[English] 日本語
Yorodumi
- EMDB-30949: Cryo EM structure of a Na+-bound Na+,K+-ATPase in the E1 state wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-30949
TitleCryo EM structure of a Na+-bound Na+,K+-ATPase in the E1 state with ATP-gamma-S
Map data
Sample
  • Complex: cryo EM structure of a Na+-bound Na+,K+-ATPase in the E1 state with ATP-gamma-S
    • Protein or peptide: Sodium/potassium-transporting ATPase subunit alpha-1
    • Protein or peptide: Sodium/potassium-transporting ATPase subunit beta-1
    • Protein or peptide: Sodium/potassium-transporting ATPase subunit gamma
  • Ligand: SODIUM ION
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water
Function / homology
Function and homology information


negative regulation of glucocorticoid biosynthetic process / protein transport into plasma membrane raft / positive regulation of calcium:sodium antiporter activity / positive regulation of heart contraction / positive regulation of potassium ion transmembrane transporter activity / positive regulation of P-type sodium:potassium-exchanging transporter activity / Na+/K+-exchanging ATPase / positive regulation of striated muscle contraction / positive regulation of sodium ion export across plasma membrane / positive regulation of potassium ion import across plasma membrane ...negative regulation of glucocorticoid biosynthetic process / protein transport into plasma membrane raft / positive regulation of calcium:sodium antiporter activity / positive regulation of heart contraction / positive regulation of potassium ion transmembrane transporter activity / positive regulation of P-type sodium:potassium-exchanging transporter activity / Na+/K+-exchanging ATPase / positive regulation of striated muscle contraction / positive regulation of sodium ion export across plasma membrane / positive regulation of potassium ion import across plasma membrane / membrane repolarization during cardiac muscle cell action potential / response to glycoside / photoreceptor inner segment membrane / steroid hormone binding / membrane repolarization / P-type sodium:potassium-exchanging transporter activity / sodium ion binding / sodium:potassium-exchanging ATPase complex / negative regulation of heart contraction / establishment or maintenance of transmembrane electrochemical gradient / regulation of the force of heart contraction / sodium ion export across plasma membrane / intracellular potassium ion homeostasis / intracellular sodium ion homeostasis / cardiac muscle cell action potential involved in contraction / osmosensory signaling pathway / positive regulation of ATP-dependent activity / regulation of cardiac muscle contraction by calcium ion signaling / Basigin interactions / relaxation of cardiac muscle / cell communication by electrical coupling involved in cardiac conduction / cellular response to steroid hormone stimulus / monoatomic cation transmembrane transport / phosphatase activity / potassium ion import across plasma membrane / organelle membrane / potassium ion binding / Ion transport by P-type ATPases / ATPase activator activity / intercalated disc / sodium ion transmembrane transport / lateral plasma membrane / sperm flagellum / sodium channel regulator activity / cardiac muscle contraction / regulation of sodium ion transport / ATP metabolic process / Ion homeostasis / proton transmembrane transport / T-tubule / protein localization to plasma membrane / transmembrane transport / sarcolemma / regulation of blood pressure / intracellular calcium ion homeostasis / extracellular vesicle / melanosome / MHC class II protein complex binding / protein-macromolecule adaptor activity / protein-folding chaperone binding / ATPase binding / regulation of gene expression / basolateral plasma membrane / transmembrane transporter binding / Potential therapeutics for SARS / postsynaptic density / protein stabilization / cell adhesion / response to xenobiotic stimulus / membrane raft / apical plasma membrane / protein heterodimerization activity / axon / innate immune response / protein kinase binding / Golgi apparatus / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / extracellular exosome / 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 / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Sodium/potassium-transporting ATPase subunit alpha-1 / Sodium/potassium-transporting ATPase subunit beta-1 / Sodium/potassium-transporting ATPase subunit gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsGuo YY / Zhang YY / Yan RH / Huang BD / Ye FF / Wu LS / Chi XM / Zhou Q
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971123 China
National Natural Science Foundation of China (NSFC)31800139 China
CitationJournal: Nat Commun / Year: 2022
Title: Cryo-EM structures of recombinant human sodium-potassium pump determined in three different states.
Authors: Yingying Guo / Yuanyuan Zhang / Renhong Yan / Bangdong Huang / Fangfei Ye / Liushu Wu / Ximin Chi / Yi Shi / Qiang Zhou /
Abstract: Sodium-Potassium Pump (Na/K-ATPase, NKA) is an ion pump that generates an electrochemical gradient of sodium and potassium ions across the plasma membrane by hydrolyzing ATP. During each Post-Albers ...Sodium-Potassium Pump (Na/K-ATPase, NKA) is an ion pump that generates an electrochemical gradient of sodium and potassium ions across the plasma membrane by hydrolyzing ATP. During each Post-Albers cycle, NKA exchanges three cytoplasmic sodium ions for two extracellular potassium ions through alternating changes between the E1 and E2 states. Hitherto, several steps remained unknown during the complete working cycle of NKA. Here, we report cryo-electron microscopy (cryo-EM) structures of recombinant human NKA (hNKA) in three distinct states at 2.7-3.2 Å resolution, representing the E1·3Na and E1·3Na·ATP states with cytosolic gates open and the basic E2·[2K] state, respectively. This work provides the insights into the cytoplasmic Na entrance pathway and the mechanism of cytoplasmic gate closure coupled with ATP hydrolysis, filling crucial gaps in the structural elucidation of the Post-Albers cycle of NKA.
History
DepositionFeb 4, 2021-
Header (metadata) releaseJun 15, 2022-
Map releaseJun 15, 2022-
UpdateJul 20, 2022-
Current statusJul 20, 2022Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_30949.png

Downloads & links

-
Map

FileDownload / File: emd_30949.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.087 Å
Density
Contour LevelBy AUTHOR: 0.045
Minimum - Maximum-0.07170412 - 0.14017704
Average (Standard dev.)0.00049538445 (±0.005506758)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 217.40001 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

+
Entire : cryo EM structure of a Na+-bound Na+,K+-ATPase in the E1 state wi...

EntireName: cryo EM structure of a Na+-bound Na+,K+-ATPase in the E1 state with ATP-gamma-S
Components
  • Complex: cryo EM structure of a Na+-bound Na+,K+-ATPase in the E1 state with ATP-gamma-S
    • Protein or peptide: Sodium/potassium-transporting ATPase subunit alpha-1
    • Protein or peptide: Sodium/potassium-transporting ATPase subunit beta-1
    • Protein or peptide: Sodium/potassium-transporting ATPase subunit gamma
  • Ligand: SODIUM ION
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water

+
Supramolecule #1: cryo EM structure of a Na+-bound Na+,K+-ATPase in the E1 state wi...

SupramoleculeName: cryo EM structure of a Na+-bound Na+,K+-ATPase in the E1 state with ATP-gamma-S
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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

MacromoleculeName: Sodium/potassium-transporting ATPase subunit alpha-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: Na+/K+-exchanging ATPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 113.012828 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGKGVGRDKY EPAAVSEQGD KKGKKGKKDR DMDELKKEVS MDDHKLSLDE LHRKYGTDLS RGLTSARAAE ILARDGPNAL TPPPTTPEW IKFCRQLFGG FSMLLWIGAI LCFLAYSIQA ATEEEPQNDN LYLGVVLSAV VIITGCFSYY QEAKSSKIME S FKNMVPQQ ...String:
MGKGVGRDKY EPAAVSEQGD KKGKKGKKDR DMDELKKEVS MDDHKLSLDE LHRKYGTDLS RGLTSARAAE ILARDGPNAL TPPPTTPEW IKFCRQLFGG FSMLLWIGAI LCFLAYSIQA ATEEEPQNDN LYLGVVLSAV VIITGCFSYY QEAKSSKIME S FKNMVPQQ ALVIRNGEKM SINAEEVVVG DLVEVKGGDR IPADLRIISA NGCKVDNSSL TGESEPQTRS PDFTNENPLE TR NIAFFST NCVEGTARGI VVYTGDRTVM GRIATLASGL EGGQTPIAAE IEHFIHIITG VAVFLGVSFF ILSLILEYTW LEA VIFLIG IIVANVPEGL LATVTVCLTL TAKRMARKNC LVKNLEAVET LGSTSTICSD KTGTLTQNRM TVAHMWFDNQ IHEA DTTEN QSGVSFDKTS ATWLALSRIA GLCNRAVFQA NQENLPILKR AVAGDASESA LLKCIELCCG SVKEMRERYA KIVEI PFNS TNKYQLSIHK NPNTSEPQHL LVMKGAPERI LDRCSSILLH GKEQPLDEEL KDAFQNAYLE LGGLGERVLG FCHLFL PDE QFPEGFQFDT DDVNFPIDNL CFVGLISMID PPRAAVPDAV GKCRSAGIKV IMVTGDHPIT AKAIAKGVGI ISEGNET VE DIAARLNIPV SQVNPRDAKA CVVHGSDLKD MTSEQLDDIL KYHTEIVFAR TSPQQKLIIV EGCQRQGAIV AVTGDGVN D SPALKKADIG VAMGIAGSDV SKQAADMILL DDNFASIVTG VEEGRLIFDN LKKSIAYTLT SNIPEITPFL IFIIANIPL PLGTVTILCI DLGTDMVPAI SLAYEQAESD IMKRQPRNPK TDKLVNERLI SMAYGQIGMI QALGGFFTYF VILAENGFLP IHLLGLRVD WDDRWINDVE DSYGQQWTYE QRKIVEFTCH TAFFVSIVVV QWADLVICKT RRNSVFQQGM KNKILIFGLF E ETALAAFL SYCPGMGVAL RMYPLKPTWW FCAFPYSLLI FVYDEVRKLI IRRRPGGWVE KETYY

+
Macromolecule #2: Sodium/potassium-transporting ATPase subunit beta-1

MacromoleculeName: Sodium/potassium-transporting ATPase subunit beta-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.108258 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MARGKAKEEG SWKKFIWNSE KKEFLGRTGG SWFKILLFYV IFYGCLAGIF IGTIQVMLLT ISEFKPTYQD RVAPPGLTQI PQIQKTEIS FRPNDPKSYE AYVLNIVRFL EKYKDSAQRD DMIFEDCGDV PSEPKERGDF NHERGERKVC RFKLEWLGNC S GLNDETYG ...String:
MARGKAKEEG SWKKFIWNSE KKEFLGRTGG SWFKILLFYV IFYGCLAGIF IGTIQVMLLT ISEFKPTYQD RVAPPGLTQI PQIQKTEIS FRPNDPKSYE AYVLNIVRFL EKYKDSAQRD DMIFEDCGDV PSEPKERGDF NHERGERKVC RFKLEWLGNC S GLNDETYG YKEGKPCIII KLNRVLGFKP KPPKNESLET YPVMKYNPNV LPVQCTGKRD EDKDKVGNVE YFGLGNSPGF PL QYYPYYG KLLQPKYLQP LLAVQFTNLT MDTEIRIECK AYGENIGYSE KDRFQGRFDV KIEVKS

+
Macromolecule #3: Sodium/potassium-transporting ATPase subunit gamma

MacromoleculeName: Sodium/potassium-transporting ATPase subunit gamma / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.292322 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MTGLSMDGGG SPKGDVDPFY YDYETVRNGG LIFAGLAFIV GLLILLSRRF RCGGNKKRRQ INEDEP

+
Macromolecule #5: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 5 / Number of copies: 4
Molecular weightTheoretical: 22.99 Da

+
Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #7: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 7 / Number of copies: 1 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

+
Macromolecule #8: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 8 / Number of copies: 6 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

+
Macromolecule #9: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 9 / Number of copies: 2 / Formula: PC1
Molecular weightTheoretical: 790.145 Da
Chemical component information

ChemComp-PC1:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

+
Macromolecule #10: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 10 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

+
Macromolecule #11: water

MacromoleculeName: water / type: ligand / ID: 11 / Number of copies: 5 / 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

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.6) / Number images used: 51044
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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