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- PDB-2k1r: The solution NMR structure of the complex between MNK1 and HAH1 m... -

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Basic information

Entry
Database: PDB / ID: 2k1r
TitleThe solution NMR structure of the complex between MNK1 and HAH1 mediated by Cu(I)
Components
  • Copper transport protein ATOX1
  • Copper-transporting ATPase 1
KeywordsHYDROLASE/CHAPERONE / MNK1 / HAH1 / protein-protein interaction / ATP7A / SPINE 2 / Structural Proteomics in Europe / Alternative splicing / ATP-binding / Copper / Copper transport / Cytoplasm / Disease mutation / Endoplasmic reticulum / Glycoprotein / Golgi apparatus / Hydrolase / Ion transport / Magnesium / Membrane / Metal-binding / Nucleotide-binding / Phosphoprotein / Polymorphism / Transmembrane / Transport / Chaperone / HYDROLASE-CHAPERONE COMPLEX / Structural Genomics
Function / homology
Function and homology information


peptidyl-lysine modification / epinephrine metabolic process / : / positive regulation of response to wounding / metallochaperone activity / 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 ...peptidyl-lysine modification / epinephrine metabolic process / : / positive regulation of response to wounding / metallochaperone activity / 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 / copper chaperone activity / 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 / response to oxidative stress / 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 / Alpha-Beta Plaits - #100 ...: / 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 transport protein ATOX1 / Copper-transporting ATPase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsBertini, I. / Banci, L.C. / Felli, I.C. / Pavelkova, A. / Rosato, A. / Structural Proteomics in Europe (SPINE)
CitationJournal: To be Published
Title: The solution structure of the copper(I)-mediated complex between the first soluble domain of the Menkes protein and the metallochaperone HAH1.
Authors: Bertini, I. / Banci, L.C. / Felli, I.C. / Pavelkova, A. / Rosato, A.
History
DepositionMar 14, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Copper-transporting ATPase 1
B: Copper transport protein ATOX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5253
Polymers15,4622
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 / 100structures with the least restraint violations
RepresentativeModel #20closest to the average

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Components

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


Mass: 8049.171 Da / Num. of mol.: 1 / Fragment: HMA 1 domain: Residues 5-77
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATP7A, MC1, MNK / Plasmid: pET20 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta pLysS(DE3) / References: UniProt: Q04656, Cu2+-exporting ATPase
#2: Protein Copper transport protein ATOX1 / Metal transport protein ATX1


Mass: 7412.646 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATOX1, HAH1 / Plasmid: pET20 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta pLysS(DE3) / References: UniProt: O00244
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1222D 1H-13C HSQC
1323D CBCA(CO)NH
1423D HNCO
1523D HN(CA)CB
1623D (H)CCH-TOCSY
1723D 1H-15N NOESY
1823D 1H-13C NOESY
2912D 1H-15N HSQC
21012D 1H-13C HSQC
21113D CBCA(CO)NH
21213D HNCO
21313D HN(CA)CB
21413D (H)CCH-TOCSY
21513D 1H-15N NOESY
21613D 1H-13C NOESY
117213C-edited,13C-edited,13C,15N-filtered NOESY
218113C-edited,13C-edited,13C,15N-filtered NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6 mM MNK1, 0.6 mM [U-100% 13C; U-100% 15N] HAH1, 0.6 mM COPPER(I) ION, 90% H2O/10% D2O90% H2O/10% D2O
20.6 mM [U-100% 13C; U-100% 15N] MNK1, 0.6 mM HAH1, 0.6 mM COPPER(I) ION, 90% H2O/10% D2O90% H2O/10% D2O
30.6 mM [U-100% 13C; U-100% 15N] MNK1, 1.0 mM HAH1, 1.0 mM COPPER(I) ION, 90% H2O/10% D2O90% H2O/10% D2O
41.0 mM MNK1, 0.6 mM [U-100% 13C; U-100% 15N] HAH1, 1.0 mM COPPER(I) ION, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMMNK11
0.6 mMHAH1[U-100% 13C; U-100% 15N]1
0.6 mMCOPPER(I) ION1
0.6 mMMNK1[U-100% 13C; U-100% 15N]2
0.6 mMHAH12
0.6 mMCOPPER(I) ION2
0.6 mMMNK1[U-100% 13C; U-100% 15N]3
1.0 mMHAH13
1.0 mMCOPPER(I) ION3
1.0 mMMNK14
0.6 mMHAH1[U-100% 13C; U-100% 15N]4
1.0 mMCOPPER(I) ION4
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
17ambient 298 K
27ambient 298 K
37ambient 298 K
47ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE4001
Bruker AvanceBrukerAVANCE5002
Bruker AvanceBrukerAVANCE6003
Bruker AvanceBrukerAVANCE7004
Bruker AvanceBrukerAVANCE8005
Bruker AvanceBrukerAVANCE9006

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, et.al, and Kollmrefinement
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.data analysis
XEASYBartels et al.peak picking
RefinementMethod: molecular dynamics / Software ordinal: 1 / Details: MD in explicit solvent
NMR constraintsNOE constraints total: 2206 / NOE intraresidue total count: 452 / NOE long range total count: 784 / NOE medium range total count: 413 / NOE sequential total count: 557 / Protein phi angle constraints total count: 91 / Protein psi angle constraints total count: 91
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20
NMR ensemble rmsDistance rms dev: 0.0088 Å / Distance rms dev error: 0.001 Å

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