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- PDB-2lqb: Metal binding repeat 2 of the Wilson disease protein (ATP7B) -

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Basic information

Entry
Database: PDB / ID: 2lqb
TitleMetal binding repeat 2 of the Wilson disease protein (ATP7B)
ComponentsCopper-transporting ATPase 2
KeywordsHYDROLASE / copper binding
Function / homology
Function and homology information


protein maturation by copper ion transfer / P-type divalent copper transporter activity / copper ion export / copper ion transmembrane transporter activity / copper ion import / P-type Cu+ transporter / P-type monovalent copper transporter activity / sequestering of calcium ion / copper ion transport / xenobiotic detoxification by transmembrane export across the plasma membrane ...protein maturation by copper ion transfer / P-type divalent copper transporter activity / copper ion export / copper ion transmembrane transporter activity / copper ion import / P-type Cu+ transporter / P-type monovalent copper transporter activity / sequestering of calcium ion / 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 / lactation / trans-Golgi network membrane / establishment of localization in cell / late endosome / monoatomic ion transmembrane transport / copper ion binding / viral translational frameshifting / 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 / torsion angle dynamics
Model detailsclosest to the average, model 1
AuthorsNokhrin, S. / Dolgova, N.V. / Yu, C. / Dmitriev, O.Y.
CitationJournal: Biochem.J. / Year: 2013
Title: Copper chaperone Atox1 interacts with the metal-binding domain of Wilson's disease protein in cisplatin detoxification.
Authors: Dolgova, N.V. / Nokhrin, S. / Yu, C.H. / George, G.N. / Dmitriev, O.Y.
History
DepositionFeb 28, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Aug 14, 2013Group: Database references
Revision 1.3Jun 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 1.4May 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

Downloads & links

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Assembly

Deposited unit
A: Copper-transporting ATPase 2


Theoretical massNumber of molelcules
Total (without water)8,4281
Polymers8,4281
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 / 100target function
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: 8427.712 Da / Num. of mol.: 1 / Fragment: HMA 2 domain residues 141-212
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
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HNCA
1413D HN(CA)CB
1513D HN(COCA)CB
1613D C(CO)NH
1713D H(CCO)NH
1813D 1H-15N TOCSY
1913D 1H-15N NOESY
11013D 1H-13C NOESY
11113D HN(CA)CO

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Sample preparation

DetailsContents: 50 mM [U-2H] Tris-Cl, 0.5 mM DSS, 0.05 mM sodium azide, 5 % [U-2H] D2O, 5 mM TCEP (tris(2-carboxyethyl)phosphine), 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMTris-Cl-1[U-2H]1
0.5 mMDSS-21
0.05 mMsodium azide-31
5 %D2O-4[U-2H]1
5 mMTCEP (tris(2-carboxyethyl)phosphine)-51
Sample conditionsIonic strength: 50 / pH: 7.4 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
CARA1.9.0F. Damberger, R. Kellerchemical shift assignment
FelixAccelrys Software Inc.processing
FelixAccelrys Software Inc.peak picking
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 894 / NOE intraresidue total count: 253 / NOE long range total count: 227 / NOE medium range total count: 145 / NOE sequential total count: 269 / Protein phi angle constraints total count: 66 / Protein psi angle constraints total count: 66
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum upper distance constraint violation: 0.56 Å
NMR ensemble rmsDistance rms dev: 0.37 Å / Distance rms dev error: 0.12 Å

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