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- PDB-7e21: Cryo EM structure of a Na+-bound Na+,K+-ATPase in the E1 state wi... -

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Basic information

Entry
Database: PDB / ID: 7.0E+21
TitleCryo EM structure of a Na+-bound Na+,K+-ATPase in the E1 state with ATP-gamma-S
Components(Sodium/potassium-transporting ATPase subunit ...) x 3
KeywordsMEMBRANE PROTEIN / Na+ / K+-ATPase
Function / homology
Function and homology information


negative regulation of glucocorticoid biosynthetic process / protein transport into plasma membrane raft / Na+/K+-exchanging ATPase / positive regulation of striated muscle contraction / positive regulation of sodium ion export across plasma membrane / positive regulation of heart contraction / positive regulation of potassium ion import across plasma membrane / photoreceptor inner segment membrane / membrane repolarization during cardiac muscle cell action potential / steroid hormone binding ...negative regulation of glucocorticoid biosynthetic process / protein transport into plasma membrane raft / Na+/K+-exchanging ATPase / positive regulation of striated muscle contraction / positive regulation of sodium ion export across plasma membrane / positive regulation of heart contraction / positive regulation of potassium ion import across plasma membrane / photoreceptor inner segment membrane / membrane repolarization during cardiac muscle cell action potential / steroid hormone binding / sodium ion binding / P-type sodium:potassium-exchanging transporter activity / sodium:potassium-exchanging ATPase complex / negative regulation of heart contraction / membrane repolarization / establishment or maintenance of transmembrane electrochemical gradient / regulation of the force of heart contraction / cell communication by electrical coupling involved in cardiac conduction / sodium ion export across plasma membrane / osmosensory signaling pathway / regulation of calcium ion transmembrane transport / intracellular sodium ion homeostasis / cardiac muscle cell action potential involved in contraction / relaxation of cardiac muscle / regulation of cardiac muscle contraction by calcium ion signaling / response to glycoside / Basigin interactions / cellular hyperosmotic salinity response / cellular response to steroid hormone stimulus / organelle membrane / potassium ion import across plasma membrane / potassium ion binding / intracellular potassium ion homeostasis / phosphatase activity / ATPase activator activity / Ion transport by P-type ATPases / intercalated disc / lateral plasma membrane / sodium channel regulator activity / sperm flagellum / transporter activator activity / ATP metabolic process / regulation of sodium ion transport / cardiac muscle contraction / Ion homeostasis / potassium ion transmembrane transport / T-tubule / sodium ion transmembrane transport / proton transmembrane transport / protein localization to plasma membrane / sarcolemma / caveola / transmembrane transport / regulation of blood pressure / intracellular calcium ion homeostasis / MHC class II protein complex binding / melanosome / extracellular vesicle / protein-folding chaperone binding / ATPase binding / regulation of gene expression / protein-macromolecule adaptor activity / basolateral plasma membrane / Potential therapeutics for SARS / transmembrane transporter binding / response to hypoxia / cell adhesion / postsynaptic density / protein stabilization / apical plasma membrane / membrane raft / response to xenobiotic stimulus / protein heterodimerization activity / negative regulation of cell population proliferation / axon / innate immune response / protein kinase binding / endoplasmic reticulum / Golgi apparatus / protein-containing complex / ATP hydrolysis activity / extracellular exosome / 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
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / CHOLESTEROL HEMISUCCINATE / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsGuo, Y.Y. / Zhang, Y.Y. / Yan, R.H. / Huang, B.D. / Ye, F.F. / Wu, L.S. / Chi, X.M. / Zhou, Q.
Funding support China, 2items
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, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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 gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,19919
Polymers155,4133
Non-polymers5,78616
Water905
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Sodium/potassium-transporting ATPase subunit ... , 3 types, 3 molecules ABC

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


Mass: 113012.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATP1A1 / Production host: Homo sapiens (human) / References: UniProt: P05023, Na+/K+-exchanging ATPase
#2: Protein Sodium/potassium-transporting ATPase subunit beta-1 / Sodium/potassium-dependent ATPase subunit beta-1


Mass: 35108.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATP1B1, ATP1B / Production host: Homo sapiens (human) / References: UniProt: P05026
#3: Protein Sodium/potassium-transporting ATPase subunit gamma / Na(+)/K(+) ATPase subunit gamma / FXYD domain-containing ion transport regulator 2 / Sodium pump gamma chain


Mass: 7292.322 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FXYD2, ATP1C, ATP1G1 / Production host: Homo sapiens (human) / References: UniProt: P54710

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Sugars , 2 types, 2 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.: 1
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.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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, 19 molecules

#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#8: Chemical
ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C31H50O4
#9: Chemical ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: cryo EM structure of a Na+-bound Na+,K+-ATPase in the E1 state with ATP-gamma-S
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: RELION / Version: 3.0.6 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 51044 / Symmetry type: POINT

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