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- PDB-2n7y: NMR structure of metal-binding domain 1 of ATP7B -

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Basic information

Entry
Database: PDB / ID: 2n7y
TitleNMR structure of metal-binding domain 1 of ATP7B
ComponentsCopper-transporting ATPase 2
KeywordsMETAL BINDING PROTEIN / copper binding / hydrolase
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 / Alpha-Beta Plaits - #100 / E1-E2 ATPase ...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 / Alpha-Beta Plaits - #100 / 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 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Copper-transporting ATPase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsYu, C. / Lee, W. / Dmitriev, O.
CitationJournal: Sci Rep / Year: 2018
Title: The Structure of Metal Binding Domain 1 of the Copper Transporter ATP7B Reveals Mechanism of a Singular Wilson Disease Mutation.
Authors: Yu, C.H. / Lee, W. / Nokhrin, S. / Dmitriev, O.Y.
History
DepositionSep 27, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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)8,1221
Polymers8,1221
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 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

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


Mass: 8122.464 Da / Num. of mol.: 1 / Fragment: Metal binding domain (UNP residues 56-127)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATP7B, PWD, WC1, WND / Plasmid: pTYB12 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P35670

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HNCA
1413D HN(CA)CB
1513D HN(COCA)CB
1613D HN(CA)CO
1713D C(CO)NH
1813D H(CCO)NH
1913D 1H-15N TOCSY
11013D 1H-15N NOESY
11113D 1H-13C NOESY

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Sample preparation

DetailsContents: 50 mM HEPES, 0.5 mM DSS, 5 mM TCEP, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
50 mMHEPES-11
0.5 mMDSS-21
5 mMTCEP-31
Sample conditionsIonic strength: 50 / pH: 7.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 750 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CARAKeller and Wuthrichchemical shift assignment
PONDEROSA-C/SLee and Markleypeak picking
PONDEROSA-C/SLee and Markleystructure solution
PONDEROSA-C/SLee and Markleyrefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: EXPLICIT WATER REFINEMENT
NMR constraintsNOE constraints total: 628 / NOE intraresidue total count: 305 / NOE long range total count: 91 / NOE medium range total count: 49 / NOE sequential total count: 143 / Protein phi angle constraints total count: 54 / Protein psi angle constraints total count: 65
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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