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- PDB-1y3j: Solution structure of the copper(I) form of the fifth domain of M... -

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Basic information

Entry
Database: PDB / ID: 1y3j
TitleSolution structure of the copper(I) form of the fifth domain of Menkes protein
ComponentsCopper-transporting ATPase 1
KeywordsHYDROLASE / ferrodoxin-like fold / beta-alpha-beta-beta-alpha-beta structure / Structural Proteomics in Europe / SPINE / Structural Genomics
Function / homology
Function and homology information


epinephrine metabolic process / negative regulation of catecholamine metabolic process / L-tryptophan metabolic process / Ion influx/efflux at host-pathogen interface / copper-dependent protein binding / cerebellar Purkinje cell differentiation / elastic fiber assembly / tyrosine metabolic process / norepinephrine biosynthetic process / P-type divalent copper transporter activity ...epinephrine metabolic process / negative regulation of catecholamine metabolic process / L-tryptophan metabolic process / Ion influx/efflux at host-pathogen interface / copper-dependent protein binding / cerebellar Purkinje cell differentiation / elastic fiber assembly / tyrosine metabolic process / norepinephrine biosynthetic process / P-type divalent copper transporter activity / copper ion import / glycoprotein biosynthetic process / copper ion transmembrane transporter activity / P-type Cu+ transporter / P-type monovalent copper transporter activity / copper ion export / positive regulation of melanin biosynthetic process / superoxide dismutase copper chaperone activity / regulation of oxidative phosphorylation / catecholamine metabolic process / copper ion transport / serotonin metabolic process / trans-Golgi network transport vesicle / melanosome membrane / detoxification of copper ion / pyramidal neuron development / norepinephrine metabolic process / T-helper cell differentiation / cartilage development / collagen fibril organization / lung alveolus development / hair follicle morphogenesis / skin development / dendrite morphogenesis / pigmentation / Detoxification of Reactive Oxygen Species / blood vessel development / central nervous system neuron development / dopamine metabolic process / cuprous ion binding / Ion transport by P-type ATPases / blood vessel remodeling / intracellular copper ion homeostasis / ATP metabolic process / extracellular matrix organization / removal of superoxide radicals / release of cytochrome c from mitochondria / neuron projection morphogenesis / trans-Golgi network membrane / mitochondrion organization / locomotory behavior / trans-Golgi network / establishment of localization in cell / neuron cellular homeostasis / phagocytic vesicle membrane / late endosome / regulation of gene expression / early endosome membrane / neuron apoptotic process / basolateral plasma membrane / negative regulation of neuron apoptotic process / neuron projection / postsynaptic density / copper ion binding / axon / neuronal cell body / dendrite / perinuclear region of cytoplasm / endoplasmic reticulum / Golgi apparatus / 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 (II) ION / Copper-transporting ATPase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsBanci, L. / Chasapis, C.T. / Ciofi-Baffoni, S. / Hadjiliadis, N. / Rosato, A. / Structural Proteomics in Europe (SPINE)
CitationJournal: Febs J. / Year: 2005
Title: An NMR study of the interaction between the human copper(I) chaperone and the second and fifth metal-binding domains of the Menkes protein
Authors: Banci, L. / Bertini, I. / Ciofi-Baffoni, S. / Chasapis, C.T. / Hadjiliadis, N. / Rosato, A.
History
DepositionNov 25, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 8, 2005Provider: 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_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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)8,5492
Polymers8,4861
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)20 / 200target function
RepresentativeModel #1fewest violations

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Components

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


Mass: 8485.839 Da / Num. of mol.: 1 / Fragment: fifth domain of the menkes protein
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)pLys / References: UniProt: Q04656, Cu2+-exporting ATPase
#2: Chemical ChemComp-CU / COPPER (II) 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 13C-separated NOESY
1213D 15N-separated NOESY
131HNHA
141CBCANH
151CBCA(CO)NH
161(H)CCH-TOCSY
171HNCO
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 1mM MNK5 domain U-15N,13C; 50mM phosphate buffer NA
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 50mM sodium phosphate / 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 AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE9002
Bruker AVANCEBrukerAVANCE6003

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Processing

NMR software
NameVersionClassification
XwinNMR3.1collection
NEASYdata analysis
DYANAstructure solution
Amber5refinement
XwinNMR3.1processing
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on NOE-derived distance constraints and dihedral angle restraints.
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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