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- PDB-7d93: Crystal Structure of the Na+,K+-ATPase in the E2P state with boun... -

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Basic information

Entry
Database: PDB / ID: 7d93
TitleCrystal Structure of the Na+,K+-ATPase in the E2P state with bound Mg2+ and anthroylouabain (P2(1)2(1)2(1) symmetry)
Components
  • (Sodium/potassium-transporting ATPase subunit ...) x 2
  • FXYD domain-containing ion transport regulator
KeywordsTRANSPORT PROTEIN / Na+ / K+-ATPase / membrane protein / ion transport / Cardiotonic steroids
Function / homology
Function and homology information


Basigin interactions / Ion homeostasis / Na+/K+-exchanging ATPase / positive regulation of sodium ion export across plasma membrane / positive regulation of potassium ion import across plasma membrane / regulation of monoatomic ion transport / Ion transport by P-type ATPases / transporter activator activity / P-type sodium:potassium-exchanging transporter activity / sodium ion binding ...Basigin interactions / Ion homeostasis / Na+/K+-exchanging ATPase / positive regulation of sodium ion export across plasma membrane / positive regulation of potassium ion import across plasma membrane / regulation of monoatomic ion transport / Ion transport by P-type ATPases / transporter activator activity / P-type sodium:potassium-exchanging transporter activity / sodium ion binding / sodium:potassium-exchanging ATPase complex / membrane repolarization / establishment or maintenance of transmembrane electrochemical gradient / sodium ion export across plasma membrane / positive regulation of potassium ion transmembrane transport / regulation of calcium ion transmembrane transport / intracellular sodium ion homeostasis / ion channel regulator activity / intracellular potassium ion homeostasis / regulation of cardiac muscle contraction by calcium ion signaling / relaxation of cardiac muscle / positive regulation of sodium ion transmembrane transport / organelle membrane / potassium ion import across plasma membrane / potassium ion binding / ATPase activator activity / sperm flagellum / intercalated disc / lateral plasma membrane / ATP metabolic process / regulation of sodium ion transport / cardiac muscle contraction / T-tubule / proton transmembrane transport / protein localization to plasma membrane / sarcolemma / transmembrane transport / intracellular calcium ion homeostasis / melanosome / ATPase binding / regulation of gene expression / protein-macromolecule adaptor activity / basolateral plasma membrane / cell adhesion / protein stabilization / apical plasma membrane / axon / innate immune response / 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/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/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. / Sodium and potassium ATPases beta subunits signature 2. / 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 / Cation transport ATPase (P-type) / 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
CHOLESTEROL / Chem-H0C / 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: 3.65 Å
AuthorsKanai, R. / Cornelius, F. / Ogawa, H. / Motoyama, K. / Vilsen, B. / Toyoshima, C.
Funding support Japan, Denmark, 7items
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
Danish Council for Independent ResearchDFF7016-00193B Denmark
Danish Council for Independent ResearchDFF4183-00011A Denmark
Novo Nordisk FoundationNNF13OC0013409 Denmark
Novo Nordisk FoundationNNF13OC0006555 Denmark
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 12, 2020Deposition site: PDBJ / Processing site: PDBJ
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

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


Theoretical massNumber of molelcules
Total (without water)323,85736
Polymers309,4056
Non-polymers14,45330
Water21612
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)161,72918
Polymers154,7023
Non-polymers7,02615
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10600 Å2
ΔGint-78 kcal/mol
Surface area59820 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)162,12918
Polymers154,7023
Non-polymers7,42715
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11380 Å2
ΔGint-68 kcal/mol
Surface area59070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.620, 117.890, 494.300
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
14
24

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain 'A'A21 - 1016
211chain 'C'C21 - 1016
112chain 'B'B13 - 303
122chain 'B'B1001 - 1002
132chain 'B'B1011 - 1012
142chain 'B'B1021
212chain 'D'D13 - 303
222chain 'D'D1001 - 1002
232chain 'D'D1011 - 1012
242chain 'D'D1021
113chain 'E'E17 - 48
213chain 'G'G17 - 48
114(chain 'H' and (resid 1106 through 1107 or resid 1203 through 3000))H1106 - 1107
124(chain 'H' and (resid 1106 through 1107 or resid 1203 through 3000))H1203 - 1205
134(chain 'H' and (resid 1106 through 1107 or resid 1203 through 3000))H1211
144(chain 'H' and (resid 1106 through 1107 or resid 1203 through 3000))H1215
154(chain 'H' and (resid 1106 through 1107 or resid 1203 through 3000))H3000
214(chain 'I' and (resid 1105 through 1106 or resid 1203 through 3000))I1105 - 1106
224(chain 'I' and (resid 1105 through 1106 or resid 1203 through 3000))I1203
234(chain 'I' and (resid 1105 through 1106 or resid 1203 through 3000))I1205
244(chain 'I' and (resid 1105 through 1106 or resid 1203 through 3000))I1211
254(chain 'I' and (resid 1105 through 1106 or resid 1203 through 3000))I1215 - 1216
264(chain 'I' and (resid 1105 through 1106 or resid 1203 through 3000))I3000

NCS ensembles :
ID
1
2
3
4

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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: 112403.945 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 EG

#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-ROHGlycam 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
[][D-1-deoxy-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, 36 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.: 5 / 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.: 11 / Source method: obtained synthetically / Formula: C44H85NO8P / Comment: DOPC, phospholipid*YM
#9: Chemical ChemComp-H0C / [(2~{R},3~{R},4~{R},5~{S},6~{S})-2-[[(1~{R},3~{S},5~{S},8~{R},9~{S},10~{R},11~{R},13~{R},14~{S},17~{R})-10-(hydroxymethyl)-13-methyl-1,5,11,14-tetrakis(oxidanyl)-17-(5-oxidanylidene-2~{H}-furan-3-yl)-2,3,4,6,7,8,9,11,12,15,16,17-dodecahydro-1~{H}-cyclopenta[a]phenanthren-3-yl]oxy]-6-methyl-3,5-bis(oxidanyl)oxan-4-yl] anthracene-9-carboxylate


Mass: 788.876 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C44H52O13 / Feature type: SUBJECT OF INVESTIGATION
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 5.44 Å3/Da / Density % sol: 77.41 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 125-150 mM MgCl2, 18% (w/v) PEG2000MME, 10% (w/v) glycerol, 5 mM GSH, 0.1 mM DTT and 1 mg/ml butylhydroxytoluen, 100 mM MES

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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 EIGER X 16M / Detector: PIXEL / Date: Jul 20, 2020
RadiationMonochromator: Si double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.65→50 Å / Num. obs: 35168 / % possible obs: 46.3 % / Redundancy: 7.7 % / Biso Wilson estimate: 131.74 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.044 / Rrim(I) all: 0.127 / Net I/σ(I): 8.5
Reflection shellResolution: 3.65→3.96 Å / Redundancy: 5 % / Rmerge(I) obs: 1.24 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1758 / CC1/2: 0.105 / Rpim(I) all: 0.588 / Rrim(I) all: 1.381 / % possible all: 11

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Processing

Software
NameVersionClassification
BSSdata collection
DENZOdata reduction
SCALEPACKdata scaling
STARANISOdata scaling
PHASERphasing
Cootmodel building
PHENIX1.17.1_3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KPZ

6kpz
PDB Unreleased entry


Resolution: 3.65→15 Å / SU ML: 0.5951 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 34.6884
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2742 1698 4.99 %
Rwork0.2334 32296 -
obs0.2355 33994 45.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 140.6 Å2
Refinement stepCycle: LAST / Resolution: 3.65→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20742 0 642 12 21396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005221836
X-RAY DIFFRACTIONf_angle_d0.932729665
X-RAY DIFFRACTIONf_chiral_restr0.31893390
X-RAY DIFFRACTIONf_plane_restr0.0086373
X-RAY DIFFRACTIONf_dihedral_angle_d16.80988253
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.65-3.760.4974240.3695506X-RAY DIFFRACTION8.61
3.76-3.880.2911350.3766687X-RAY DIFFRACTION11.77
3.88-4.020.3705460.3657863X-RAY DIFFRACTION14.85
4.02-4.170.3582590.35181088X-RAY DIFFRACTION18.64
4.17-4.360.3792670.3091360X-RAY DIFFRACTION23.07
4.36-4.580.3022910.27041593X-RAY DIFFRACTION27.14
4.58-4.860.32471030.26081976X-RAY DIFFRACTION33.59
4.86-5.220.32231580.26452965X-RAY DIFFRACTION50.27
5.22-5.720.32552060.28213854X-RAY DIFFRACTION65.08
5.72-6.490.3252700.28315229X-RAY DIFFRACTION87.65
6.49-7.960.2773140.23466024X-RAY DIFFRACTION99.78
7.97-150.21033250.17486151X-RAY DIFFRACTION99.58

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