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- PDB-7lu8: Structure of the cryptic HMA domain of the human copper transport... -

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Basic information

Entry
Database: PDB / ID: 7lu8
TitleStructure of the cryptic HMA domain of the human copper transporter ATP7A
ComponentsCopper-transporting ATPase 1
KeywordsMETAL TRANSPORT / copper transport / heavy metal associated domain / ATP7A / membrane transporter
Function / homology
Function and homology information


peptidyl-lysine modification / epinephrine metabolic process / : / positive regulation of response to wounding / cellular response to cobalt ion / L-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 / : / positive regulation of response to wounding / cellular response to cobalt ion / L-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 / 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 / regulation of oxidative phosphorylation / positive regulation of catalytic activity / catecholamine metabolic process / copper ion transport / pyramidal neuron development / serotonin metabolic process / trans-Golgi network transport vesicle / melanosome membrane / detoxification of copper ion / norepinephrine metabolic process / T-helper cell differentiation / positive regulation of vascular associated smooth muscle cell migration / collagen fibril organization / negative regulation of iron ion transmembrane transport / response to manganese ion / cartilage development / 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 / dopamine metabolic process / central nervous system neuron development / 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 / secretory granule / liver development / positive regulation of epithelial cell proliferation / trans-Golgi network membrane / cellular response to iron ion / female pregnancy / mitochondrion organization / 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 / neuron projection / postsynaptic density / apical plasma membrane / 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 / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain ...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 / 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
Similarity search - Domain/homology
Copper-transporting ATPase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsLee, W. / Uhlemann, E.E. / Tonelli, M. / Dmitriev, O.Y.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2017-06822 Canada
CitationJournal: Biophys.J. / Year: 2021
Title: At sixes and sevens: cryptic domain in the metal binding chain of the human copper transporter ATP7A.
Authors: Uhlemann, E.E. / Lee, W. / Tonelli, M. / Dmitriev, O.Y.
History
DepositionFeb 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 10, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Copper-transporting ATPase 1


Theoretical massNumber of molelcules
Total (without water)8,3681
Polymers8,3681
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 2000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 8367.748 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATP7A, MC1, MNK / Plasmid: pTYB12 / Production host: Escherichia coli (E. coli) / Strain (production host): Arctic Express DE3 / References: UniProt: Q04656, P-type Cu+ transporter

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic32D 1H-15N HSQC
121isotropic33D HNCA
131isotropic33D HN(CA)CB
141isotropic33D 1H-15N NOESY
171isotropic33D CBCA(CO)NH

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Sample preparation

DetailsType: solution
Contents: 0.35 mM [U-13C; U-15N] HMA2A, 50 mM HEPES, 150 mM sodium chloride, 5 mM TCEP, 95% H2O/5% D2O
Label: 13C_15N_sample / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.35 mMHMA2A[U-13C; U-15N]1
50 mMHEPESnatural abundance1
150 mMsodium chloridenatural abundance1
5 mMTCEPnatural abundance1
Sample conditionsIonic strength: 210 mM / Ionic strength err: 10 / Label: 13C_15N_sample / pH: 7.4 / PH err: 0.02 / Pressure: 1 atm / Temperature: 298 K / Temperature err: 0.1

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III9001
Varian Uniform NMR SystemVarianUniform NMR System6002
Bruker AVANCE IIIBrukerAVANCE III6003

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Processing

NMR software
NameDeveloperClassification
VNMRVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
APESLeepeak picking
NMRFAM-SPARKYLee, Tonelli, Markleychemical shift assignment
I-PINELee, Bahrami, Dashti, Eghbalnia, Tonelli, Westler and Markleychemical shift assignment
CS-ROSETTAShen, Vernon, Baker and Baxstructure calculation
PONDEROSA-C/SLee, Stark, Markleystructure calculation
AUDANALee, Petit, Cornilescu, Stark, Markleydata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 5 / Details: torsion angle dynamics
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 2000 / Conformers submitted total number: 20

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