[English] 日本語
Yorodumi
- EMDB-62260: Cryo-EM structure of human sodium pump E1003K complexed with NDRG... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-62260
TitleCryo-EM structure of human sodium pump E1003K complexed with NDRG3 in (2Na+)E1 state
Map data
Sample
  • Complex: human sodium pump alpha-beta-gamma protomer
    • 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: 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: 3.2 Å
AuthorsAbe K / Matsui R / 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 / Matsui R / Abe K / Suzuki J
History
DepositionNov 2, 2024-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_62260.png

Downloads & links

-
Map

FileDownload / File: emd_62260.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.13 Å/pix.
x 300 pix.
= 338.4 Å		1.13 Å/pix.
x 300 pix.
= 338.4 Å		1.13 Å/pix.
x 300 pix.
= 338.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.128 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.412
Minimum - Maximum-2.8515375 - 4.4231153
Average (Standard dev.)-0.0029424136 (±0.079013914)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 338.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_62260_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_62260_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_62260_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : human sodium pump alpha-beta-gamma protomer

EntireName: human sodium pump alpha-beta-gamma protomer
Components
  • Complex: human sodium pump alpha-beta-gamma protomer
    • 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: water

-
Supramolecule #1: human sodium pump alpha-beta-gamma protomer

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

-
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

-
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

-
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

-
Macromolecule #4: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 4 / Number of copies: 1
Molecular weightTheoretical: 22.99 Da

-
Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 2 / 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: 6.5
VitrificationCryogen name: ETHANE

-
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

+
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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 106301
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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