun 96  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transport Protein, Gdp-Binding, Membrane Trafficking, Homodimer (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. E. Greasley, H. Jhoti, C. Teahan, R. Solari, A. Fensome, G. M. Thomas, S. Cockcroft, B. Bax
The Structure Of Rat Adp-Ribosylation Factor-1 (Arf-1) Complexed To Gdp Determined From Two Different Crystal Forms.
Nat. Struct. Biol. V. 2 797 1995
PubMed-ID: 7552752  |  Reference-DOI: 10.1038/NSB0995-797
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RAT ADP-RIBOSYLATION FACTOR-1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET
    Expression System Taxid562
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymARF-1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:31 , GLU A:54 , GDP A:183 , HOH A:246 , HOH A:253 , HOH B:223BINDING SITE FOR RESIDUE MG A 182
2AC2SOFTWARETHR B:31 , GDP B:183 , HOH B:254 , HOH B:259 , HOH B:260BINDING SITE FOR RESIDUE MG B 182
3AC3SOFTWAREALA A:27 , ALA A:28 , GLY A:29 , LYS A:30 , THR A:31 , THR A:32 , ASN A:126 , LYS A:127 , ASP A:129 , LEU A:130 , CYS A:159 , ALA A:160 , THR A:161 , MG A:182 , HOH A:189 , HOH A:221 , HOH A:226 , HOH A:230 , HOH A:246 , HOH A:253 , GLY B:50 , ASN B:52BINDING SITE FOR RESIDUE GDP A 183
4AC4SOFTWAREILE A:49 , GLY A:50 , ASP B:26 , ALA B:27 , ALA B:28 , GLY B:29 , LYS B:30 , THR B:31 , THR B:32 , ASN B:126 , LYS B:127 , ASP B:129 , LEU B:130 , CYS B:159 , ALA B:160 , MG B:182 , HOH B:193 , HOH B:213 , HOH B:219 , HOH B:225 , HOH B:254 , HOH B:260BINDING SITE FOR RESIDUE GDP B 183

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ARFPS51417 small GTPase Arf family profile.ARF1_RAT11-177
 
  2A:11-177
B:11-177

(-) Exons   (0, 0)

(no "Exon" information available for 1RRG)

(-) 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:177
 aligned with ARF1_RAT | P84079 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:180
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181
             ARF1_RAT     2 GNIFANLFKGLFGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQLRNQK 181
               SCOP domains d1rrga_ A: ADP-ribosylation factor                                                                                                                                                   SCOP domains
               CATH domains 1rrgA00 A:2-181 P-loop containing nucleotide triphosphate hydrolases                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhh.......eeeeeee.....hhhhhhhh....eeeeeee..eeeeeee...eeeeeee...---...hhhhhh..eeeeeeeee......hhhhhhhhhhhh........eeeeeee.........hhhhhhh............eee........hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------ARF  PDB: A:11-177 UniProt: 11-177                                                                                                                                     ---- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1rrg A   2 GNIFANLFKGLFGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGG---IRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQLRNQK 181
                                    11        21        31        41        51        61        |-  |     81        91       101       111       121       131       141       151       161       171       181
                                                                                               70  74                                                                                                           

Chain B from PDB  Type:PROTEIN  Length:177
 aligned with ARF1_RAT | P84079 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:180
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181
             ARF1_RAT     2 GNIFANLFKGLFGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQLRNQK 181
               SCOP domains d1rrgb_ B: ADP-ribosylation factor                                                                                                                                                   SCOP domains
               CATH domains 1rrgB00 B:2-181 P-loop containing nucleotide triphosphate hydrolases                                                                                                                 CATH domains
           Pfam domains (1) -Arf-1rrgB01 B:3-177                                                                                                                                                            ---- Pfam domains (1)
           Pfam domains (2) -Arf-1rrgB02 B:3-177                                                                                                                                                            ---- Pfam domains (2)
         Sec.struct. author .hhhhhhhh.......eeeeeee.....hhhhhhhh....eeeeeee..eeeeeee...eeeeeee...---..hhhhhhh..eeeeeeeee......hhhhhhhhhhhhh.......eeeeeee.........hhhhhhh..........eeeee........hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------ARF  PDB: B:11-177 UniProt: 11-177                                                                                                                                     ---- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1rrg B   2 GNIFANLFKGLFGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGG---IRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQLRNQK 181
                                    11        21        31        41        51        61        |-  |     81        91       101       111       121       131       141       151       161       171       181
                                                                                               70  74                                                                                                           

   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/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (51, 51)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ARF1_RAT | P84079)
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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    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:1990583    phospholipase D activator activity    Increases the activity of the enzyme phospholipase D.
    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:0055108    Golgi to transport vesicle transport    The directed movement of proteins from the Golgi to a transport vesicle. Continuously secreted proteins are sorted into transport vesicles that fuse with the plasma membrane, releasing their contents by exocytosis.
    GO:0007015    actin filament organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments. Includes processes that control the spatial distribution of actin filaments, such as organizing filaments into meshworks, bundles, or other structures, as by cross-linking.
    GO:0006878    cellular copper ion homeostasis    Any process involved in the maintenance of an internal steady state of copper ions at the level of a cell.
    GO:0097061    dendritic spine organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a dendritic spine. A dendritic spine is a specialized protrusion from a neuronal dendrite and is involved in synaptic transmission.
    GO:0060292    long term synaptic depression    A process that modulates synaptic plasticity such that synapses are changed resulting in the decrease in the rate, or frequency of synaptic transmission at the synapse.
    GO:0097212    lysosomal membrane organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a lysosomal membrane. A lysosomal membrane is the lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm.
    GO:1902953    positive regulation of ER to Golgi vesicle-mediated transport    Any process that activates or increases the frequency, rate or extent of ER to Golgi vesicle-mediated transport.
    GO:0045956    positive regulation of calcium ion-dependent exocytosis    Any process that activates or increases the frequency, rate or extent of calcium ion-dependent exocytosis.
    GO:0043085    positive regulation of catalytic activity    Any process that activates or increases the activity of an enzyme.
    GO:0060999    positive regulation of dendritic spine development    Any process that increases the rate, frequency, or extent of dendritic spine development, the process whose specific outcome is the progression of the dendritic spine over time, from its formation to the mature structure.
    GO:0045807    positive regulation of endocytosis    Any process that activates or increases the frequency, rate or extent of endocytosis.
    GO:1902824    positive regulation of late endosome to lysosome transport    Any process that activates or increases the frequency, rate or extent of late endosome to lysosome transport.
    GO:0050714    positive regulation of protein secretion    Any process that activates or increases the frequency, rate or extent of the controlled release of a protein from a cell.
    GO:1902307    positive regulation of sodium ion transmembrane transport    Any process that activates or increases the frequency, rate or extent of sodium ion transmembrane transport.
    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:0034315    regulation of Arp2/3 complex-mediated actin nucleation    Any process that modulates the frequency, rate or extent of actin nucleation mediated by the Arp2/3 complex and interacting proteins.
    GO:1903725    regulation of phospholipid metabolic process    Any process that modulates the frequency, rate or extent of phospholipid metabolic process.
    GO:0002090    regulation of receptor internalization    Any process that modulates the frequency, rate or extent of receptor internalization.
    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:0070142    synaptic vesicle budding    Evagination of a membrane to form a synaptic vesicle.
    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:0034379    very-low-density lipoprotein particle assembly    The non-covalent aggregation and arrangement of proteins and lipids in the liver to form a very-low-density lipoprotein particle.
    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:0030137    COPI-coated vesicle    A vesicle with a coat formed of the COPI coat complex proteins. COPI-coated vesicles are found associated with Golgi membranes at steady state, are involved in Golgi to endoplasmic reticulum (retrograde) vesicle transport, and possibly also in intra-Golgi transport.
    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:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0031252    cell leading edge    The area of a motile cell closest to the direction of movement.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0012505    endomembrane system    A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.
    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:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    GO:0005778    peroxisomal membrane    The lipid bilayer surrounding a peroxisome.
    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:0014069    postsynaptic density of dendrite    An electron dense network of proteins within and adjacent to the postsynaptic membrane of the dendrite of asymetric synapses. Its major components include neurotransmitter receptors and the proteins that spatially and functionally organize them such as anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components.
    GO:0045211    postsynaptic membrane    A specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters cross the synaptic cleft and transmit the signal to the postsynaptic membrane.
    GO:0030017    sarcomere    The repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs.
    GO:0045202    synapse    The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic 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.

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 Related Entries

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        ARF1_RAT | P840791re0 1rrf

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