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- PDB-6a71: Crystal Structure of Human ATP7B and TM Complex -

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Basic information

Entry
Database: PDB / ID: 6a71
TitleCrystal Structure of Human ATP7B and TM Complex
ComponentsATP7B protein
KeywordsMETAL TRANSPORT / Copper transporter protein
Function / homology
Function and homology information


P-type divalent copper transporter activity / copper ion transmembrane transporter activity / P-type Cu+ transporter / P-type monovalent copper transporter activity / copper ion import / copper ion export / : / copper ion transport / xenobiotic detoxification by transmembrane export across the plasma membrane / intracellular zinc ion homeostasis ...P-type divalent copper transporter activity / copper ion transmembrane transporter activity / P-type Cu+ transporter / P-type monovalent copper transporter activity / copper ion import / copper ion export / : / copper ion transport / xenobiotic detoxification by transmembrane export across the plasma membrane / intracellular zinc ion homeostasis / response to copper ion / Ion transport by P-type ATPases / intracellular copper ion homeostasis / lactation / trans-Golgi network membrane / protein maturation / establishment of localization in cell / late endosome / monoatomic ion transmembrane transport / Golgi membrane / copper ion binding / viral translational frameshifting / Golgi apparatus / ATP hydrolysis activity / mitochondrion / 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 ...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 / P-type ATPase actuator domain / 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
dioxo(di-mu-sulfide)dimolybdenum / DI(HYDROXYETHYL)ETHER / Copper-transporting ATPase 2 / Copper-transporting ATPase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsChen, W.B.
Funding support China, 1items
OrganizationGrant numberCountry
China
CitationJournal: Nat Commun / Year: 2019
Title: Tetrathiomolybdate induces dimerization of the metal-binding domain of ATPase and inhibits platination of the protein.
Authors: Fang, T. / Chen, W. / Sheng, Y. / Yuan, S. / Tang, Q. / Li, G. / Huang, G. / Su, J. / Zhang, X. / Zang, J. / Liu, Y.
History
DepositionJun 30, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP7B protein
B: ATP7B protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3416
Polymers14,8112
Non-polymers5304
Water3,837213
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.267, 87.740, 78.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-211-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ATP7B protein


Mass: 7405.412 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATP7B / Production host: Escherichia coli (E. coli) / References: UniProt: B7ZLR3, UniProt: P35670*PLUS

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Non-polymers , 5 types, 217 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-9UX / dioxo(di-mu-sulfide)dimolybdenum


Mass: 292.041 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4Mo2O2S2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.71 Å3/Da / Density % sol: 54.54 %
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20%PEG8000,0.1M MES pH6.0,0.2M Ca(OAc)2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.37906 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.37906 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 20975 / % possible obs: 97.8 % / Redundancy: 8 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 24.4
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.292 / Num. unique obs: 3284

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CJK

3cjk


Resolution: 1.6→43.87 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.505 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19537 1029 4.9 %RANDOM
Rwork0.16521 ---
obs0.16676 19928 97.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.334 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å20 Å2
2--0.17 Å20 Å2
3----0.75 Å2
Refinement stepCycle: 1 / Resolution: 1.6→43.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1017 0 20 219 1256
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191137
X-RAY DIFFRACTIONr_bond_other_d0.0030.021080
X-RAY DIFFRACTIONr_angle_refined_deg1.6221.9761561
X-RAY DIFFRACTIONr_angle_other_deg1.00432518
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4815166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.21127.14335
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.41815190
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.831152
X-RAY DIFFRACTIONr_chiral_restr0.0920.2200
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021334
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02212
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7882.04629
X-RAY DIFFRACTIONr_mcbond_other1.7732.038628
X-RAY DIFFRACTIONr_mcangle_it2.5143.041802
X-RAY DIFFRACTIONr_mcangle_other2.5123.044803
X-RAY DIFFRACTIONr_scbond_it3.1462.391508
X-RAY DIFFRACTIONr_scbond_other3.1122.391508
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6123.445758
X-RAY DIFFRACTIONr_long_range_B_refined8.75919.511460
X-RAY DIFFRACTIONr_long_range_B_other8.77819.5451454
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 54 -
Rwork0.26 1176 -
obs--80.6 %

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