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- PDB-7ddf: Crystal structures of Na+,K+-ATPase in complex with beryllium fluoride -

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Basic information

Entry
Database: PDB / ID: 7ddf
TitleCrystal structures of Na+,K+-ATPase in complex with beryllium fluoride
Components
  • (Sodium/potassium-transporting ATPase subunit ...) x 2
  • FXYD domain-containing ion transport regulator
KeywordsMEMBRANE PROTEIN / Na+ / K+-ATPase / ion transport / Cardiotonic steroids
Function / homology
Function and homology information


Ion homeostasis / Ion transport by P-type ATPases / regulation of monoatomic ion transport / Na+/K+-exchanging ATPase / ion channel regulator activity / positive regulation of sodium ion export across plasma membrane / positive regulation of potassium ion import across plasma membrane / sodium ion binding / P-type sodium:potassium-exchanging transporter activity / sodium:potassium-exchanging ATPase complex ...Ion homeostasis / Ion transport by P-type ATPases / regulation of monoatomic ion transport / Na+/K+-exchanging ATPase / ion channel regulator activity / positive regulation of sodium ion export across plasma membrane / positive regulation of potassium ion import across plasma membrane / sodium ion binding / P-type sodium:potassium-exchanging transporter activity / sodium:potassium-exchanging ATPase complex / regulation of calcium ion transmembrane transport / membrane repolarization / establishment or maintenance of transmembrane electrochemical gradient / sodium ion export across plasma membrane / positive regulation of potassium ion transmembrane transport / intracellular sodium ion homeostasis / relaxation of cardiac muscle / regulation of cardiac muscle contraction by calcium ion signaling / positive regulation of sodium ion transmembrane transport / regulation of sodium ion transport / ATPase activator activity / potassium ion binding / potassium ion import across plasma membrane / intracellular potassium ion homeostasis / intercalated disc / lateral plasma membrane / transporter activator activity / sperm flagellum / cardiac muscle contraction / ATP metabolic process / proton transmembrane transport / T-tubule / protein localization to plasma membrane / sarcolemma / transmembrane transport / intracellular calcium ion homeostasis / regulation of gene expression / melanosome / ATPase binding / basolateral plasma membrane / protein-macromolecule adaptor activity / protein stabilization / apical plasma membrane / axon / lysosomal membrane / protein kinase binding / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
: / Ion-transport regulator, FXYD motif / : / ATP1G1/PLM/MAT8 family / FXYD family signature. / Sodium and potassium ATPases beta subunits signature 2. / Sodium/potassium-transporting ATPase subunit beta / Sodium/potassium-transporting ATPase subunit beta superfamily / Sodium / potassium ATPase beta chain / Sodium and potassium ATPases beta subunits signature 1. ...: / Ion-transport regulator, FXYD motif / : / ATP1G1/PLM/MAT8 family / FXYD family signature. / Sodium and potassium ATPases beta subunits signature 2. / Sodium/potassium-transporting ATPase subunit beta / Sodium/potassium-transporting ATPase subunit beta superfamily / Sodium / potassium ATPase beta chain / Sodium and potassium ATPases beta subunits signature 1. / : / P-type ATPase subfamily IIC, subunit alpha / Cation-transporting P-type ATPase, C-terminal / Cation transporting ATPase, C-terminus / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / P-type ATPase, cytoplasmic domain N / : / 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 / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
BERYLLIUM TRIFLUORIDE ION / CHOLESTEROL / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Sodium/potassium-transporting ATPase subunit alpha-1 / Sodium/potassium-transporting ATPase subunit beta-1 / FXYD domain-containing ion transport regulator
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.62 Å
AuthorsOgawa, H. / Cornelius, F. / Kanai, R. / Motoyama, K. / Vilsen, B. / Toyoshima, C.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)16K18500 Japan
Japan Society for the Promotion of Science (JSPS)16H02499 Japan
Japan Society for the Promotion of Science (JSPS)19H00975 Japan
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Binding of cardiotonic steroids to Na + ,K + -ATPase in the E2P state.
Authors: Kanai, R. / Cornelius, F. / Ogawa, H. / Motoyama, K. / Vilsen, B. / Toyoshima, C.
History
DepositionOct 29, 2020Deposition site: PDBJ / Processing site: PDBJ
SupersessionJan 27, 2021ID: 6KPU
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.3Mar 12, 2025Group: Database references / Category: pdbx_database_related
Revision 2.0Aug 12, 2026Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Polymer sequence / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_poly / entity_poly_seq / pdbx_entity_nonpoly / pdbx_modification_feature / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_rmsd_bond / struct_asym / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _pdbx_modification_feature.auth_asym_id / _pdbx_modification_feature.auth_comp_id / _pdbx_modification_feature.auth_seq_id / _pdbx_modification_feature.category / _pdbx_modification_feature.comp_id_linking_atom / _pdbx_modification_feature.label_asym_id / _pdbx_modification_feature.label_comp_id / _pdbx_modification_feature.label_seq_id / _pdbx_modification_feature.modified_residue_auth_asym_id / _pdbx_modification_feature.modified_residue_auth_comp_id / _pdbx_modification_feature.modified_residue_auth_seq_id / _pdbx_modification_feature.modified_residue_id / _pdbx_modification_feature.modified_residue_id_linking_atom / _pdbx_modification_feature.modified_residue_label_asym_id / _pdbx_modification_feature.modified_residue_label_comp_id / _pdbx_modification_feature.modified_residue_label_seq_id / _pdbx_modification_feature.modified_residue_symmetry / _pdbx_modification_feature.ref_comp_id / _pdbx_modification_feature.ref_pcm_id / _pdbx_modification_feature.type / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id
Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sodium/potassium-transporting ATPase subunit alpha-1
B: Sodium/potassium-transporting ATPase subunit beta-1
G: FXYD domain-containing ion transport regulator
C: Sodium/potassium-transporting ATPase subunit alpha-1
D: Sodium/potassium-transporting ATPase subunit beta-1
E: FXYD domain-containing ion transport regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)320,27734
Polymers309,2456
Non-polymers11,03228
Water18010
1
A: Sodium/potassium-transporting ATPase subunit alpha-1
B: Sodium/potassium-transporting ATPase subunit beta-1
G: FXYD domain-containing ion transport regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,92618
Polymers154,6223
Non-polymers6,30315
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10730 Å2
ΔGint-68 kcal/mol
Surface area60380 Å2
MethodPISA
2
C: Sodium/potassium-transporting ATPase subunit alpha-1
D: Sodium/potassium-transporting ATPase subunit beta-1
E: FXYD domain-containing ion transport regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,35116
Polymers154,6223
Non-polymers4,72913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10040 Å2
ΔGint-61 kcal/mol
Surface area59290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.481, 118.371, 495.388
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain 'A'A21 - 1016
211chain 'C'C21 - 1016
112(chain 'B' and (resid 13 through 161 or resid 168 through 303 or resid 1001 through 1021))B13 - 160
122(chain 'B' and (resid 13 through 161 or resid 168 through 303 or resid 1001 through 1021))B168 - 303
132(chain 'B' and (resid 13 through 161 or resid 168 through 303 or resid 1001 through 1021))B1001 - 1002
142(chain 'B' and (resid 13 through 161 or resid 168 through 303 or resid 1001 through 1021))B1011 - 1012
152(chain 'B' and (resid 13 through 161 or resid 168 through 303 or resid 1001 through 1021))B1021
212chain 'D'D13 - 160
222chain 'D'D168 - 303
232chain 'D'D1001 - 1002
242chain 'D'D1011 - 1012
252chain 'D'D1021
113chain 'E'E17 - 48
213chain 'G'G17 - 48

NCS ensembles :
ID
1
2
3

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Components

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Sodium/potassium-transporting ATPase subunit ... , 2 types, 4 molecules ACBD

#1: Protein Sodium/potassium-transporting ATPase subunit alpha-1 / Na(+)/K(+) ATPase alpha-1 subunit / Sodium pump subunit alpha-1


Mass: 112323.961 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P05024, Na+/K+-exchanging ATPase
#2: Protein Sodium/potassium-transporting ATPase subunit beta-1 / Sodium/potassium-dependent ATPase subunit beta-1


Mass: 35204.402 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P05027

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Protein , 1 types, 2 molecules GE

#3: Protein FXYD domain-containing ion transport regulator / Na+/K+ ATPase gamma subunit transcript variant a


Mass: 7094.115 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q58K79

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Sugars , 2 types, 6 molecules

#4: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#10: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 32 molecules

#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Chemical
ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C27H46O
#8: Chemical
ChemComp-PCW / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / (Z,Z)-4-HYDROXY-N,N,N-TRIMETHYL-10-OXO-7-[(1-OXO-9-OCTADECENYL)OXY]-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-18-EN-1-AMINIUM-4-OXIDE


Mass: 787.121 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C44H85NO8P / Comment: DOPC, phospholipid*YM
#9: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 5.42 Å3/Da / Density % sol: 77.33 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 16% PEG 2000 MME, 10% GLYCEROL, 200mM MAGNESIUM CHLORIDE, 5mM GSH, 0.1mM DTT, 0.0001% BHT, 100mM MES-NMDG, PH 6.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 18, 2014
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.6→50 Å / Num. obs: 12110 / % possible obs: 31.8 % / Redundancy: 4.6 % / Biso Wilson estimate: 88.45 Å2 / Rmerge(I) obs: 0.161 / Net I/σ(I): 6.9
Reflection shellResolution: 4.6→5.27 Å / Rmerge(I) obs: 0.612 / Num. unique obs: 583

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.17.1_3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A3Y

3a3y


Resolution: 4.62→15.99 Å / SU ML: 0.4882 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.7358
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2415 470 4.52 %
Rwork0.1936 9925 -
obs0.1957 10395 28.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 143.08 Å2
Refinement stepCycle: LAST / Resolution: 4.62→15.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20692 0 490 10 21192
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00721622
X-RAY DIFFRACTIONf_angle_d1.020529346
X-RAY DIFFRACTIONf_chiral_restr0.05553338
X-RAY DIFFRACTIONf_plane_restr0.00766346
X-RAY DIFFRACTIONf_dihedral_angle_d15.82488106
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.62-5.270.2642170.2284566X-RAY DIFFRACTION4.81
5.27-6.560.311640.26741470X-RAY DIFFRACTION12.56
6.56-15.990.23483890.18477889X-RAY DIFFRACTION66.1

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