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- PDB-6vqc: Mammalian V-ATPase from rat brain membrane-embedded Vo region rot... -

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Basic information

Entry
Database: PDB / ID: 6vqc
TitleMammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 1 (from focused refinement)
Components
  • (V-type proton ATPase ...) x 6
  • ATPase H+-transporting V1 subunit D
  • ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a
  • Renin receptor
  • Ribonuclease K
KeywordsPROTON TRANSPORT / membrane protein complex / rotary 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 / plasma membrane proton-transporting V-type ATPase complex / Insulin receptor recycling / RHOA GTPase cycle / eye pigmentation / transporter activator activity ...Metabolism of Angiotensinogen to Angiotensins / Ion channel transport / Transferrin endocytosis and recycling / Amino acids regulate mTORC1 / negative regulation of autophagic cell death / plasma membrane proton-transporting V-type ATPase complex / Insulin receptor recycling / RHOA GTPase cycle / eye pigmentation / transporter activator activity / central nervous system maturation / rostrocaudal neural tube patterning / cellular response to increased oxygen levels / positive regulation of transforming growth factor beta1 production / proton-transporting V-type ATPase, V0 domain / synaptic vesicle lumen acidification / vacuolar transport / extrinsic component of synaptic vesicle membrane / endosome to plasma membrane protein transport / vacuolar proton-transporting V-type ATPase, V1 domain / clathrin-coated vesicle membrane / vacuolar proton-transporting V-type ATPase, V0 domain / lysosomal lumen acidification / endosomal lumen acidification / NURF complex / head morphogenesis / osteoclast development / vacuolar proton-transporting V-type ATPase complex / protein localization to cilium / vacuolar acidification / proton-transporting V-type ATPase complex / dendritic spine membrane / regulation of cellular pH / ROS and RNS production in phagocytes / Neutrophil degranulation / ATPase activator activity / regulation of MAPK cascade / MLL1 complex / autophagosome membrane / positive regulation of Wnt signaling pathway / cilium assembly / regulation of macroautophagy / angiotensin maturation / receptor-mediated endocytosis of virus by host cell / axon terminus / proton-transporting ATPase activity, rotational mechanism / endoplasmic reticulum-Golgi intermediate compartment membrane / RNA endonuclease activity / receptor-mediated endocytosis / proton transmembrane transport / terminal bouton / cilium / small GTPase binding / transmembrane transport / synaptic vesicle membrane / positive regulation of canonical Wnt signaling pathway / melanosome / synaptic vesicle / signaling receptor activity / cell body / ATPase binding / intracellular iron ion homeostasis / postsynaptic membrane / positive regulation of ERK1 and ERK2 cascade / early endosome / lysosome / endosome / endosome membrane / apical plasma membrane / axon / lysosomal membrane / external side of plasma membrane / centrosome / ubiquitin protein ligase binding / endoplasmic reticulum membrane / protein-containing complex binding / perinuclear region of cytoplasm / protein-containing complex / extracellular space / nucleoplasm / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
ATPase, V1 complex, subunit F / 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 / Ribonuclease kappa / V-type proton ATPase subunit S1/VOA1, transmembrane domain / V0 complex accessory subunit Ac45/VOA1 transmembrane domain ...ATPase, V1 complex, subunit F / 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 / Ribonuclease kappa / V-type proton ATPase subunit S1/VOA1, transmembrane domain / V0 complex accessory subunit Ac45/VOA1 transmembrane domain / ATPase, V1 complex, subunit F, eukaryotic / ATPase, V0 complex, subunit e1/e2 / ATP synthase subunit H / ATPase, V0 complex, subunit d / V-ATPase proteolipid subunit C, eukaryotic / ATPase, V0 complex, subunit 116kDa, eukaryotic / ATPase, V0 complex, c/d subunit / V-type ATPase subunit C/d / V-type ATP synthase subunit c/d subunit superfamily / V-type ATP synthase c/d subunit, domain 3 superfamily / ATP synthase (C/AC39) subunit / V-ATPase proteolipid subunit / V-type ATPase, V0 complex, 116kDa subunit family / V-type ATPase 116kDa subunit family / ATPase, V1 complex, subunit D / ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F superfamily / ATP synthase subunit D / ATP synthase (F/14-kDa) subunit / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a / Similar to RIKEN cDNA 1110020A23 / V-type proton ATPase subunit S1 / V-type proton ATPase 116 kDa subunit a 1 / V-type proton ATPase subunit F / V-type proton ATPase 16 kDa proteolipid subunit c / V-type proton ATPase subunit e 2 / V-type proton ATPase subunit / Renin receptor / V-type proton ATPase subunit D
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsAbbas, Y.M. / Rubinstein, J.L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Science / Year: 2020
Title: Structure of V-ATPase from the mammalian brain.
Authors: Yazan M Abbas / Di Wu / Stephanie A Bueler / Carol V Robinson / John L Rubinstein /
Abstract: In neurons, the loading of neurotransmitters into synaptic vesicles uses energy from proton-pumping vesicular- or vacuolar-type adenosine triphosphatases (V-ATPases). These membrane protein complexes ...In neurons, the loading of neurotransmitters into synaptic vesicles uses energy from proton-pumping vesicular- or vacuolar-type adenosine triphosphatases (V-ATPases). These membrane protein complexes possess numerous subunit isoforms, which complicates their analysis. We isolated homogeneous rat brain V-ATPase through its interaction with SidK, a effector protein. Cryo-electron microscopy allowed the construction of an atomic model, defining the enzyme's ATP:proton ratio as 3:10 and revealing a homolog of yeast subunit f in the membrane region, which we tentatively identify as RNAseK. The c ring encloses the transmembrane anchors for cleaved ATP6AP1/Ac45 and ATP6AP2/PRR, the latter of which is the (pro)renin receptor that, in other contexts, is involved in both Wnt signaling and the renin-angiotensin system that regulates blood pressure. This structure shows how ATP6AP1/Ac45 and ATP6AP2/PRR enable assembly of the enzyme's catalytic and membrane regions.
History
DepositionFeb 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
H: ATPase H+-transporting V1 subunit D
L: V-type proton ATPase subunit F
a: V-type proton ATPase 116 kDa subunit a isoform 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
h: V-type proton ATPase 16 kDa proteolipid subunit
i: V-type proton ATPase 16 kDa proteolipid subunit
j: V-type proton ATPase 16 kDa proteolipid subunit
k: V-type proton ATPase 16 kDa proteolipid subunit
l: V-type proton ATPase 16 kDa proteolipid subunit
m: V-type proton ATPase 16 kDa proteolipid subunit
n: V-type proton ATPase 16 kDa proteolipid subunit
o: V-type proton ATPase 16 kDa proteolipid subunit
p: Renin receptor


Theoretical massNumber of molelcules
Total (without water)452,96318
Polymers452,96318
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 4 types, 4 molecules Hbfp

#1: Protein ATPase H+-transporting V1 subunit D / ATPase / H+ transporting / V1 subunit D / isoform CRA_c / lysosomal V1 subunit D


Mass: 28359.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q6P503
#4: Protein ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a / ATPase / H+ transporting / lysosomal V0 subunit B / Atp6v0b protein


Mass: 21618.553 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: B0K022
#8: Protein Ribonuclease K / Rnasek protein


Mass: 11000.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: D3ZIM6
#10: Protein Renin receptor / ATPase H(+)-transporting lysosomal accessory protein 2 / ATPase H(+)-transporting lysosomal- ...ATPase H(+)-transporting lysosomal accessory protein 2 / ATPase H(+)-transporting lysosomal-interacting protein 2 / Renin/prorenin receptor


Mass: 39118.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q6AXS4

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V-type proton ATPase ... , 6 types, 14 molecules Lacdeghijklmno

#2: Protein V-type proton ATPase subunit F / V-ATPase subunit F / V-ATPase 14 kDa subunit / Vacuolar proton pump subunit F


Mass: 13389.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P50408
#3: Protein V-type proton ATPase 116 kDa subunit a isoform 1 / V-ATPase 116 kDa isoform a1 / Clathrin-coated vesicle/synaptic vesicle proton pump 116 kDa subunit ...V-ATPase 116 kDa isoform a1 / 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: 96429.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P25286
#5: 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: 51160.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: O54715
#6: Protein V-type proton ATPase subunit


Mass: 40341.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q5M7T6
#7: Protein V-type proton ATPase subunit e 2 / V-ATPase subunit e 2 / Vacuolar proton pump subunit e 2


Mass: 9203.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q5EB76
#9: Protein
V-type proton ATPase 16 kDa proteolipid subunit / V-ATPase 16 kDa proteolipid subunit / Vacuolar proton pump 16 kDa proteolipid subunit


Mass: 15815.833 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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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Membrane embedded region of rat brain V-ATPase composed of subunits a, c", c1-9, d, e, f, atp6ap1, atp6ap2, as well as subunits F and part of subunit D from the V1 region.
Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Rattus norvegicus (Norway rat)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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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
Image recordingElectron dose: 43 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM softwareName: cryoSPARC / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 90648 / Algorithm: BACK PROJECTION / Symmetry type: POINT

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