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- PDB-2ga7: Solution structure of the copper(I) form of the third metal-bindi... -

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Basic information

Entry
Database: PDB / ID: 2ga7
TitleSolution structure of the copper(I) form of the third metal-binding domain of ATP7A protein (menkes disease protein)
ComponentsCopper-transporting ATPase 1
KeywordsHYDROLASE / solution structure / Menkes disease-associated protein / copper(I) / Structural Genomics / Structural Proteomics in Europe / SPINE
Function / homology
Function and homology information


peptidyl-lysine modification / epinephrine metabolic process / elastin biosynthetic process / positive regulation of response to wounding / tryptophan metabolic process / cellular response to cobalt ion / Ion influx/efflux at host-pathogen interface / positive regulation of tyrosinase activity / copper-dependent protein binding / cerebellar Purkinje cell differentiation ...peptidyl-lysine modification / epinephrine metabolic process / elastin biosynthetic process / positive regulation of response to wounding / tryptophan metabolic process / cellular response to cobalt ion / Ion influx/efflux at host-pathogen interface / positive regulation of tyrosinase activity / copper-dependent protein binding / cerebellar Purkinje cell differentiation / elastic fiber assembly / response to iron(III) ion / P-type divalent copper transporter activity / P-type monovalent copper transporter activity / P-type Cu+ transporter / copper ion export / copper ion import / copper ion transmembrane transporter activity / positive regulation of melanin biosynthetic process / superoxide dismutase copper chaperone activity / pyramidal neuron development / cellular response to lead ion / copper ion homeostasis / melanosome membrane / copper ion transport / serotonin metabolic process / catecholamine metabolic process / regulation of oxidative phosphorylation / detoxification of copper ion / trans-Golgi network transport vesicle / norepinephrine metabolic process / T-helper cell differentiation / positive regulation of vascular associated smooth muscle cell migration / collagen fibril organization / cartilage development / response to manganese ion / negative regulation of iron ion transmembrane transport / pigmentation / skin development / cellular response to antibiotic / dopamine metabolic process / hair follicle morphogenesis / lung alveolus development / response to zinc ion / positive regulation of catalytic activity / central nervous system neuron development / cellular response to platelet-derived growth factor stimulus / blood vessel development / Detoxification of Reactive Oxygen Species / cuprous ion binding / cell leading edge / microvillus / Ion transport by P-type ATPases / intracellular copper ion homeostasis / positive regulation of cell size / removal of superoxide radicals / blood vessel remodeling / positive regulation of lamellipodium assembly / cellular response to copper ion / cellular response to cadmium ion / mitochondrion organization / lactation / extracellular matrix organization / neuron projection morphogenesis / trans-Golgi network membrane / locomotory behavior / liver development / secretory granule / female pregnancy / positive regulation of epithelial cell proliferation / brush border membrane / cellular response to amino acid stimulus / trans-Golgi network / cellular response to iron ion / small GTPase binding / phagocytic vesicle membrane / late endosome / cellular response to hypoxia / perikaryon / protein-folding chaperone binding / early endosome membrane / basolateral plasma membrane / in utero embryonic development / postsynaptic density / neuron projection / copper ion binding / apical plasma membrane / axon / dendrite / neuronal cell body / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / membrane / plasma membrane / cytosol
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 (I) ION / Copper-transporting ATPase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Torsion angle dynamics, simulated annealing, restrained energy minimization
AuthorsBanci, L. / Bertini, I. / Cantini, F. / DellaMalva, N. / Rosato, A. / Herrmann, T. / Wuthrich, K. / Structural Proteomics in Europe (SPINE)
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Solution structure and intermolecular interactions of the third metal-binding domain of ATP7A, the Menkes disease protein.
Authors: Banci, L. / Bertini, I. / Cantini, F. / DellaMalva, N. / Herrmann, T. / Rosato, A. / Wuthrich, K.
History
DepositionMar 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Copper-transporting ATPase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9372
Polymers9,8731
Non-polymers641
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 300target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Copper-transporting ATPase 1 / Copper pump 1 / Menkes disease-associated protein


Mass: 9873.033 Da / Num. of mol.: 1 / Fragment: Third soluble domain, residues 275-352 / Mutation: K46V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATP7A, MC1, MNK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q04656, Cu2+-exporting ATPase
#2: Chemical ChemComp-CU1 / COPPER (I) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1323D 15N-separated NOESY
143CBCA(CO)NH
153CBCANH
163h(CCH)-TOCSY
1733D 13C-separated NOESY
18215N-HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM copper(I)MNK3 unlabelled sample, 100mM phosphate buffer, pH 7.0, 90% H2O, 10% D2O90% H2O/10% D2O
20.5mM copper(I)MNK3 15N labeled sample, 100mM phosphate buffer, pH 7.0, 90% H2O, 10% D2O90% H2O/10% D2O
30.5mM copper(I)MNK3 15N,13C labeled sample, 100mM phosphate buffer, pH 7.0, 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 100mM phosphate buffer / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker AVANCEBrukerAVANCE7002
Bruker AVANCEBrukerAVANCE8003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR1.3collection
XEASY1.3data analysis
CARA1.5data analysis
CYANA2.1Guntert, P. et al.structure solution
Amber8Case, D.A. et al.refinement
RefinementMethod: Torsion angle dynamics, simulated annealing, restrained energy minimization
Software ordinal: 1
Details: 1011 meaningful proton-proton distance restraints, 143 dihedral angles restraints were used for structure calculations
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 300 / Conformers submitted total number: 30

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