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- EMDB-62255: Cryo-EM structure of human sodium pump E1003K complexed with NDRG... -

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Basic information

Entry
Database: EMDB / ID: EMD-62255
TitleCryo-EM structure of human sodium pump E1003K complexed with NDRG3 in (2Na+)E1-AMPPCP state
Map data
Sample
  • Complex: human sodium pump alpha-beta complexed with NDRG3
    • Protein or peptide: Sodium/potassium-transporting ATPase subunit alpha-1
    • Protein or peptide: Sodium/potassium-transporting ATPase subunit beta-3
    • Protein or peptide: Protein NDRG3
  • Ligand: SODIUM ION
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
  • Ligand: water
KeywordsP-type ATPase / Na+ / K+-ATPase / sodium pump / human / MEMBRANE PROTEIN
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 / photoreceptor inner segment membrane / membrane repolarization during cardiac muscle cell action potential / steroid hormone binding / sodium ion 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 / 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 / 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 / sarcolemma / 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 / Golgi apparatus / signal transduction / protein-containing complex / ATP hydrolysis activity / extracellular exosome / ATP binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
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 ...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 / 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 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Sodium/potassium-transporting ATPase subunit alpha-1 / Sodium/potassium-transporting ATPase subunit beta-3 / Protein NDRG3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsAbe K / Dou Y / Suzuki J
Funding support Japan, 1 items
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: Dou Y / Abe K / Suzuki J
History
DepositionNov 1, 2024-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62255.png

Downloads & links

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Map

FileDownload / File: emd_62255.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.75 Å/pix.
x 450 pix.
= 338.4 Å		0.75 Å/pix.
x 450 pix.
= 338.4 Å		0.75 Å/pix.
x 450 pix.
= 338.4 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.752 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.255
Minimum - Maximum-2.6588793 - 4.4777427
Average (Standard dev.)-0.0028717099 (±0.059985533)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 338.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_62255_msk_1.map
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Half map: #1

Fileemd_62255_half_map_1.map
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Half map: #2

Fileemd_62255_half_map_2.map
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Sample components

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Entire : human sodium pump alpha-beta complexed with NDRG3

EntireName: human sodium pump alpha-beta complexed with NDRG3
Components
  • Complex: human sodium pump alpha-beta complexed with NDRG3
    • Protein or peptide: Sodium/potassium-transporting ATPase subunit alpha-1
    • Protein or peptide: Sodium/potassium-transporting ATPase subunit beta-3
    • Protein or peptide: Protein NDRG3
  • Ligand: SODIUM ION
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
  • Ligand: water

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Supramolecule #1: human sodium pump alpha-beta complexed with NDRG3

SupramoleculeName: human sodium pump alpha-beta complexed with NDRG3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 150 KDa

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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: 108.781023 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VSMDDHKLSL DELHRKYGTD LSRGLTSARA AEILARDGPN ALTPPPTTPE WIKFCRQLFG GFSMLLWIGA ILCFLAYSIQ AATEEEPQN DNLYLGVVLS AVVIITGCFS YYQEAKSSKI MESFKNMVPQ QALVIRNGEK MSINAEEVVV GDLVEVKGGD R IPADLRII ...String:
VSMDDHKLSL DELHRKYGTD LSRGLTSARA AEILARDGPN ALTPPPTTPE WIKFCRQLFG GFSMLLWIGA ILCFLAYSIQ AATEEEPQN DNLYLGVVLS AVVIITGCFS YYQEAKSSKI MESFKNMVPQ QALVIRNGEK MSINAEEVVV GDLVEVKGGD R IPADLRII SANGCKVDNS SLTGESEPQT RSPDFTNENP LETRNIAFFS TNCVEGTARG IVVYTGDRTV MGRIATLASG LE GGQTPIA AEIEHFIHII TGVAVFLGVS FFILSLILEY TWLEAVIFLI GIIVANVPEG LLATVTVCLT LTAKRMARKN CLV KNLEAV ETLGSTSTIC SDKTGTLTQN RMTVAHMWFD NQIHEADTTE NQSGVSFDKT SATWLALSRI AGLCNRAVFQ ANQE NLPIL KRAVAGDASE SALLKCIELC CGSVKEMRER YAKIVEIPFN STNKYQLSIH KNPNTSEPQH LLVMKGAPER ILDRC SSIL LHGKEQPLDE ELKDAFQNAY LELGGLGERV LGFCHLFLPD EQFPEGFQFD TDDVNFPIDN LCFVGLISMI DPPRAA VPD AVGKCRSAGI KVIMVTGDHP ITAKAIAKGV GIISEGNETV EDIAARLNIP VSQVNPRDAK ACVVHGSDLK DMTSEQL DD ILKYHTEIVF ARTSPQQKLI IVEGCQRQGA IVAVTGDGVN DSPALKKADI GVAMGIAGSD VSKQAADMIL LDDNFASI V TGVEEGRLIF DNLKKSIAYT LTSNIPEITP FLIFIIANIP LPLGTVTILC IDLGTDMVPA ISLAYEQAES DIMKRQPRN PKTDKLVNER LISMAYGQIG MIQALGGFFT YFVILAENGF LPIHLLGLRV DWDDRWINDV EDSYGQQWTY EQRKIVEFTC HTAFFVSIV VVQWADLVIC KTRRNSVFQQ GMKNKILIFG LFEETALAAF LSYCPGMGVA LRMYPLKPTW WFCAFPYSLL I FVYDKVRK LIIRRRPGGW VEKETYY

UniProtKB: Sodium/potassium-transporting ATPase subunit alpha-1

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Macromolecule #2: Sodium/potassium-transporting ATPase subunit beta-3

MacromoleculeName: Sodium/potassium-transporting ATPase subunit beta-3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.545518 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTKNEKKSLN QSLAEWKLFI YNPTTGEFLG RTAKSWGLIL LFYLVFYGFL AALFSFTMWV MLQTLNDEVP KYRDQIPSPG LMVFPKPVT ALEYTFSRSD PTSYAGYIED LKKFLKPYTL EEQKNLTVCP DGALFEQKGP VYVACQFPIS LLQACSGMND P DFGYSQGN ...String:
MTKNEKKSLN QSLAEWKLFI YNPTTGEFLG RTAKSWGLIL LFYLVFYGFL AALFSFTMWV MLQTLNDEVP KYRDQIPSPG LMVFPKPVT ALEYTFSRSD PTSYAGYIED LKKFLKPYTL EEQKNLTVCP DGALFEQKGP VYVACQFPIS LLQACSGMND P DFGYSQGN PCILVKMNRI IGLKPEGVPR IDCVSKNEDI PNVAVYPHNG MIDLKYFPYY GKKLHVGYLQ PLVAVQVSFA PN NTGKEVT VECKIDGSAN LKSQDDRDKF LGRVMFKITA RA

UniProtKB: Sodium/potassium-transporting ATPase subunit beta-3

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Macromolecule #3: Protein NDRG3

MacromoleculeName: Protein NDRG3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.907508 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: CQEHDIETTH GVVHVTIRGL PKGNRPVILT YHDIGLNHKS CFNAFFNFED MQEITQHFAV CHVDAPGQQE GAPSFPTGYQ YPTMDELAE MLPPVLTHLS LKSIIGIGVG AGAYILSRFA LNHPELVEGL VLINVDPCAK GWIDWAASKL SGLTTNVVDI I LAHHFGQE ...String:
CQEHDIETTH GVVHVTIRGL PKGNRPVILT YHDIGLNHKS CFNAFFNFED MQEITQHFAV CHVDAPGQQE GAPSFPTGYQ YPTMDELAE MLPPVLTHLS LKSIIGIGVG AGAYILSRFA LNHPELVEGL VLINVDPCAK GWIDWAASKL SGLTTNVVDI I LAHHFGQE ELQANLDLIQ TYRMHIAQDI NQDNLQLFLN SYNGRRDLEI ERPILGQNDN KSKTLKCSTL LVVGDNSPAV EA VVECNSR LNPINTTLLK MADCGGLPQV VQPGKLTEAF KYFLQGMGYI PSASMTRLAR S

UniProtKB: Protein NDRG3

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Macromolecule #4: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 4 / Number of copies: 2
Molecular weightTheoretical: 22.99 Da

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Macromolecule #5: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER

MacromoleculeName: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / type: ligand / ID: 5 / Number of copies: 1 / Formula: ACP
Molecular weightTheoretical: 505.208 Da
Chemical component information

ChemComp-ACP:
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / AMP-PCP, energy-carrying molecule analogue*YM

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 12 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 6.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3wgu

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 187081
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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