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- PDB-1yjv: Solution structure of the Cu(I) form of the sixth soluble domain ... -

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Basic information

Entry
Database: PDB / ID: 1yjv
TitleSolution structure of the Cu(I) form of the sixth soluble domain of Menkes protein
ComponentsCopper-transporting ATPase 1
KeywordsHYDROLASE / metallochaperone / protein-protein interaction / copper(I) / metal homeostasis
Function / homology
Function and homology information


peptidyl-lysine modification / epinephrine metabolic process / elastin biosynthetic process / positive regulation of response to wounding / cellular response to cobalt ion / tryptophan metabolic process / 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 / cellular response to cobalt ion / tryptophan metabolic process / Ion influx/efflux at host-pathogen interface / positive regulation of tyrosinase activity / copper-dependent protein binding / cerebellar Purkinje cell differentiation / elastic fiber assembly / P-type divalent copper transporter activity / response to iron(III) ion / pyramidal neuron development / copper ion export / copper ion transmembrane transporter activity / copper ion import / P-type Cu+ transporter / P-type monovalent copper transporter activity / superoxide dismutase copper chaperone activity / positive regulation of melanin biosynthetic process / cellular response to lead ion / copper ion homeostasis / copper ion transport / catecholamine metabolic process / detoxification of copper ion / serotonin metabolic process / melanosome membrane / trans-Golgi network transport vesicle / regulation of oxidative phosphorylation / norepinephrine metabolic process / T-helper cell differentiation / response to manganese ion / positive regulation of catalytic activity / positive regulation of vascular associated smooth muscle cell migration / collagen fibril organization / cartilage development / negative regulation of iron ion transmembrane transport / cellular response to antibiotic / hair follicle morphogenesis / pigmentation / lung alveolus development / skin development / response to zinc ion / blood vessel development / Detoxification of Reactive Oxygen Species / cell leading edge / central nervous system neuron development / dopamine metabolic process / cellular response to platelet-derived growth factor stimulus / cuprous ion binding / Ion transport by P-type ATPases / microvillus / positive regulation of cell size / intracellular copper ion homeostasis / blood vessel remodeling / positive regulation of lamellipodium assembly / cellular response to copper ion / lactation / cellular response to cadmium ion / removal of superoxide radicals / extracellular matrix organization / positive regulation of epithelial cell proliferation / liver development / neuron projection morphogenesis / trans-Golgi network membrane / secretory granule / mitochondrion organization / female pregnancy / locomotory behavior / cellular response to iron ion / cellular response to amino acid stimulus / brush border membrane / trans-Golgi network / small GTPase binding / phagocytic vesicle membrane / late endosome / protein-folding chaperone binding / cellular response to hypoxia / early endosome membrane / basolateral plasma membrane / perikaryon / in utero embryonic development / postsynaptic density / neuron projection / apical plasma membrane / copper ion binding / axon / neuronal cell body / dendrite / 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. / Migliardi, M. / Rosato, A. / Wang, S.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: An atomic-level investigation of the disease-causing A629P mutant of the Menkes protein, ATP7A
Authors: Banci, L. / Bertini, I. / Cantini, F. / Migliardi, M. / Rosato, A. / Wang, S.
History
DepositionJan 15, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 3, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: 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_conn / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 29, 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 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2552
Polymers8,1921
Non-polymers641
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 300target function
RepresentativeModel #1lowest energy

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Components

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


Mass: 8191.593 Da / Num. of mol.: 1 / Fragment: Sixth soluble domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATP7A / Plasmid: pET20b+ / 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


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
1113D 15N-separated NOESY
222CBCANH; CBCA(CO)NH; HNCO; HN(CA)CO
3332D NOESY
3432D TOCSY
151HNHA

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8mM 15N labeled sample; 5mM DTT; 100mM phosphate buffer90% H2O/10% D2O
20.8mM 15N 13C labeled sample; 5mM DTT; 100mM phosphate buffer90% H2O/10% D2O
31.0mM unlabeled sample; 5mM DTT; 100mM phosphate buffer90% H2O/10% D2O
Sample conditionsIonic strength: 100mM phosphate buffer / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE9001
Bruker AVANCEBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMRcollection
CARA1.2Keller, Rochus (2004): the computer aided resonance tutorial ISBN 3-85600-112-3, first editiondata analysis
DYANA1.5structure solution
Amber5refinement
RefinementMethod: torsion angle dynamics, simulated annealing, restrained energy minimization
Software ordinal: 1
Details: the structures were based on a total of 1947 meaningful distance constraints, 81 dihedral angle restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 300 / Conformers submitted total number: 30

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