[English] 日本語
Yorodumi
- PDB-8xli: Structure of the Vo sector of V-ATPase in the adult cortex and hi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8xli
TitleStructure of the Vo sector of V-ATPase in the adult cortex and hippocampus
Components
  • (V-type proton ATPase ...) x 5
  • ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a
  • Renin receptor cytoplasmic fragment
  • Ribonuclease K
KeywordsMEMBRANE PROTEIN / Vo sector of V-ATPase
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsZhang, M. / Feng, J. / Li, Y. / Zhu, S.
Funding support China, 1items
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, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
a: V-type proton ATPase 116 kDa subunit a 1
b: ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a
c: V-type proton ATPase subunit S1
d: V-type proton ATPase subunit
e: V-type proton ATPase subunit e 2
f: Ribonuclease K
g: V-type proton ATPase 16 kDa proteolipid subunit c
h: V-type proton ATPase 16 kDa proteolipid subunit c
i: V-type proton ATPase 16 kDa proteolipid subunit c
j: V-type proton ATPase 16 kDa proteolipid subunit c
k: V-type proton ATPase 16 kDa proteolipid subunit c
l: V-type proton ATPase 16 kDa proteolipid subunit c
m: V-type proton ATPase 16 kDa proteolipid subunit c
n: V-type proton ATPase 16 kDa proteolipid subunit c
o: V-type proton ATPase 16 kDa proteolipid subunit c
p: Renin receptor cytoplasmic fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)342,59920
Polymers340,90216
Non-polymers1,6984
Water00
1


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

-
Components

-
V-type proton ATPase ... , 5 types, 13 molecules acdeghijklmno

#1: Protein V-type proton ATPase 116 kDa subunit a 1 / V-ATPase 116 kDa subunit a 1 / Clathrin-coated vesicle/synaptic vesicle proton pump 116 kDa subunit ...V-ATPase 116 kDa subunit a 1 / Clathrin-coated vesicle/synaptic vesicle proton pump 116 kDa subunit / Vacuolar adenosine triphosphatase subunit Ac116 / Vacuolar proton pump subunit 1 / Vacuolar proton translocating ATPase 116 kDa subunit a isoform 1


Mass: 95248.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P25286
#3: Protein V-type proton ATPase subunit S1 / V-ATPase subunit S1 / C7-1 protein / V-ATPase Ac45 subunit / V-ATPase S1 accessory protein / ...V-ATPase subunit S1 / C7-1 protein / V-ATPase Ac45 subunit / V-ATPase S1 accessory protein / Vacuolar proton pump subunit S1


Mass: 23360.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: O54715
#4: Protein V-type proton ATPase subunit


Mass: 39285.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat)
#5: Protein V-type proton ATPase subunit e 2 / V-ATPase subunit e 2 / Vacuolar proton pump subunit e 2


Mass: 8655.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q5EB76
#7: Protein
V-type proton ATPase 16 kDa proteolipid subunit c / V-ATPase 16 kDa proteolipid subunit c / Vacuolar proton pump 16 kDa proteolipid subunit c


Mass: 15256.132 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P63081

-
Protein , 2 types, 2 molecules bf

#2: Protein ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a / Atp6v0b protein


Mass: 21372.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: B0K022
#6: Protein Ribonuclease K


Mass: 9933.642 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat)

-
Protein/peptide / Sugars , 2 types, 5 molecules p

#8: Protein/peptide Renin receptor cytoplasmic fragment


Mass: 5740.624 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q6AXS4
#9: 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.: 4 / Source method: obtained synthetically
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

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Mammalian V0-ATPase from rat brain / Type: COMPLEX / Entity ID: #1-#8 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
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: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: DIRECT ELECTRON DE-10 (5k x 4k)

-
Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 34147 / Symmetry type: POINT

+
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