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- PDB-2kmx: Solution structure of the nucleotide binding domain of the human ... -

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Basic information

Entry
Database: PDB / ID: 2kmx
TitleSolution structure of the nucleotide binding domain of the human Menkes protein in the ATP-bound form
ComponentsCopper-transporting ATPase 1
KeywordsHYDROLASE / ATP7A / Menkes / ATPase / nucleotide binding protein / Alternative splicing / ATP-binding / Cell membrane / Copper / Copper transport / Cytoplasm / Disease mutation / Endoplasmic reticulum / Glycoprotein / Golgi apparatus / Ion transport / Magnesium / Membrane / Metal-binding / Nucleotide-binding / Phosphoprotein / Polymorphism / Transmembrane / Transport
Function / homology
Function and homology information


peptidyl-lysine modification / epinephrine metabolic process / : / positive regulation of response to wounding / 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 ...peptidyl-lysine modification / epinephrine metabolic process / : / positive regulation of response to wounding / 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 / copper ion export / copper ion import / copper ion transmembrane transporter activity / P-type Cu+ transporter / P-type monovalent copper transporter activity / positive regulation of melanin biosynthetic process / cellular response to lead ion / superoxide dismutase copper chaperone activity / copper ion homeostasis / positive regulation of catalytic activity / copper ion transport / pyramidal neuron development / catecholamine metabolic process / serotonin metabolic process / trans-Golgi network transport vesicle / melanosome membrane / detoxification of copper ion / regulation of oxidative phosphorylation / norepinephrine metabolic process / T-helper cell differentiation / positive regulation of vascular associated smooth muscle cell migration / L-tryptophan metabolic process / collagen fibril organization / cartilage development / negative regulation of iron ion transmembrane transport / response to manganese ion / cellular response to antibiotic / hair follicle morphogenesis / pigmentation / response to zinc ion / skin development / lung alveolus development / cellular response to cadmium ion / Detoxification of Reactive Oxygen Species / blood vessel development / cell leading edge / central nervous system neuron development / dopamine metabolic process / cuprous ion binding / Ion transport by P-type ATPases / microvillus / blood vessel remodeling / intracellular copper ion homeostasis / positive regulation of cell size / positive regulation of lamellipodium assembly / cellular response to copper ion / cellular response to platelet-derived growth factor stimulus / lactation / extracellular matrix organization / removal of superoxide radicals / neuron projection morphogenesis / positive regulation of epithelial cell proliferation / liver development / secretory granule / trans-Golgi network membrane / mitochondrion organization / female pregnancy / cellular response to iron ion / locomotory behavior / cellular response to amino acid stimulus / trans-Golgi network / brush border membrane / small GTPase binding / phagocytic vesicle membrane / late endosome / protein-folding chaperone binding / early endosome membrane / basolateral plasma membrane / cellular response to hypoxia / 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 / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA ...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 / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Copper-transporting ATPase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsBanci, L. / Bertini, I. / Cantini, F. / Inagaki, S. / Migliardi, M. / Rosato, A.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: The binding mode of ATP revealed by the solution structure of the N-domain of human ATP7A.
Authors: Banci, L. / Bertini, I. / Cantini, F. / Inagaki, S. / Migliardi, M. / Rosato, A.
History
DepositionAug 5, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)20,7772
Polymers20,2701
Non-polymers5071
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500target function
RepresentativeModel #1fewest violations

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Components

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


Mass: 20269.803 Da / Num. of mol.: 1 / Fragment: nucleotide binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta2 / References: UniProt: Q04656, Cu2+-exporting ATPase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1312D 1H-1H TOCSY
1412D 1H-1H NOESY
1523D HNCO
1623D HNCA
1723D CBCA(CO)NH
1823D HN(CA)CB
1913D 1H-15N NOESY
11023D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM [U-99% 15N] ATPfree N-MNK-1, 90% H2O/10% D2O90% H2O/10% D2O
20.8 mM [U-95% 13C; U-95% 15N] ATPfree N-MNK-2, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMATPfree N-MNK-1[U-99% 15N]1
0.8 mMATPfree N-MNK-2[U-95% 13C; U-95% 15N]2
Sample conditionsIonic strength: phospate 0.05 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE7002
Bruker AvanceBrukerAVANCE9003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
CARAKeller and Wuthrichchemical shift assignment
XEASYBartels et al.data analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
Amber10Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, Kollmrefinement
PSVSBhattacharya and Montelionedata analysis
ProcheckNMRLaskowski and MacArthurdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 500 / Conformers submitted total number: 20 / Representative conformer: 1

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