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- PDB-8xli: Structure of the Vo sector of V-ATPase in the adult cortex and hi... -

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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 / positive regulation of transforming growth factor beta1 production / synaptic vesicle lumen acidification / proton-transporting V-type ATPase, V0 domain / cellular response to increased oxygen levels / endosome to plasma membrane protein transport / vacuolar proton-transporting V-type ATPase, V0 domain / clathrin-coated vesicle membrane / lysosomal lumen acidification / proton-transporting V-type ATPase complex / head morphogenesis / vacuolar proton-transporting V-type ATPase complex / osteoclast development / vacuolar acidification / regulation of cellular pH / dendritic spine membrane / ROS and RNS production in phagocytes / Neutrophil degranulation / ATPase activator activity / regulation of MAPK cascade / autophagosome membrane / proton-transporting ATPase activity, rotational mechanism / regulation of macroautophagy / positive regulation of Wnt signaling pathway / transporter activator activity / angiotensin maturation / endoplasmic reticulum-Golgi intermediate compartment membrane / proton transmembrane transport / small GTPase binding / transmembrane transport / terminal bouton / synaptic vesicle / synaptic vesicle membrane / positive regulation of canonical Wnt signaling pathway / melanosome / signaling receptor activity / cell body / ATPase binding / intracellular iron ion homeostasis / postsynaptic membrane / positive regulation of ERK1 and ERK2 cascade / lysosome / endosome / endosome membrane / apical plasma membrane / axon / lysosomal membrane / external side of plasma 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 / Renin receptor N-terminal domain / V-type proton ATPase subunit S1/VOA1, transmembrane domain / V0 complex accessory subunit Ac45/VOA1 transmembrane domain ...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 / Renin receptor N-terminal domain / 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
V-type proton ATPase 21 kDa proteolipid subunit c'' / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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Components

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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

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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)

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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

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

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

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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

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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)

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Processing

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

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