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Title :   STRUCTURE OF ESPG-ARF6 COMPLEX

Authors :   D. R. Tomchick, N. M. Alto, A. S. Selyunin

Date :   21 Oct 10 (Deposition) - 05 Jan 11 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A,B

Keywords :   Bacterial Effector, Small G Protein, Small Gtp-Binding Protein, Arf, Adp-Ribosylation Factor 6, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. S. Selyunin, S. E. Sutton, B. A. Weigele, L. E. Reddick, R. C. Orchard S. M. Bresson, D. R. Tomchick, N. M. Alto
The Assembly Of A Gtpase-Kinase Signalling Complex By A Bacterial Catalytic Scaffold.
Nature V. 469 107 2011
PubMed-ID: 21170023 | Reference-DOI: 10.1038/NATURE09593

Molecule 1 - ESPG
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PPRO-EX-HTB
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 42-398
	Gene	:	ECS4590, ESPG, Z5142
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83334
	Synonym	:	ESPG PROTEIN

Molecule 2 - ADP-RIBOSYLATION FACTOR 6
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PPRO-EX-HTB
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 14-175
	Gene	:	ARF6
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 15)

No.	Name	Count	Type	Full Name
1	GTP	1	Ligand/Ion	GUANOSINE-5'-TRIPHOSPHATE
2	MG	1	Ligand/Ion	MAGNESIUM ION
3	MSE	13	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP B:22 , ALA B:23 , ALA B:24 , GLY B:25 , LYS B:26 , THR B:27 , THR B:28 , THR B:41 , THR B:44 , GLY B:65 , GLY B:66 , GLN B:67 , ASN B:122 , LYS B:123 , ASP B:125 , LEU B:126 , CYS B:155 , ALA B:156 , HOH B:189 , HOH B:192 , HOH B:197 , MG B:1231	BINDING SITE FOR RESIDUE GTP B 1230
2	AC2	SOFTWARE	THR B:27 , THR B:44 , ASP B:63 , HOH B:197 , GTP B:1230	BINDING SITE FOR RESIDUE MG B 1231

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

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

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

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

Asymmetric/Biological Unit (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000298316	1	ENSE00001093805	chr14:50359810-50359875	66	ARF6_HUMAN	-	0	0	-	-
1.2	ENST00000298316	2	ENSE00001093803	chr14:50359974-50361490	1517	ARF6_HUMAN	1-336	336	1	B:14-173	160

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:349
 aligned with Q7DB50_ECO57 | Q7DB50 from UniProtKB/TrEMBL  Length:398

    Alignment length:349
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386         
         Q7DB50_ECO57    47 EMSCAEKLFKVLSFGLWNPTYSRSERQSFQELLTVLEPVYPLPNELGRVSARFSDGSSLRISVTNSELVEAEIRTANNEKITVLLESNEQNRLLQSLPIDRHMPYIQVHRALSEMDLTDTTSMRNLLGFTSKLSTTLIPHNAQTDPLSGPTPFSSIFMDTCRGLGNAKLSLNGVDIPANAQKLLRDALGLKDTHSSPTRNVIDHGISRHDAEQIARESSGSDKQKAEVVEFLCHPEAATAICSAFYQSFNVPALTLTHERISKASEYNAERSLDTPNACINISISQSSDGNIYVTSHTGVLIMAPEDRPNEMGMLTNRTSYEVPQGVKCIIDEMVSALQPRYAASETYL 395
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains EspG-3pcrA01 A:47-395                                                                                                                                                                                                                                                                                                                                         Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh.......hhhhhhhhhhhh..eee.....eeeeeeee.....eeeeeee...eeeeeee.....eeeeee..............ee.....eeee........hhhhhhhhhhhhh...eee.................hhhhhhhhhh...eeee..eeehhhhhhhhhhhhh..........hhhhhh.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeeee.....eeeeeeeeeeee........eeeeeeeeeeee......hhhhhhhhh..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pcr A  47 EmSCAEKLFKVLSFGLWNPTYSRSERQSFQELLTVLEPVYPLPNELGRVSARFSDGSSLRISVTNSELVEAEIRTANNEKITVLLESNEQNRLLQSLPIDRHmPYIQVHRALSEmDLTDTTSmRNLLGFTSKLSTTLIPHNAQTDPLSGPTPFSSIFmDTCRGLGNAKLSLNGVDIPANAQKLLRDALGLKDTHSSPTRNVIDHGISRHDAEQIARESSGSDKQKAEVVEFLCHPEAATAICSAFYQSFNVPALTLTHERISKASEYNAERSLDTPNACINISISQSSDGNIYVTSHTGVLImAPEDRPNEmGmLTNRTSYEVPQGVKCIIDEmVSALQPRYAASETYL 395
                             |      56        66        76        86        96       106       116       126       136       146  |    156    |  166  |    176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346  |    356 | |   366       376   |   386         
                            48-MSE                                                                                              149-MSE     161-MSE 169-MSE                            204-MSE                                                                                                                                          349-MSE  358-MSE               380-MSE           
                                                                                                                                                                                                                                                                                                                                                   360-MSE

Chain B from PDB  Type:PROTEIN  Length:160
 aligned with ARF6_HUMAN | P62330 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:160
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173
           ARF6_HUMAN    14 MRILMLGLDAAGKTTILYKLKLGQSVTTIPTVGFNVETVTYKNVKFNVWDVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFANKQDLPDAMKPHEIQEKLGLTRIRDRNWYVQPSCATSGDGLYEGLTWLTSNY 173
               SCOP domains d3pcrb_ B: ADP-ribosylation factor                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Arf-3pcrB01 B:14-173                                                                                                                                             Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhh...........eeeeeee....eeeeeee.........hhhhhh....eeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeee........hhhhhhhhh.........eeeeee......hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.2  PDB: B:14-173 UniProt: 1-336 [INCOMPLETE]                                                                                                              Transcript 1
                 3pcr B  14 mRILmLGLDAAGKTTILYKLKLGQSVTTIPTVGFNVETVTYKNVKFNVWDVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREmRDAIILIFANKQDLPDAmKPHEIQEKLGLTRIRDRNWYVQPSCATSGDGLYEGLTWLTSNY 173
                            |   |   23        33        43        53        63        73        83        93       103       113       123      |133       143       153       163       173
                            |   |                                                                                           112-MSE           130-MSE                                       
                           14-MSE                                                                                                                                                           
                               18-MSE

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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)

Human (Homo sapiens), ARF1 [TaxId: 9606] (12)

d3pcrb_

(no "CATH Domain" information available for 3PCR)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: Arf (26)

Homo sapiens (Human) (9)

Arf-3pcrB01

B:14-173

Clan: no clan defined [family: EspG] (3)

Family: EspG (3)

Escherichia coli O157:H7 (2)

EspG-3pcrA01

A:47-395

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (Q7DB50_ECO57 | Q7DB50)

molecular function
	GO:0004197	cysteine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
	GO:0008234	cysteine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
biological process
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Chain B (ARF6_HUMAN | P62330)

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:0047485	protein N-terminus binding	Interacting selectively and non-covalently with a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
	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).
	GO:0031996	thioesterase binding	Interacting selectively and non-covalently with any thioesterase enzyme.
biological process
	GO:0007155	cell adhesion	The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
	GO:0007049	cell cycle	The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
	GO:0030154	cell differentiation	The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
	GO:0051301	cell division	The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
	GO:0030866	cortical 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 actin-based cytoskeletal structures in the cell cortex, i.e. just beneath the plasma membrane.
	GO:0090162	establishment of epithelial cell polarity	The specification and formation of anisotropic intracellular organization of an epithelial cell.
	GO:0097284	hepatocyte apoptotic process	Any apoptotic process in a hepatocyte, the main structural component of the liver.
	GO:0001889	liver development	The process whose specific outcome is the progression of the liver over time, from its formation to the mature structure. The liver is an exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes.
	GO:0006928	movement of cell or subcellular component	The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore.
	GO:0033028	myeloid cell apoptotic process	Any apoptotic process in a myeloid cell, a cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage.
	GO:2000171	negative regulation of dendrite development	Any process that stops, prevents, or reduces the frequency, rate or extent of dendrite development.
	GO:0048261	negative regulation of receptor-mediated endocytosis	Any process that stops, prevents, or reduces the frequency, rate or extent of receptor mediated endocytosis, the uptake of external materials by cells, utilizing receptors to ensure specificity of transport.
	GO:0007399	nervous system development	The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
	GO:0030838	positive regulation of actin filament polymerization	Any process that activates or increases the frequency, rate or extent of actin polymerization.
	GO:0090004	positive regulation of establishment of protein localization to plasma membrane	Any process that increases the frequency, rate or extent of the directed movement of a protein to a specific location in the plasma membrane.
	GO:0034394	protein localization to cell surface	A process in which a protein is transported to, or maintained in, a location within the external part of the cell wall and/or plasma membrane.
	GO:0036010	protein localization to endosome	A process in which a protein is transported to, or maintained in, a location within an endosome.
	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:0035020	regulation of Rac protein signal transduction	Any process that modulates the frequency, rate or extent of Rac protein signal transduction.
	GO:0060998	regulation of dendritic spine development	Any process that modulates 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:0051489	regulation of filopodium assembly	Any process that modulates the frequency, rate or extent of the assembly of a filopodium, a thin, stiff protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal growth cone.
	GO:0031529	ruffle organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a ruffle, a projection at the leading edge of a crawling cell.
	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:0005938	cell cortex	The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.
	GO:0042995	cell projection	A prolongation or process extending from a cell, e.g. a flagellum or axon.
	GO:0032154	cleavage furrow	The cleavage furrow is a plasma membrane invagination at the cell division site. The cleavage furrow begins as a shallow groove and eventually deepens to divide the cytoplasm.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005769	early endosome	A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
	GO:0030139	endocytic vesicle	A membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance. Endocytic vesicles fuse with early endosomes to deliver the cargo for further sorting.
	GO:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	GO:0010008	endosome membrane	The lipid bilayer surrounding an endosome.
	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:0031527	filopodium membrane	The portion of the plasma membrane surrounding a filopodium.
	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:0030496	midbody	A thin cytoplasmic bridge formed between daughter cells at the end of cytokinesis. The midbody forms where the contractile ring constricts, and may persist for some time before finally breaking to complete cytokinesis.
	GO:0043209	myelin sheath	An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system.
	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: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:0055038	recycling endosome membrane	The lipid bilayer surrounding a recycling endosome.
	GO:0001726	ruffle	Projection at the leading edge of a crawling cell; the protrusions are supported by a microfilament meshwork.

Asymmetric/Biological Unit
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	3pcr
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UniProtKB/Swiss-Prot
	ARF6_HUMAN \| P62330	:	1e0s 2a5d 2a5f 2a5g 2bao 2bau 2j5x 2w83 3lvq 3lvr 3n5c 4fme 4kax
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	Q7DB50_ECO57 \| Q7DB50	:	3pcs 4fmc 4fmd 4fme

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 15)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (1, 1)

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Gene Ontology (58, 58)

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