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- PDB-9kcm: Cryo-EM structure of human sodium pump E1003K complexed with NDRG... -

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Basic information

Entry
Database: PDB / ID: 9kcm
TitleCryo-EM structure of human sodium pump E1003K complexed with NDRG3 and TMX2 in (2Na+)E1-AMPPCP state
Components
  • (Sodium/potassium-transporting ATPase subunit ...) x 2
  • Protein NDRG3
  • Thioredoxin-related transmembrane protein 2
KeywordsMEMBRANE PROTEIN / P-type ATPase / Na+ / K+-ATPase / sodium pump / human
Function / homology
Function and homology information


negative regulation of glucocorticoid biosynthetic process / 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 / mitochondria-associated endoplasmic reticulum membrane contact site / photoreceptor inner segment membrane / membrane repolarization during cardiac muscle cell action potential / steroid hormone binding ...negative regulation of glucocorticoid biosynthetic process / 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 / mitochondria-associated endoplasmic reticulum membrane contact site / photoreceptor inner segment membrane / membrane repolarization during cardiac muscle cell action potential / steroid hormone binding / disulfide oxidoreductase activity / 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 / intracellular sodium ion homeostasis / cardiac muscle cell action potential involved in contraction / relaxation of cardiac muscle / response to glycoside / Basigin interactions / 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 / lateral plasma membrane / sperm flagellum / transporter activator activity / regulation of sodium ion transport / Ion homeostasis / potassium ion transmembrane transport / T-tubule / sodium ion transmembrane transport / proton transmembrane transport / protein localization to plasma membrane / negative regulation of cell growth / brain development / sarcolemma / mitochondrial membrane / regulation of blood pressure / melanosome / extracellular vesicle / protein-folding chaperone binding / ATPase binding / spermatogenesis / protein-macromolecule adaptor activity / basolateral plasma membrane / Potential therapeutics for SARS / transmembrane transporter binding / cell differentiation / postsynaptic density / protein stabilization / apical plasma membrane / membrane raft / response to xenobiotic stimulus / protein heterodimerization activity / axon / endoplasmic reticulum membrane / endoplasmic reticulum / Golgi apparatus / signal transduction / protein-containing complex / ATP hydrolysis activity / mitochondrion / extracellular exosome / ATP binding / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Thioredoxin-related transmembrane protein 2, thioredoxin domain / Thioredoxin-related transmembrane protein 2 / NDRG / Ndr family / 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 ...Thioredoxin-related transmembrane protein 2, thioredoxin domain / Thioredoxin-related transmembrane protein 2 / NDRG / Ndr family / 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 / Thioredoxin / 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 / Thioredoxin domain profile. / Thioredoxin domain / HAD superfamily / HAD-like superfamily / Alpha/Beta hydrolase fold / Thioredoxin-like superfamily
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Sodium/potassium-transporting ATPase subunit alpha-1 / Sodium/potassium-transporting ATPase subunit beta-3 / Protein NDRG3 / Thioredoxin-related transmembrane protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsAbe, K. / Matsui, R. / Dou, Y. / Suzuki, J.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21H02426 Japan
CitationJournal: To Be Published
Title: Structural basis of a sodium pump quaternary complex leading phospholipid scrambling in the living cell
Authors: Matsui, R. / Dou, Y. / Abe, K. / Suzuki, J.
History
DepositionNov 1, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Sodium/potassium-transporting ATPase subunit beta-3
N: Protein NDRG3
A: Sodium/potassium-transporting ATPase subunit alpha-1
T: Thioredoxin-related transmembrane protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,8637
Polymers207,3124
Non-polymers5513
Water36020
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Sodium/potassium-transporting ATPase subunit ... , 2 types, 2 molecules BA

#1: Protein Sodium/potassium-transporting ATPase subunit beta-3 / Sodium/potassium-dependent ATPase subunit beta-3 / ATPB-3


Mass: 31545.518 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATP1B3 / Production host: Homo sapiens (human) / References: UniProt: P54709
#3: Protein Sodium/potassium-transporting ATPase subunit alpha-1 / Na(+)/K(+) ATPase alpha-1 subunit / Sodium pump subunit alpha-1


Mass: 108781.023 Da / Num. of mol.: 1 / Mutation: E1003K
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

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Protein , 2 types, 2 molecules NT

#2: Protein Protein NDRG3 / N-myc downstream-regulated gene 3 protein


Mass: 32907.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NDRG3 / Production host: Homo sapiens (human) / References: UniProt: Q9UGV2
#4: Protein Thioredoxin-related transmembrane protein 2 / Cell proliferation-inducing gene 26 protein / Thioredoxin domain-containing protein 14


Mass: 34077.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: TMX2, TXNDC14, CGI-31, My009, PIG26, PSEC0045, UNQ237/PRO270
Production host: Homo sapiens (human) / References: UniProt: Q9Y320

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Non-polymers , 3 types, 23 molecules

#5: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: human sodium pump alpha-beta-gamma protomer / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightValue: 0.15 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 6.5
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 48 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 274429 / Symmetry type: POINT
RefinementCross valid method: NONE

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