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- PDB-2koy: Structure of the E1064A mutant of the N-domain of Wilson Disease ... -

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Basic information

Entry
Database: PDB / ID: 2koy
TitleStructure of the E1064A mutant of the N-domain of Wilson Disease Associated Protein
ComponentsCopper-transporting ATPase 2
KeywordsMETAL TRANSPORT / ATP7B / Wilson disease / ATPase / copper transport / ATP binding / ATP-binding / Disease mutation / Golgi apparatus / Hydrolase / Ion transport / Magnesium / Membrane / Metal-binding / Mitochondrion / Nucleotide-binding / Phosphoprotein / Transmembrane / Transport
Function / homology
Function and homology information


protein maturation by copper ion transfer / copper ion transmembrane transporter activity / P-type divalent copper transporter activity / P-type monovalent copper transporter activity / P-type Cu+ transporter / sequestering of calcium ion / copper ion export / copper ion import / copper ion transport / xenobiotic detoxification by transmembrane export across the plasma membrane ...protein maturation by copper ion transfer / copper ion transmembrane transporter activity / P-type divalent copper transporter activity / P-type monovalent copper transporter activity / P-type Cu+ transporter / sequestering of calcium ion / copper ion export / copper ion import / copper ion transport / xenobiotic detoxification by transmembrane export across the plasma membrane / intracellular zinc ion homeostasis / response to copper ion / Ion transport by P-type ATPases / intracellular copper ion homeostasis / monoatomic ion transmembrane transport / lactation / trans-Golgi network membrane / establishment of localization in cell / late endosome / copper ion binding / Golgi membrane / Golgi apparatus / ATP hydrolysis activity / mitochondrion / ATP binding / membrane / plasma membrane
Similarity search - Function
Heavy metal-associated domain, copper ion-binding / P-type ATPase, subfamily IB / Heavy-metal-associated, conserved site / Heavy-metal-associated domain. / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain ...Heavy metal-associated domain, copper ion-binding / P-type ATPase, subfamily IB / Heavy-metal-associated, conserved site / Heavy-metal-associated domain. / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Copper-transporting ATPase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailslowest energy, model 1
AuthorsDmitriev, O.Y.
CitationJournal: J. Biol. Chem. / Year: 2011
Title: Difference in stability of the N-domain underlies distinct intracellular properties of the E1064A and H1069Q mutants of copper-transporting ATPase ATP7B.
Authors: Dmitriev, O.Y. / Bhattacharjee, A. / Nokhrin, S. / Uhlemann, E.M. / Lutsenko, S.
History
DepositionOct 3, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Copper-transporting ATPase 2


Theoretical massNumber of molelcules
Total (without water)14,7521
Polymers14,7521
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Copper-transporting ATPase 2 / Copper pump 2 / Wilson disease-associated protein / WND/140 kDa


Mass: 14752.179 Da / Num. of mol.: 1 / Fragment: N-domain / Mutation: E1064A, deletion H1115-D1138
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATP7B, PWD, WC1, WND / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P35670, Cu2+-exporting ATPase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: The E1064A variant of the ATP7B N-domain (residues 1032-1196) modified to delete the disordered loop A1115-H1138
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HNCA
1413D HN(COCA)CB
1513D HN(CA)CB
1613D C(CO)NH
1713D H(CCO)NH
1813D 1H-15N TOCSY
1913D 1H-15N NOESY
11013D 1H-13C NOESY

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Sample preparation

DetailsContents: 50 mM sodium phosphate, 5 mM DTT, 0.3 mM DSS, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
50 mMsodium phosphate-11
5 mMDTT-21
0.3 mMDSS-31
Sample conditionsIonic strength: 0.1 / pH: 6.0 / Pressure: ambient atm / Temperature: 300 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
Felix2007Accelrys Software Inc.peak picking
TALOSCornilescu, Delaglio and Baxrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 20

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