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Asym./Biol. Unit (Jmol Viewer)

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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)

Molecule 1 - RAT ADP-RIBOSYLATION FACTOR-1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET
	Expression System Taxid	:	562
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	ARF-1

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	GDP	2	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
2	MG	2	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:31 , GLU A:54 , GDP A:183 , HOH A:246 , HOH A:253 , HOH B:223	BINDING SITE FOR RESIDUE MG A 182
2	AC2	SOFTWARE	THR B:31 , GDP B:183 , HOH B:254 , HOH B:259 , HOH B:260	BINDING SITE FOR RESIDUE MG B 182
3	AC3	SOFTWARE	ALA 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:52	BINDING SITE FOR RESIDUE GDP A 183
4	AC4	SOFTWARE	ILE 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:260	BINDING SITE FOR RESIDUE GDP B 183

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

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

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ARF	PS51417	small GTPase Arf family profile.	ARF1_RAT	11-177	2	A:11-177 B:11-177

(no "Exon" information available for 1RRG)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

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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)
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	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 '\|'

Asymmetric/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

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Class: Alpha and beta proteins (a/b) (23833)

Fold: P-loop containing nucleoside triphosphate hydrolases (2083)

Superfamily: P-loop containing nucleoside triphosphate hydrolases (2083)

Family: G proteins (693)

Protein domain: ADP-ribosylation factor (40)

Norway rat (Rattus norvegicus), ARF1 [TaxId: 10116] (2)

1a	d1rrga_	A:
1b	d1rrgb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

Norway rat (Rattus norvegicus) (38)

1a	1rrgA00	A:2-181
1b	1rrgB00	B:2-181

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: Arf (26)

Rattus norvegicus (Rat) (3)

1a	Arf-1rrgB01	B:3-177
1b	Arf-1rrgB02	B:3-177

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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