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Theoretical Model (Jmol Viewer)

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Title :   HADDOCK MODEL OF THE COMPLEX BETWEEN THE COPPER CHAPERONE ATX1 AND THE ATPASE CCC2 FROM YEAST

Authors :   F. Arnesano, L. Banci, I. Bertini, A. M. J. J. Bonvin

Date :   13 Jan 04 (Deposition) - 08 Apr 04 (Release) - 08 Apr 04 (Revision)

Method :   THEORETICAL MODEL

Resolution :   NOT APPLICABLE

Chains :   Theor. Model : A,B  (10x)

Keywords :   Copper Chaperone, P-Type Atpase, Copper Transport, Ferredoxin-Like Fold, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Arnesano, L. Banci, I. Bertini, A. Bonvin
A Docking Approach To The Study Of Copper Trafficking Proteins; Interaction Between Metallochaperones And Soluble Domains Of Copper Atpases
Structure V. 12 669 2004
PubMed: search
(for further references see the PDB file header)

Molecule 1 - METAL HOMEOSTASIS FACTOR ATX1
	Chains	:	A
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE

Molecule 2 - PROBABLE COPPER-TRANSPORTING ATPASE
	Chains	:	B
	EC Number	:	3.6.3.4
	Fragment	:	FIRST SOLUBLE COPPER BINDING DOMAIN OF THE ATPASE CCC2, RESIDUES 1-72
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Synonym	:	CU(2+)-ATPASE


Theoretical Model (10x)	:

Summary Information (see also Sequences/Alignments below)

Theoretical Model (1, 1)

No.	Name	Count	Type	Full Name
1	CU1	1	Ligand/Ion	COPPER (I) ION

Theoretical Model (1, 1)

No.	Name	Evidence	Residues	Description
1	CU	not defined	CYS B:13 , CYS B:16	MODEL OBTAINED STARTING FROM CU(I) BOUND TO ATX1

(no "SS Bond" information available for 1UV2)

(no "Cis Peptide Bond" information available for 1UV2)

(no "SAP(SNP)/Variant" information available for 1UV2)

Theoretical Model (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HMA_2	PS50846	Heavy-metal-associated domain profile.	ATU2_YEAST	3-68 81-147	1	B:3-68 -
1	HMA_2	PS50846	Heavy-metal-associated domain profile.	ATX1_YEAST	13-69	1	A:13-69
2	HMA_1	PS01047	Heavy-metal-associated domain.	ATU2_YEAST	8-37 86-115	1	B:8-37 -
2	HMA_1	PS01047	Heavy-metal-associated domain.	ATX1_YEAST	10-40	1	A:10-40

Theoretical Model (2, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YDR270W	1	YDR270W.1	IV:1005672-1008686	3015	ATU2_YEAST	1-1004	1004	1	B:1-72	72

2.1	YNL259C	1	YNL259C.1	XIV:157866-157645	222	ATX1_YEAST	1-73	73	1	A:1-73	73

Theoretical Model

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:73
 aligned with ATX1_YEAST | P38636 from UniProtKB/Swiss-Prot  Length:73

    Alignment length:73
                                    10        20        30        40        50        60        70   
            ATX1_YEAST    1 MAEIKHYQFNVVMTCSGCSGAVNKVLTKLEPDVSKIDISLEKQLVDVYTTLPYDFILEKIKKTGKEVRSGKQL 73
               SCOP domains ------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee........hhhhhhhhhhh..eeeeee.....eeeeee..hhhhhhhhhhhh...eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ---------HMA_1  PDB: A:10-40            --------------------------------- PROSITE (3)
                PROSITE (4) ------------HMA_2  PDB: A:13-69 UniProt: 13-69                       ---- PROSITE (4)
               Transcript 2 Exon 2.1  PDB: A:1-73 UniProt: 1-73                                       Transcript 2
                  1uv2 A  1 MAEIKHYQFNVVMTCSGCSGAVNKVLTKLEPDVSKIDISLEKQLVDVYTTLPYDFILEKIKKTGKEVRSGKQL 73
                                    10        20        30        40        50        60        70

Chain B from PDB  Type:PROTEIN  Length:72
 aligned with ATU2_YEAST | P38995 from UniProtKB/Swiss-Prot  Length:1004

    Alignment length:72
                                    10        20        30        40        50        60        70  
            ATU2_YEAST    1 MREVILAVHGMTCSACTNTINTQLRALKGVTKCDISLVTNECQVTYDNEVTADSIKEIIEDCGFDCEILRDS 72
               SCOP domains ------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee........hhhhhhhh......eeeeeee....eeeeee....hhhhhhhhhhh.....eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --HMA_2  PDB: B:3-68 UniProt: 3-68                                  ---- PROSITE (1)
                PROSITE (2) -------HMA_1  PDB: B:8-37            ----------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: B:1-72 UniProt: 1-1004 [INCOMPLETE]                       Transcript 1
                  1uv2 B  1 AREVILAVHGMTCSACTNTINTQLRALKGVTKCDISLVTNECQVTYDNEVTADSIKEIIEDCGFDCEILRDS 72
                                    10        20        30        40        50        60        70

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 '\|'

(no "SCOP Domain" information available for 1UV2)

(no "CATH Domain" information available for 1UV2)

(no "Pfam Domain" information available for 1UV2)

Theoretical Model(hide GO term definitions)

Chain A (ATX1_YEAST | P38636)

molecular function
	GO:0016531	copper chaperone activity	Assists in the delivery of copper ions to target proteins or compartments.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
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:0006879	cellular iron ion homeostasis	Any process involved in the maintenance of an internal steady state of iron ions at the level of a cell.
	GO:0034599	cellular response to oxidative stress	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
	GO:0006825	copper ion transport	The directed movement of copper (Cu) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0015680	intracellular copper ion transport	The directed movement of copper (Cu) ions within a cell.
	GO:0006811	ion transport	The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0030001	metal ion transport	The directed movement of metal ions, any metal ion with an electric charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	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.
cellular component
	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.

Chain B (ATU2_YEAST | P38995)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0019829	cation-transporting ATPase activity	Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + cation(out) = ADP + phosphate + cation(in).
	GO:0005507	copper ion binding	Interacting selectively and non-covalently with copper (Cu) ions.
	GO:0043682	copper-transporting ATPase activity	Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + Cu2+ = ADP + phosphate + Cu2+, directly driving the transport of the copper ions across a membrane.
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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.
biological process
	GO:0006812	cation transport	The directed movement of cations, atoms or small molecules with a net positive charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006879	cellular iron ion homeostasis	Any process involved in the maintenance of an internal steady state of iron ions at the level of a cell.
	GO:0060003	copper ion export	The directed movement of copper ions out of a cell or organelle.
	GO:0006825	copper ion transport	The directed movement of copper (Cu) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006811	ion transport	The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0030001	metal ion transport	The directed movement of metal ions, any metal ion with an electric charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0055085	transmembrane transport	The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
	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.
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:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0005887	integral component of plasma membrane	The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0012510	trans-Golgi network transport vesicle membrane	The lipid bilayer surrounding a vesicle transporting substances between the trans-Golgi network and other parts of the cell.

Theoretical Model
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		CU	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1uv2)

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	1uv2
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	ATU2_YEAST \| P38995
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	ATX1_YEAST \| P38636
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	3.6.3.4
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	ATU2_YEAST \| P38995
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UniProtKB/Swiss-Prot
	ATU2_YEAST \| P38995	:	1fvq 1fvs 1uv1 2ggp
	ATX1_YEAST \| P38636	:	1cc7 1cc8 1fd8 1fes 1uv1 2ggp 3k7r

1cc7	CRYSTAL STRUCTURE OF THE ATX1 METALLOCHAPERONE PROTEIN
1cc8	CRYSTAL STRUCTURE OF THE ATX1 METALLOCHAPERONE PROTEIN
1fd8	SOLUTION STRUCTURE OF THE CU(I) FORM OF THE YEAST METALLOCHAPERONE, ATX1
1fes	SOLUTION STRUCTURE OF THE APO FORM OF THE YEAST METALLOCHAPERONE, ATX1
1fvq	SOLUTION STRUCTURE OF THE YEAST COPPER TRANSPORTER DOMAINCCC2A IN THE APO AND CU(I) LOADED STATES
1fvs	SOLUTION STRUCTURE OF THE YEAST COPPER TRANSPORTER DOMAINCCC2A IN THE APO AND CU(I) LOAD STATES
1uv1	HADDOCK MODEL OF THE COMPLEX BETWEEN THE COPPER CHAPERONE ATX1 AND THE ATPASE CCC2 FROM YEAST

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (2, 2)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (26, 32)

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