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- PDB-5t7l: Pt(II)-mediated copper-dependent interactions between ATOX1 and MNK1 -

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Basic information

Entry
Database: PDB / ID: 5t7l
TitlePt(II)-mediated copper-dependent interactions between ATOX1 and MNK1
Components
  • Copper transport protein ATOX1
  • Copper-transporting ATPase 1
KeywordsTRANSPORT PROTEIN / Atox1-MNK1 / Pt-binding / heterodimer
Function / homology
Function and homology information


metallochaperone activity / 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 ...metallochaperone activity / 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 / copper chaperone activity / 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 / pyramidal neuron development / cellular response to lead ion / copper ion homeostasis / melanosome membrane / copper ion transport / serotonin metabolic process / catecholamine metabolic process / regulation of oxidative phosphorylation / detoxification of copper ion / 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 / skin development / cellular response to antibiotic / dopamine metabolic process / hair follicle morphogenesis / lung alveolus development / response to zinc ion / positive regulation of catalytic activity / central nervous system neuron development / cellular response to platelet-derived growth factor stimulus / 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 / removal of superoxide radicals / blood vessel remodeling / positive regulation of lamellipodium assembly / cellular response to copper ion / cellular response to cadmium ion / mitochondrion organization / lactation / extracellular matrix 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 / perikaryon / protein-folding chaperone binding / early endosome membrane / basolateral plasma membrane / response to oxidative stress / in utero embryonic development / postsynaptic density / neuron projection / copper ion binding / apical plasma membrane / axon / dendrite / neuronal cell body / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
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 transport protein ATOX1 / Copper-transporting ATPase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å
AuthorsCaliandro, R. / Mirabelli, V. / Caliandro, R. / Rosato, A. / Lasorsa, A. / Galliani, A. / Arnesano, F. / Natile, G.
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Mechanistic and Structural Basis for Inhibition of Copper Trafficking by Platinum Anticancer Drugs.
Authors: Lasorsa, A. / Nardella, M.I. / Rosato, A. / Mirabelli, V. / Caliandro, R. / Caliandro, R. / Natile, G. / Arnesano, F.
History
DepositionSep 5, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)16,2296
Polymers15,7122
Non-polymers5174
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-77 kcal/mol
Surface area7640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.617, 54.659, 63.719
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Copper transport protein ATOX1 / Metal transport protein ATX1


Mass: 7394.608 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATOX1, HAH1 / Production host: Escherichia coli (E. coli) / References: UniProt: O00244
#2: Protein Copper-transporting ATPase 1 / Copper pump 1 / Menkes disease-associated protein


Mass: 8317.440 Da / Num. of mol.: 1 / Fragment: UNP residues 7-77
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATP7A, MC1, MNK / Production host: Escherichia coli (E. coli) / References: UniProt: Q04656, EC: 3.6.3.54
#3: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Pt
#4: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: PEG-6000 10 to 30 % w/v and sodium citrate 0.1M at pH 4.7

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID23-111.0597
SYNCHROTRONDiamond I0220.9795
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M-F1PIXELApr 28, 2016
DECTRIS PILATUS 6M2PIXELJan 18, 2016
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.05971
20.97951
ReflectionResolution: 2.83→41.49 Å / Num. obs: 4184 / % possible obs: 98.1 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 7.58
Reflection shellResolution: 2.83→2.931 Å / Mean I/σ(I) obs: 2.41 / Num. unique all: 385 / % possible all: 92.77

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
Sir2014phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CJK

3cjk


Resolution: 2.83→41.486 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 0.15 / Phase error: 31.76
RfactorNum. reflection% reflection
Rfree0.2734 341 4.51 %
Rwork0.2002 --
obs0.2035 4184 98.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.83→41.486 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1093 0 4 13 1110
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091140
X-RAY DIFFRACTIONf_angle_d1.151544
X-RAY DIFFRACTIONf_dihedral_angle_d15.562697
X-RAY DIFFRACTIONf_chiral_restr0.064184
X-RAY DIFFRACTIONf_plane_restr0.006196
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8298-3.56490.36841740.24643579X-RAY DIFFRACTION98
3.5649-41.49090.23961670.18183634X-RAY DIFFRACTION99

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