[English] 日本語
Yorodumi
- EMDB-38449: Structure of the Vo sector of V-ATPase in the adult cortex and hi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-38449
TitleStructure of the Vo sector of V-ATPase in the adult cortex and hippocampus
Map data
Sample
  • Complex: Mammalian V0-ATPase from rat brain
    • Protein or peptide: V-type proton ATPase 116 kDa subunit a 1
    • Protein or peptide: ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a
    • Protein or peptide: V-type proton ATPase subunit S1
    • Protein or peptide: V-type proton ATPase subunit
    • Protein or peptide: V-type proton ATPase subunit e 2
    • Protein or peptide: Ribonuclease K
    • Protein or peptide: V-type proton ATPase 16 kDa proteolipid subunit c
    • Protein or peptide: Renin receptor cytoplasmic fragment
KeywordsVo sector of V-ATPase / MEMBRANE PROTEIN
Function / homology
Function and homology information


Metabolism of Angiotensinogen to Angiotensins / Ion channel transport / Transferrin endocytosis and recycling / Amino acids regulate mTORC1 / negative regulation of autophagic cell death / Insulin receptor recycling / RHOA GTPase cycle / eye pigmentation / central nervous system maturation / rostrocaudal neural tube patterning ...Metabolism of Angiotensinogen to Angiotensins / Ion channel transport / Transferrin endocytosis and recycling / Amino acids regulate mTORC1 / negative regulation of autophagic cell death / Insulin receptor recycling / RHOA GTPase cycle / eye pigmentation / central nervous system maturation / rostrocaudal neural tube patterning / cellular response to increased oxygen levels / positive regulation of transforming growth factor beta1 production / transporter activator activity / proton-transporting V-type ATPase, V0 domain / synaptic vesicle lumen acidification / clathrin-coated vesicle membrane / endosome to plasma membrane protein transport / vacuolar proton-transporting V-type ATPase, V0 domain / lysosomal lumen acidification / proton-transporting V-type ATPase complex / vacuolar proton-transporting V-type ATPase complex / osteoclast development / head morphogenesis / vacuolar acidification / dendritic spine membrane / regulation of cellular pH / ROS and RNS production in phagocytes / Neutrophil degranulation / ATPase activator activity / regulation of MAPK cascade / autophagosome membrane / positive regulation of Wnt signaling pathway / regulation of macroautophagy / angiotensin maturation / proton-transporting ATPase activity, rotational mechanism / endoplasmic reticulum-Golgi intermediate compartment membrane / proton transmembrane transport / terminal bouton / small GTPase binding / transmembrane transport / synaptic vesicle membrane / positive regulation of canonical Wnt signaling pathway / synaptic vesicle / melanosome / signaling receptor activity / ATPase binding / cell body / postsynaptic membrane / intracellular iron ion homeostasis / lysosome / positive regulation of ERK1 and ERK2 cascade / endosome / endosome membrane / apical plasma membrane / axon / external side of plasma membrane / lysosomal membrane / ubiquitin protein ligase binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / extracellular space / membrane / plasma membrane / cytoplasm
Similarity search - Function
ATPase, V0 complex, subunit e1/e2, metazoa / V0 complex accessory subunit Ac45 / V-type proton ATPase subunit S1, luminal domain / V-type proton ATPase subunit S1, luminal domain / Renin receptor-like / Renin receptor-like transmembrane spanning segment / V-type proton ATPase subunit S1/VOA1, transmembrane domain / V0 complex accessory subunit Ac45/VOA1 transmembrane domain / ATPase, V0 complex, subunit e1/e2 / ATP synthase subunit H ...ATPase, V0 complex, subunit e1/e2, metazoa / V0 complex accessory subunit Ac45 / V-type proton ATPase subunit S1, luminal domain / V-type proton ATPase subunit S1, luminal domain / Renin receptor-like / Renin receptor-like transmembrane spanning segment / V-type proton ATPase subunit S1/VOA1, transmembrane domain / V0 complex accessory subunit Ac45/VOA1 transmembrane domain / ATPase, V0 complex, subunit e1/e2 / ATP synthase subunit H / V-ATPase proteolipid subunit C, eukaryotic / ATPase, V0 complex, subunit 116kDa, eukaryotic / V-ATPase proteolipid subunit / V-type ATPase, V0 complex, 116kDa subunit family / V-type ATPase 116kDa subunit family / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C
Similarity search - Domain/homology
ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a / V-type proton ATPase subunit S1 / V-type proton ATPase 116 kDa subunit a 1 / V-type proton ATPase 16 kDa proteolipid subunit c / V-type proton ATPase subunit e 2 / Renin receptor
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsZhang M / Feng J / Li Y / Zhu S
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: To Be Published
Title: Structure of the Vo sector of V-ATPase in the adult cortex and hippocampus
Authors: Zhang M / Feng J
History
DepositionDec 26, 2023-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_38449.png

Downloads & links

-
Map

FileDownload / File: emd_38449.map.gz / Format: CCP4 / Size: 303.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 430 pix.
= 460.53 Å		1.07 Å/pix.
x 430 pix.
= 460.53 Å		1.07 Å/pix.
x 430 pix.
= 460.53 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.071 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-0.25220707 - 0.4690498
Average (Standard dev.)0.00042637618 (±0.011495095)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions430430430
Spacing430430430
CellA=B=C: 460.53 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_38449_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_38449_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_38449_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Mammalian V0-ATPase from rat brain

EntireName: Mammalian V0-ATPase from rat brain
Components
  • Complex: Mammalian V0-ATPase from rat brain
    • Protein or peptide: V-type proton ATPase 116 kDa subunit a 1
    • Protein or peptide: ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a
    • Protein or peptide: V-type proton ATPase subunit S1
    • Protein or peptide: V-type proton ATPase subunit
    • Protein or peptide: V-type proton ATPase subunit e 2
    • Protein or peptide: Ribonuclease K
    • Protein or peptide: V-type proton ATPase 16 kDa proteolipid subunit c
    • Protein or peptide: Renin receptor cytoplasmic fragment

-
Supramolecule #1: Mammalian V0-ATPase from rat brain

SupramoleculeName: Mammalian V0-ATPase from rat brain / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rattus norvegicus (Norway rat)

-
Macromolecule #1: V-type proton ATPase 116 kDa subunit a 1

MacromoleculeName: V-type proton ATPase 116 kDa subunit a 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 95.248148 KDa
SequenceString: LFRSEEMTLA QLFLQSEAAY CCVSELEELG KVQFRDLNPD VNVFQRKFVN EVRRCEEMDR KLRFVEKEIR KANIPIMDTG ENPEVPFPR DMIDLEANFE KIENELKEIN TNQEALKRNF LELTELKFIL RKTQQFFDEM ADPDLLEESS SLLEPNEMGR G APLRLGFV ...String:
LFRSEEMTLA QLFLQSEAAY CCVSELEELG KVQFRDLNPD VNVFQRKFVN EVRRCEEMDR KLRFVEKEIR KANIPIMDTG ENPEVPFPR DMIDLEANFE KIENELKEIN TNQEALKRNF LELTELKFIL RKTQQFFDEM ADPDLLEESS SLLEPNEMGR G APLRLGFV AGVINRERIP TFERMLWRVC RGNVFLRQAE IENPLEDPVT GDYVHKSVFI IFFQGDQLKN RVKKICEGFR AS LYPCPET PQERKEMASG VNTRIDDLQM VLNQTEDHRQ RVLQAAAKNI RVWFIKVRKM KAIYHTLNLC NIDVTQKCLI AEV WCPVTD LDSIQFALRR GTEHSGSTVP SILNRMQTNQ TPPTYNKTNK FTHGFQNIVD AYGIGTYREI NPAPYTVITF PFLF AVMFG DFGHGILMTL FAVWMVLRES RILSQKNENE MFSMVFSGRY IILLMGLFSI YTGLIYNDCF SKSLNIFGSS WSVRP MFTI GNWTEETLLG SSVLQLNPAI PGVFGGPYPF GIDPIWNIAT NKLTFLNSFK MKMSVILGII HMLFGVSLSL FNHIYF KKP LNIYFGFIPE IIFMSSLFGY LVILIFYKWT AYDAHSSRNA PSLLIHFINM FLFSYPESGN AMLYSGQKGI QCFLIVV AM LCVPWMLLFK PLILRHQYLR KKHLGTLNFG GIRVGNGPTE EDAEIIQHDQ LSTHSEDAEE PTEDEVFDFG DTMVHQAI H TIEYCLGCIS NTASYLRLWA LSLAHAQLSE VLWTMVIHIG LHVRSLAGGL GLFFIFAAFA TLTVAILLIM EGLSAFLHA LRLHWVEFQN KFYTGTGFKF LPFSFEHI

UniProtKB: V-type proton ATPase 116 kDa subunit a 1

-
Macromolecule #2: ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a

MacromoleculeName: ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 21.37227 KDa
SequenceString: TGLELLYLGI FVAFWACMIV VGICYTIFDL GFRFDVAWFL TETSPFMWSN LGIGLAISLS VVGAAWGIYI TGSSIIGGGV KAPRIKTKN LVSIIFCEAV AIYGIIMAIV ISNMAEPFSA TDPKAIGHRN YHAGYSMFGA GLTVGLSNLF CGVCVGIVGS G AALADAQN ...String:
TGLELLYLGI FVAFWACMIV VGICYTIFDL GFRFDVAWFL TETSPFMWSN LGIGLAISLS VVGAAWGIYI TGSSIIGGGV KAPRIKTKN LVSIIFCEAV AIYGIIMAIV ISNMAEPFSA TDPKAIGHRN YHAGYSMFGA GLTVGLSNLF CGVCVGIVGS G AALADAQN PSLFVKILIV EIFGSAIGLF GVIVAILQTS RVKMG

UniProtKB: ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a

-
Macromolecule #3: V-type proton ATPase subunit S1

MacromoleculeName: V-type proton ATPase subunit S1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 23.360582 KDa
SequenceString: IHPPVSYNDT APRILFWAQN FSVAYKDEWK DLTSLTFGVE NLNLTGSFWN DSFAMLSLTY EPLFGATVTF KFILASRFYP VSARYWFTM ERLEIHSNGS VAHFNVSQVT GPSIYSFHCE YVSSLSKKGS LLVTNVPSLW QMTLHNFQIQ AFNVTGEQFS Y ASDCAGFF ...String:
IHPPVSYNDT APRILFWAQN FSVAYKDEWK DLTSLTFGVE NLNLTGSFWN DSFAMLSLTY EPLFGATVTF KFILASRFYP VSARYWFTM ERLEIHSNGS VAHFNVSQVT GPSIYSFHCE YVSSLSKKGS LLVTNVPSLW QMTLHNFQIQ AFNVTGEQFS Y ASDCAGFF SPGIWMGLLT TLFMLFIFTY GLHMILSLKT MDRFDD

UniProtKB: V-type proton ATPase subunit S1

-
Macromolecule #4: V-type proton ATPase subunit

MacromoleculeName: V-type proton ATPase subunit / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 39.28568 KDa
SequenceString: SFFPELYFNV DNGYLEGLVR GLKAGVLSQA DYLNLVQCET LEDLKLHLQS TDYGNFLANE ASPLTVSVID DKLKEKMVVE FRHMRNHAY EPLASFLDFI TYSYMIDNVI LLITGTLHQK CHPLGSFEQM EAVNIAQTPA ELYNAILVDT PLAAFFQDCI S EQDLDAMN ...String:
SFFPELYFNV DNGYLEGLVR GLKAGVLSQA DYLNLVQCET LEDLKLHLQS TDYGNFLANE ASPLTVSVID DKLKEKMVVE FRHMRNHAY EPLASFLDFI TYSYMIDNVI LLITGTLHQK CHPLGSFEQM EAVNIAQTPA ELYNAILVDT PLAAFFQDCI S EQDLDAMN IEIIRNTLYK AYLESFYKFC TLLGGTTADA MCPILEFEAD RRAFIITINS FGTELSKEDR AKLFPHCGRL YP EGLAQLA RADDYEQVKN VADYYPEYKL LFEGAGSNPG DKTLEDRFFE HEVKLNKLAF LNQFHFGVFY AFVKLKEQEC RNI VWIAEC IAQRHRAKID NYIPIF

-
Macromolecule #5: V-type proton ATPase subunit e 2

MacromoleculeName: V-type proton ATPase subunit e 2 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 8.655396 KDa
SequenceString:
AHSFALPVII FTTFWGLIGI AGPWFVPKGP NRGVIITMLV ATAVCCYLFW LIAILAQLNP LFGPQLKNET IWYVRFL

UniProtKB: V-type proton ATPase subunit e 2

-
Macromolecule #6: Ribonuclease K

MacromoleculeName: Ribonuclease K / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 9.933642 KDa
SequenceString:
CCGPKLAACG IVLSAWGVIM LIMLGIFFNV HSAVLIEDVP FTEKDFENGP QNIYNLYEQV SYNCFIAAGL YLLLGGFSFC QVRLNKRKE

-
Macromolecule #7: V-type proton ATPase 16 kDa proteolipid subunit c

MacromoleculeName: V-type proton ATPase 16 kDa proteolipid subunit c / type: protein_or_peptide / ID: 7 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 15.256132 KDa
SequenceString:
NNPEYSSFFG VMGASSAMVF SAMGAAYGTA KSGTGIAAMS VMRPELIMKS IIPVVMAGII AIYGLVVAVL IANSLTDGIT LYRSFLQLG AGLSVGLSGL AAGFAIGIVG DAGVRGTAQQ PRLFVGMILI LIFAEVLGLY GLIVALILST K

UniProtKB: V-type proton ATPase 16 kDa proteolipid subunit c

-
Macromolecule #8: Renin receptor cytoplasmic fragment

MacromoleculeName: Renin receptor cytoplasmic fragment / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 5.740624 KDa
SequenceString:
PYNLAYKYNL EYSVVFNLVL WIMTGLALAV IITSYNIWNM DPGYDSIIY

UniProtKB: Renin receptor

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statetissue

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: DIRECT ELECTRON DE-10 (5k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 34147
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
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