[English] 日本語
Yorodumi
- PDB-7wyt: Crystal structures of Na+,K+-ATPase in complex with ouabain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7wyt
TitleCrystal structures of Na+,K+-ATPase in complex with ouabain
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


Basigin interactions / Ion homeostasis / positive regulation of P-type sodium:potassium-exchanging transporter activity / Na+/K+-exchanging ATPase / positive regulation of sodium ion export across plasma membrane / Ion transport by P-type ATPases / positive regulation of potassium ion import across plasma membrane / membrane repolarization / P-type sodium:potassium-exchanging transporter activity / sodium ion binding ...Basigin interactions / Ion homeostasis / positive regulation of P-type sodium:potassium-exchanging transporter activity / Na+/K+-exchanging ATPase / positive regulation of sodium ion export across plasma membrane / Ion transport by P-type ATPases / positive regulation of potassium ion import across plasma membrane / membrane repolarization / P-type sodium:potassium-exchanging transporter activity / sodium ion binding / sodium:potassium-exchanging ATPase complex / establishment or maintenance of transmembrane electrochemical gradient / sodium ion export across plasma membrane / intracellular potassium ion homeostasis / intracellular sodium ion homeostasis / potassium ion import across plasma membrane / potassium ion binding / ATPase activator activity / sodium channel regulator activity / regulation of sodium ion transport / proton transmembrane transport / transmembrane transport / sarcolemma / melanosome / protein-macromolecule adaptor activity / ATPase binding / basolateral plasma membrane / cell adhesion / apical plasma membrane / axon / innate immune response / 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. / Sodium and potassium ATPases beta subunits signature 2. ...: / : / 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 / OUABAIN / 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: 2.9 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
Citation
Journal: Proc Natl Acad Sci U S A / Year: 2022
Title: Cryoelectron microscopy of Na,K-ATPase in the two E2P states with and without cardiotonic steroids.
Authors: Ryuta Kanai / Flemming Cornelius / Bente Vilsen / Chikashi Toyoshima /
Abstract: Cryoelectron microscopy (cryo-EM) was applied to Na+,K+-ATPase (NKA) to determine the structures of two E2P states, one (E2PATP) formed by ATP and Mg2+ in the forward reaction, and the other (E2PPi) ...Cryoelectron microscopy (cryo-EM) was applied to Na+,K+-ATPase (NKA) to determine the structures of two E2P states, one (E2PATP) formed by ATP and Mg2+ in the forward reaction, and the other (E2PPi) formed by inorganic phosphate (Pi) and Mg2+ in the backward reaction, with and without ouabain or istaroxime, representatives of classical and new-generation cardiotonic steroids (CTSs). These two E2P states exhibit different biochemical properties. In particular, K+-sensitive acceleration of the dephosphorylation reaction is not observed with E2PPi, attributed to the presence of a Mg2+ ion in the transmembrane cation binding sites. The cryo-EM structures of NKA demonstrate that the two E2P structures are nearly identical but Mg2+ in the transmembrane binding cavity is identified only in E2PPi, corroborating the idea that it should be denoted as E2PPi·Mg2+. We can now explain why the absence of transmembrane Mg2+ in E2PATP confers the K+ sensitivity in dephosphorylation. In addition, we show that ATP bridges the actuator (A) and nucleotide binding (N) domains, stabilizing the E2PATP state; CTS binding causes hardly any changes in the structure of NKA, both in E2PATP and E2PPi·Mg2+, indicating that the binding mechanism is conformational selection; and istaroxime binds to NKA, extending its aminoalkyloxime group deep into the cation binding site. This orientation is upside down compared to that of classical CTSs with respect to the steroid ring. Notably, mobile parts of NKA are resolved substantially better in the electron microscopy (EM) maps than in previous X-ray structures, including sugars sticking out from the β-subunit and many phospholipid molecules.
#1: Journal: Proc Natl Acad Sci U S A / 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.
#2: Journal: To Be Published
Title: Cryo-electron microscopy of Na+, K+-ATPase in the two E2P states with and without cardiotonic steroids
Authors: Kanai, R. / Cornelius, F. / Vilsen, B. / Toyoshima, C.
History
DepositionFeb 16, 2022Deposition site: PDBJ / Processing site: PDBJ
SupersessionMay 4, 2022ID: 7DDJ
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)325,02338
Polymers309,4056
Non-polymers15,61832
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)164,28621
Polymers154,7023
Non-polymers9,58418
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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)160,73717
Polymers154,7023
Non-polymers6,03514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.621, 117.810, 493.203
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-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "C"
d_1ens_2(chain "B" and (resid 13 through 161 or resid 168 through 303 or resid 1001 through 1021))
d_2ens_2chain "D"
d_1ens_3chain "E"
d_2ens_3chain "G"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LYSTYRA1 - 996
d_12ens_1MGMGB
d_13ens_1NANAC
d_21ens_1LYSTYRC1 - 996
d_22ens_1MGMGN
d_23ens_1NANAO
d_11ens_2LYSGLYB1 - 149
d_12ens_2GLYSERB156 - 291
d_13ens_2NAGNAGG
d_14ens_2NAGNAGH
d_15ens_2NAGNAGI
d_16ens_2NAGNAGJ
d_17ens_2NAGNAGK
d_21ens_2LYSSERD1 - 285
d_22ens_2NAGNAGS
d_23ens_2NAGNAGT
d_24ens_2NAGNAGU
d_25ens_2NAGNAGV
d_26ens_2NAGNAGW
d_11ens_3ASPLYSE1 - 32
d_21ens_3ASPLYSG1 - 32

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(0.59836690782, -0.795363558004, 0.0967153257018), (-0.795439333663, -0.604181024222, -0.0473450782288), (0.0960901144145, -0.0486014461709, -0.994185389825)8.28916924916, 29.1431373783, 120.245130504
2given(0.539954176602, -0.838480453789, 0.0734847996876), (-0.83724487854, -0.544014149529, -0.0554041376657), (0.086432057297, -0.0316090766554, -0.995756177859)9.29615816533, 30.183098866, 120.542127813
3given(0.540601207582, -0.83687274757, 0.0859903409466), (-0.836225865482, -0.545725849945, -0.0539406952177), (0.0920686497128, -0.0427469423086, -0.994834691124)9.87447862874, 30.4128281987, 120.126561809

-
Components

-
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

-
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

-
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

-
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.: 13 / Source method: obtained synthetically / Formula: C44H85NO8P / Comment: DOPC, phospholipid*YM
#9: Chemical ChemComp-OBN / OUABAIN


Mass: 584.652 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H44O12 / Feature type: SUBJECT OF INVESTIGATION
#11: Water ChemComp-HOH / water


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

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.43 Å3/Da / Density % sol: 77.34 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 175mM MgCl2, 18% (w/v) PEG 2000 MME, 10% (w/v) glycerol, 5mM GSH, 0.1mM DTT, 1mg/ml butylhydroxytoluen, 100mM MES

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 22, 2015
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 73353 / % possible obs: 48.8 % / Redundancy: 8.1 % / Biso Wilson estimate: 70.04 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.5
Reflection shellResolution: 2.9→3.03 Å / Redundancy: 1 % / Rmerge(I) obs: 0.374 / Num. unique obs: 297 / % possible all: 1.5

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.19.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KPU

6kpu
PDB Unreleased entry


Resolution: 2.9→15.99 Å / SU ML: 0.4947 / Cross valid method: FREE R-VALUE / σ(F): 1.48 / Phase error: 32.3872
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3074 7200 9.93 %
Rwork0.2703 65301 -
obs0.274 72501 48.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.2 Å2
Refinement stepCycle: LAST / Resolution: 2.9→15.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20690 0 654 10 21354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004621786
X-RAY DIFFRACTIONf_angle_d0.925829591
X-RAY DIFFRACTIONf_chiral_restr0.05383388
X-RAY DIFFRACTIONf_plane_restr0.0086355
X-RAY DIFFRACTIONf_dihedral_angle_d16.90258195
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.841641752054
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.498295344004
ens_3d_2EX-RAY DIFFRACTIONTorsion NCS0.498515798707
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.940.45220.402334X-RAY DIFFRACTION0.76
2.94-2.970.089220.459958X-RAY DIFFRACTION1.27
2.97-3.010.565390.395191X-RAY DIFFRACTION2.06
3.01-3.040.4702200.485126X-RAY DIFFRACTION2.99
3.04-3.080.5196240.4227198X-RAY DIFFRACTION4.62
3.08-3.130.3932240.4576294X-RAY DIFFRACTION6.46
3.13-3.170.4303430.4252395X-RAY DIFFRACTION9.01
3.17-3.220.4289550.3993498X-RAY DIFFRACTION11.34
3.22-3.270.4096820.4349621X-RAY DIFFRACTION14.41
3.27-3.320.4592680.398761X-RAY DIFFRACTION16.9
3.32-3.380.3872990.3955898X-RAY DIFFRACTION20.21
3.38-3.440.3899960.39711032X-RAY DIFFRACTION23.06
3.44-3.50.40331280.41241167X-RAY DIFFRACTION26.26
3.5-3.570.40941400.37821367X-RAY DIFFRACTION30.75
3.57-3.650.40961730.36211558X-RAY DIFFRACTION35.23
3.65-3.730.41442210.35481809X-RAY DIFFRACTION41.28
3.73-3.830.40912150.34062206X-RAY DIFFRACTION49.04
3.83-3.930.40072870.33582631X-RAY DIFFRACTION58.84
3.93-4.040.35123300.32192956X-RAY DIFFRACTION66.69
4.04-4.170.36273580.31713302X-RAY DIFFRACTION74.45
4.17-4.320.35494100.30083630X-RAY DIFFRACTION81.21
4.32-4.490.33064420.28973960X-RAY DIFFRACTION88.84
4.49-4.690.33994570.27494286X-RAY DIFFRACTION95.22
4.69-4.930.30864900.27284393X-RAY DIFFRACTION98.31
4.93-5.220.30834630.25944471X-RAY DIFFRACTION98.96
5.22-5.610.3235270.2744438X-RAY DIFFRACTION98.9
5.61-6.150.3185160.2814454X-RAY DIFFRACTION98.91
6.15-6.970.3014860.25644501X-RAY DIFFRACTION98.79
6.97-8.550.23675100.21574519X-RAY DIFFRACTION98.53
8.55-15.990.20115230.17794647X-RAY DIFFRACTION98.4

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more