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- PDB-1kvj: Solution Structure of the Cu(I) bound form of the first heavy met... -

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Basic information

Entry
Database: PDB / ID: 1kvj
TitleSolution Structure of the Cu(I) bound form of the first heavy metal binding motif of the Menkes protein
ComponentsCopper-transporting ATPase 1
KeywordsHYDROLASE / Menkes / Cu-bound
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 / cellular response to lead ion / pyramidal neuron development / copper ion homeostasis / copper ion transport / melanosome membrane / serotonin metabolic process / catecholamine metabolic process / detoxification of copper ion / regulation of oxidative phosphorylation / 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 / cellular response to antibiotic / skin development / hair follicle morphogenesis / dopamine metabolic process / lung alveolus development / response to zinc ion / cellular response to platelet-derived growth factor stimulus / positive regulation of catalytic activity / central nervous system neuron development / 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 / blood vessel remodeling / positive regulation of lamellipodium assembly / cellular response to copper ion / cellular response to cadmium ion / lactation / removal of superoxide radicals / extracellular matrix organization / mitochondrion 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 / protein-folding chaperone binding / perikaryon / early endosome membrane / basolateral plasma membrane / 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
AuthorsDe Silva, T.M. / Veglia, G. / Opella, S.J.
CitationJournal: Proteins / Year: 2005
Title: Solution structures of the reduced and Cu(I) bound forms of the first metal binding sequence of ATP7A associated with Menkes disease.
Authors: DeSilva, T.M. / Veglia, G. / Opella, S.J.
History
DepositionJan 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 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)8,7552
Polymers8,6921
Non-polymers641
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the lowest energy
Representative

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Components

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


Mass: 8691.849 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-79
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pMal / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / 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

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Sample preparation

DetailsContents: 20 mM Na Acetate buffer, 10 mM DTT, 1 mM EDTA, 0.01% Na Azide, 1 mM Protein
Solvent system: H2O/D2O
Sample conditionspH: 6.5 / Pressure: 1 atm / Temperature: 295 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
UXNMRcollection
NMRCompassdata analysis
X-PLORBrungerrefinement
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10

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