[English] 日本語
Yorodumi
- EMDB-32895: Cryo-EM structure of Na+,K+-ATPase in the E2P state formed by ATP... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-32895
TitleCryo-EM structure of Na+,K+-ATPase in the E2P state formed by ATP in the presence of 40 mM Mg2+
Map data
Sample
  • Complex: Sodium/potassium-transporting ATPase
    • Protein or peptide: Sodium/potassium-transporting ATPase subunit alpha
    • Protein or peptide: Na+,K+-ATPase beta subunit
    • Protein or peptide: FXYD domain-containing ion transport regulator
  • Ligand: MAGNESIUM ION
  • Ligand: SODIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: CHOLESTEROL
  • Ligand: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: water
Function / homology
Function and homology information


regulation of monoatomic ion transport / P-type sodium:potassium-exchanging transporter activity / sodium:potassium-exchanging ATPase complex / sodium ion export across plasma membrane / intracellular potassium ion homeostasis / intracellular sodium ion homeostasis / potassium ion import across plasma membrane / ATPase activator activity / sodium channel regulator activity / monoatomic ion transport ...regulation of monoatomic ion transport / P-type sodium:potassium-exchanging transporter activity / sodium:potassium-exchanging ATPase complex / sodium ion export across plasma membrane / intracellular potassium ion homeostasis / intracellular sodium ion homeostasis / potassium ion import across plasma membrane / ATPase activator activity / sodium channel regulator activity / monoatomic ion transport / proton transmembrane transport / ATP hydrolysis activity / ATP binding / membrane / metal ion binding / 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
Sodium/potassium-transporting ATPase subunit beta / Sodium/potassium-transporting ATPase subunit alpha / FXYD domain-containing ion transport regulator
Similarity search - Component
Biological speciesSqualus acanthias (spiny dogfish) / spiny dogfish (spiny dogfish)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsKanai R / Cornelius F / Vilsen B / Toyoshima C
Funding support Japan, Denmark, 6 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19H00975 Japan
Japan Society for the Promotion of Science (JSPS)18K06148 Japan
Danish Council for Independent ResearchDFF7016-00193B Denmark
Danish Council for Independent ResearchDFF4183-00011A Denmark
Novo Nordisk FoundationNNF14OC0013409 Denmark
Novo Nordisk FoundationNNF13OC0006555 Denmark
CitationJournal: 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.
History
DepositionFeb 16, 2022-
Header (metadata) releaseApr 27, 2022-
Map releaseApr 27, 2022-
UpdateApr 27, 2022-
Current statusApr 27, 2022Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_32895.png

Downloads & links

-
Map

FileDownload / File: emd_32895.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 240 pix.
= 258.24 Å		1.08 Å/pix.
x 240 pix.
= 258.24 Å		1.08 Å/pix.
x 240 pix.
= 258.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.076 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.019
Minimum - Maximum-0.050732736 - 0.09108368
Average (Standard dev.)0.00035229034 (±0.004049795)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 258.24 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

+
Entire : Sodium/potassium-transporting ATPase

EntireName: Sodium/potassium-transporting ATPase
Components
  • Complex: Sodium/potassium-transporting ATPase
    • Protein or peptide: Sodium/potassium-transporting ATPase subunit alpha
    • Protein or peptide: Na+,K+-ATPase beta subunit
    • Protein or peptide: FXYD domain-containing ion transport regulator
  • Ligand: MAGNESIUM ION
  • Ligand: SODIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: CHOLESTEROL
  • Ligand: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: water

+
Supramolecule #1: Sodium/potassium-transporting ATPase

SupramoleculeName: Sodium/potassium-transporting ATPase / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Squalus acanthias (spiny dogfish)

+
Macromolecule #1: Sodium/potassium-transporting ATPase subunit alpha

MacromoleculeName: Sodium/potassium-transporting ATPase subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: spiny dogfish (spiny dogfish)
Molecular weightTheoretical: 113.389859 KDa
SequenceString: MGKGTASDKY EPAATSENAT KSKKKGKKDK IDKKRDLDEL KKEVSMDDHK LSLDELHNKY GTDLTRGLTN ARAKEILARD GPNSLTPPP TTPEWIKFCR QLFGGFSILL WIGAILCFLA YGIQAATEDE PANDNLYLGV VLSTVVIVTG CFSYYQEAKS S RIMDSFKN ...String:
MGKGTASDKY EPAATSENAT KSKKKGKKDK IDKKRDLDEL KKEVSMDDHK LSLDELHNKY GTDLTRGLTN ARAKEILARD GPNSLTPPP TTPEWIKFCR QLFGGFSILL WIGAILCFLA YGIQAATEDE PANDNLYLGV VLSTVVIVTG CFSYYQEAKS S RIMDSFKN MVPQQALVIR DGEKSTINAE FVVAGDLVEV KGGDRIPADL RIISAHGCKV DNSSLTGESE PQTRSPEFSS EN PLETRNI AFFSTNCVEG TARGVVVYTG DRTVMGRIAT LASGLEVGRT PIAIEIEHFI HIITGVAVFL GVSFFILSLI LGY SWLEAV IFLIGIIVAN VPEGLLATVT VCLTLTAKRM ARKNCLVKNL EAVETLGSTS TICS(PHD)KTGTL TQNRMTVAHM WFDNQIHEA DTTENQSGAA FDKTSATWSA LSRIAALCNR AVFQAGQDNV PILKRSVAGD ASESALLKCI ELCCGSVQGM R DRNPKIVE IPFNSTNKYQ LSIHENEKSS ESRYLLVMKG APERILDRCS TILLNGAEEP LKEDMKEAFQ NAYLELGGLG ER VLGFCHF ALPEDKYNEG YPFDADEPNF PTTDLCFVGL MAMIDPPRAA VPDAVGKCRS AGIKVIMVTG DHPITAKAIA KGV GIISEG NETIEDIAAR LNIPIGQVNP RDAKACVVHG SDLKDLSTEV LDDILHYHTE IVFARTSPQQ KLIIVEGCQR QGAI VAVTG DGVNDSPALK KADIGVAMGI SGSDVSKQAA DMILLDDNFA SIVTGVEEGR LIFDNLKKSI AYTLTSNIPE ITPFL VFII GNVPLPLGTV TILCIDLGTD MVPAISLAYE QAESDIMKRQ PRNPKTDKLV NERLISMAYG QIGMIQALGG FFSYFV ILA ENGFLPMDLI GKRVRWDDRW ISDVEDSFGQ QWTYEQRKIV EFTCHTSFFI SIVVVQWADL IICKTRRNSI FQQGMKN KI LIFGLFEETA LAAFLSYCPG TDVALRMYPL KPSWWFCAFP YSLIIFLYDE MRRFIIRRSP GGWVEQETYY

+
Macromolecule #2: Na+,K+-ATPase beta subunit

MacromoleculeName: Na+,K+-ATPase beta subunit / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: spiny dogfish (spiny dogfish)
Molecular weightTheoretical: 35.176125 KDa
SequenceString: MARGKSKETD GGWKKFLWDS EKKEFLGRTG SSWFKIFLFY LIFYGCLAGI FIGTIQVLLL TLSDFEPKYQ DRVAPPGLSH APYAIKTEI SFSISNPKSY ESFVKSMHKL MDLYNESSQA GNSPFEDCSD TPADYIKRGD LDDSQGQKKA CRFSRMWLKN C SGLDDTTY ...String:
MARGKSKETD GGWKKFLWDS EKKEFLGRTG SSWFKIFLFY LIFYGCLAGI FIGTIQVLLL TLSDFEPKYQ DRVAPPGLSH APYAIKTEI SFSISNPKSY ESFVKSMHKL MDLYNESSQA GNSPFEDCSD TPADYIKRGD LDDSQGQKKA CRFSRMWLKN C SGLDDTTY GYAEGKPCVV AKLNRIIGFY PKPLKNTTDL PEELQANYNQ YVLPLRCAAK REEDREKIGS IEYFGLGGYA GF PLQYYPY YGKRLQKKYL QPLLAIQFTN LTQNMELRIE CKVYGENIDY SEKDRFRGRF EVKIEVKS

+
Macromolecule #3: FXYD domain-containing ion transport regulator

MacromoleculeName: FXYD domain-containing ion transport regulator / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: spiny dogfish (spiny dogfish)
Molecular weightTheoretical: 10.195847 KDa
SequenceString:
MLGAATGLMV LVAVTQGVWA MDPEGPDNDE RFTYDYYRLR VVGLIVAAVL CVIGIIILLA GKCRCKFNQN KRTRSNSGTA TAQHLLQPG EATEC

+
Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #9: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 9 / Number of copies: 2
Molecular weightTheoretical: 22.99 Da

+
Macromolecule #10: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 10 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

+
Macromolecule #11: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 11 / Number of copies: 8 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

+
Macromolecule #12: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 12 / Number of copies: 24 / Formula: PCW
Molecular weightTheoretical: 787.121 Da
Chemical component information

ChemComp-PCW:
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / DOPC, phospholipid*YM

+
Macromolecule #13: water

MacromoleculeName: water / type: ligand / ID: 13 / Number of copies: 10 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
13.0 mMNaClsodium chloride
1.0 mMC10H14N5O13P3Na2ATP.2Na
40.0 mMMgCl2magnesium chloride
20.0 mMC3H4N2imidazole
1.0 mMC4H10O2S2DTT
0.01 %C28H58O9C12E8
GridModel: C-flat-1.2/1.3 / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 20.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 99.9 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.1.14)
Startup modelType of model: OTHER
Details: Deposition ID: D_1300027386 was used as the startup model.
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.3) / Number images used: 31645
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)
Final 3D classificationSoftware - Name: RELION (ver. 3.1.3)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

7d91

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 68.6 / Target criteria: Correlation Coeeficient
Output model

PDB-7wyv:
Cryo-EM structure of Na+,K+-ATPase in the E2P state formed by ATP in the presence of 40 mM Mg2+

+
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://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