1R8S - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   ARF1[DELTA1-17]-GDP IN COMPLEX WITH A SEC7 DOMAIN CARRYING THE MUTATION OF THE CATALYTIC GLUTAMATE TO LYSINE

Authors :   L. Renault, B. Guibert, J. Cherfils

Date :   28 Oct 03 (Deposition) - 20 Jan 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.46

Chains :   Asym. Unit : A,E
Biol. Unit 1: A,E  (1x)
Biol. Unit 2: A,E  (2x)

Keywords :   Protein Transport/Exchange Factor, Protein Transport-Exchange Factor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Renault, B. Guibert, J. Cherfils
Structural Snapshots Of The Mechanism And Inhibition Of A Guanine Nucleotide Exchange Factor
Nature V. 426 525 2003
PubMed-ID: 14654833 | Reference-DOI: 10.1038/NATURE02197

Molecule 1 - ADP-RIBOSYLATION FACTOR 1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	BL21 GOLD
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 18-181
	Gene	:	ARF1
	Organism Common	:	CATTLE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913

Molecule 2 - ARNO
	Chains	:	E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11D
	Expression System Strain	:	BL21 GOLD
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	SEC7 DOMAIN (RESIDUES 50-252)
	Gene	:	PSCD2, ARNO
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ARF NUCLEOTIDE-BINDING SITE OPENER, CYTOHESIN 2, ARF EXCHANGE FACTOR

		1	2
Asymmetric Unit	:	A	E
Biological Unit 1 (1x)	:	A	E
Biological Unit 2 (2x)	:	A	E

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 7)

No.	Name	Count	Type	Full Name
1	BME	1	Ligand/Ion	BETA-MERCAPTOETHANOL
2	FMT	3	Ligand/Ion	FORMIC ACID
3	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
4	SO3	1	Ligand/Ion	SULFITE ION
5	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (5, 7)

No.	Name	Count	Type	Full Name
1	BME	1	Ligand/Ion	BETA-MERCAPTOETHANOL
2	FMT	3	Ligand/Ion	FORMIC ACID
3	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
4	SO3	1	Ligand/Ion	SULFITE ION
5	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (5, 14)

No.	Name	Count	Type	Full Name
1	BME	2	Ligand/Ion	BETA-MERCAPTOETHANOL
2	FMT	6	Ligand/Ion	FORMIC ACID
3	GDP	2	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
4	SO3	2	Ligand/Ion	SULFITE ION
5	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:538 , GLY E:116 , ARG E:118 , LYS E:156 , GLN E:158 , LYS E:159 , ARG E:162 , HOH E:564	BINDING SITE FOR RESIDUE SO4 E 501
2	AC2	SOFTWARE	ASN A:52 , PRO E:154 , GLY E:155 , LYS E:156	BINDING SITE FOR RESIDUE SO3 E 502
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 , HOH A:521 , HOH A:532 , HOH A:538 , HOH A:542 , HOH A:546 , HOH A:550 , HOH A:566 , HOH A:648 , LYS E:156	BINDING SITE FOR RESIDUE GDP A 401
4	AC4	SOFTWARE	ARG A:19 , HOH A:610	BINDING SITE FOR RESIDUE BME A 506
5	AC5	SOFTWARE	ARG A:149 , HIS A:150 , ARG A:151	BINDING SITE FOR RESIDUE FMT A 503
6	AC6	SOFTWARE	ARG A:79	BINDING SITE FOR RESIDUE FMT A 504
7	AC7	SOFTWARE	ASN E:139 , SER E:237	BINDING SITE FOR RESIDUE FMT E 505

(no "SS Bond" information available for 1R8S)

(no "Cis Peptide Bond" information available for 1R8S)

(no "SAP(SNP)/Variant" information available for 1R8S)

(no "PROSITE Motif" information available for 1R8S)

Asymmetric Unit (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSBTAT00000010159	1	ENSBTAE00000286249	chr7:2936881-2936828	54	ARF1_BOVIN	-	0	0	-	-
1.2	ENSBTAT00000010159	2	ENSBTAE00000180606	chr7:2920879-2920695	185	ARF1_BOVIN	1-50	50	1	A:18-50	33
1.3	ENSBTAT00000010159	3	ENSBTAE00000400733	chr7:2920620-2920510	111	ARF1_BOVIN	50-87	38	1	A:50-87	38
1.4	ENSBTAT00000010159	4	ENSBTAE00000286243	chr7:2920421-2920297	125	ARF1_BOVIN	87-128	42	1	A:87-128	42
1.5	ENSBTAT00000010159	5	ENSBTAE00000082548	chr7:2920140-2918819	1322	ARF1_BOVIN	129-181	53	1	A:129-177	49

Asymmetric 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:160
 aligned with ARF1_BOVIN | P84080 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:160
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177
           ARF1_BOVIN    18 MRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQL 177
               SCOP domains d1r8sa_ A: ADP-ribosylation factor                                                                                                                               SCOP domains
               CATH domains 1r8sA00 A:18-177 P-loop containing nucleotide triphosphate hydrolases                                                                                            CATH domains
               Pfam domains Arf-1r8sA01 A:18-177                                                                                                                                             Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhhh...........eeeee....eeeeee...hhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhhhhhhhhh..eeeeeee........hhhhhhhhhhhhhh....eeeee.......hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:18-50           ------------------------------------Exon 1.4  PDB: A:87-128 UniProt: 87-128   Exon 1.5  PDB: A:129-177 UniProt: 129-181         Transcript 1 (1)
           Transcript 1 (2) --------------------------------Exon 1.3  PDB: A:50-87 UniProt: 50-87 ------------------------------------------------------------------------------------------ Transcript 1 (2)
                 1r8s A  18 MRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQL 177
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177

Chain E from PDB  Type:PROTEIN  Length:187
 aligned with CYH2_HUMAN | Q99418 from UniProtKB/Swiss-Prot  Length:400

    Alignment length:187
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       
           CYH2_HUMAN    62 NRKMAMGRKKFNMDPKKGIQFLVENELLQNTPEEIARFLYKGEGLNKTAIGDYLGEREELNLAVLHAFVDLHEFTDLNLVQALRQFLWSFRLPGEAQKIDRMMEAFAQRYCLCNPGVFQSTDTCYVLSFAVIMLNTSLHNPNVRDKPGLERFVAMNRGINEGGDLPEELLRNLYDSIRNEPFKIPED 248
               SCOP domains d1r8se_ E: Exchange factor ARNO                                                                                                                                                             SCOP domains
               CATH domains 1r8sE01 E:62-133  [code=1.10.220.20, no name defined]                   1r8sE02 E:134-246 Arf Nucleotide-binding Site Opener,domain 2                                                    -- CATH domains
               Pfam domains Sec7-1r8sE01 E:62-243                                                                                                                                                                 ----- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh...hhhhhhhhhh..hhhhhhhhhhhhhh......hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhh.........hhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r8s E  62 NRKMAMGRKKFNMDPKKGIQFLVENELLQNTPEEIARFLYKGEGLNKTAIGDYLGEREELNLAVLHAFVDLHEFTDLNLVQALRQFLWSFRLPGKAQKIDRMMEAFAQRYCLCNPGVFQSTDTCYVLSYSVIMLNTDLHNPNVRDKMGLERFVAMNRGINEGGDLPEELLRNLYDSIRNEPFKIPED 248
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241

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 '\|'

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: Arf (26)

Bos taurus (Bovine) (3)

Arf-1r8sA01

A:18-177

Clan: no clan defined [family: Sec7] (12)

Family: Sec7 (12)

Homo sapiens (Human) (7)

Sec7-1r8sE01

E:62-243

Asymmetric Unit(hide GO term definitions)

Chain A (ARF1_BOVIN | P84080)

molecular function
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	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: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: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: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: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: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:0042583	chromaffin granule	Specialized secretory vesicle found in the cells of adrenal glands and various other organs, which is concerned with the synthesis, storage, metabolism, and secretion of epinephrine and norepinephrine.
	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: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: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.

Chain E (CYH2_HUMAN | Q99418)

molecular function
	GO:0005086	ARF guanyl-nucleotide exchange factor activity	Stimulates the exchange of guanyl nucleotides associated with the GTPase ARF. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
	GO:0005085	guanyl-nucleotide exchange factor activity	Stimulates the exchange of guanyl nucleotides associated with a GTPase. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
	GO:0070679	inositol 1,4,5 trisphosphate binding	Interacting selectively and non-covalently with inositol 1,4,5 trisphosphate.
	GO:0008289	lipid binding	Interacting selectively and non-covalently with a lipid.
	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:0030036	actin cytoskeleton 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 and their associated proteins.
	GO:0006897	endocytosis	A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
	GO:0043547	positive regulation of GTPase activity	Any process that activates or increases the activity of a GTPase.
	GO:0032012	regulation of ARF protein signal transduction	Any process that modulates the frequency, rate or extent of ARF protein signal transduction.
cellular component
	GO:0000139	Golgi membrane	The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
	GO:0042995	cell projection	A prolongation or process extending from a cell, e.g. a flagellum or axon.
	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:0030426	growth cone	The migrating motile tip of a growing nerve cell axon or dendrite.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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.

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UniProtKB/Swiss-Prot
	ARF1_BOVIN \| P84080	:	1r8q 1re0 1s9d 4c0a
	CYH2_HUMAN \| Q99418	:	1pbv 1r8m 1r8q 1s9d 4jmi 4jmo 4jwl 4jxh 4l5m 4z21

1r8m	CRYSTAL STRUCTURE OF ISOLATED ARNO-SEC7[F190Y/A191S/S198D/ P208M]
1r8q	CRYSTAL STRUCTURE OF AN ABORTIVE ARF1/GDP/MG/AFB/ARNO- SEC7[F190Y/A191S/S198D/P208M] COMPLEX
1r8r	CRYSTAL STRUCTURE OF AN ABORTIVE ARF1[D1-17]/GDP/MG/AFB/ ARNO-SEC7[F190Y/A191S/S198D/P208M] COMPLEX

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (4, 4)

Sequences/Alignments

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SCOP Domains (2, 2)

CATH Domains (3, 3)

Pfam Domains (2, 2)

Gene Ontology (41, 46)

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