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- PDB-9det: Human V-ATPase Vo subcomplex (containing subunit isoform a4) boun... -

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Basic information

Entry
Database: PDB / ID: 9det
TitleHuman V-ATPase Vo subcomplex (containing subunit isoform a4) bound to nanobody and inhibitor
Components
  • (V-type proton ATPase ...) x 6
  • Anti V-ATPase Nanobody 2CAS66
  • Renin receptor
  • Ribonuclease kappa
KeywordsMEMBRANE PROTEIN / V-ATPase / lipid nanodisc / Vo subcomplex / inhibitor
Function / homology
Function and homology information


proton-transporting two-sector ATPase complex / Ion channel transport / Regulation of MITF-M-dependent genes involved in lysosome biogenesis and autophagy / renal tubular secretion / intracellular pH reduction / plasma membrane proton-transporting V-type ATPase complex / eye pigmentation / central nervous system maturation / ATPase-coupled ion transmembrane transporter activity / rostrocaudal neural tube patterning ...proton-transporting two-sector ATPase complex / Ion channel transport / Regulation of MITF-M-dependent genes involved in lysosome biogenesis and autophagy / renal tubular secretion / intracellular pH reduction / plasma membrane proton-transporting V-type ATPase complex / eye pigmentation / central nervous system maturation / ATPase-coupled ion transmembrane transporter activity / rostrocaudal neural tube patterning / positive regulation of transforming growth factor beta1 production / Golgi lumen acidification / synaptic vesicle lumen acidification / proton-transporting V-type ATPase, V0 domain / Transferrin endocytosis and recycling / cellular response to increased oxygen levels / vacuolar transport / endosome to plasma membrane protein transport / vacuolar proton-transporting V-type ATPase, V0 domain / clathrin-coated vesicle membrane / lysosomal lumen acidification / endosomal lumen acidification / regulation of pH / XBP1(S) activates chaperone genes / proton-transporting V-type ATPase complex / Amino acids regulate mTORC1 / vacuolar proton-transporting V-type ATPase complex / head morphogenesis / osteoclast development / vacuolar acidification / ROS and RNS production in phagocytes / regulation of cellular pH / dendritic spine membrane / azurophil granule membrane / ATPase activator activity / regulation of MAPK cascade / autophagosome membrane / tertiary granule membrane / proton-transporting ATPase activity, rotational mechanism / ficolin-1-rich granule membrane / cilium assembly / RHOA GTPase cycle / positive regulation of Wnt signaling pathway / regulation of macroautophagy / transporter activator activity / Metabolism of Angiotensinogen to Angiotensins / angiotensin maturation / Insulin receptor recycling / proton-transporting ATP synthase activity, rotational mechanism / receptor-mediated endocytosis of virus by host cell / axon terminus / endoplasmic reticulum-Golgi intermediate compartment membrane / RNA endonuclease activity / proton transmembrane transport / ossification / receptor-mediated endocytosis / brush border membrane / sensory perception of sound / small GTPase binding / transmembrane transport / phagocytic vesicle membrane / apical part of cell / synaptic vesicle membrane / positive regulation of canonical Wnt signaling pathway / signaling receptor activity / ATPase binding / basolateral plasma membrane / Hydrolases; Acting on ester bonds / intracellular iron ion homeostasis / postsynaptic membrane / early endosome / lysosome / endosome / endosome membrane / apical plasma membrane / Golgi membrane / axon / lysosomal membrane / external side of plasma membrane / focal adhesion / ubiquitin protein ligase binding / Neutrophil degranulation / endoplasmic reticulum membrane / protein-containing complex binding / extracellular exosome / membrane / plasma membrane
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 f-like ...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 f-like / Ribonuclease kappa / 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 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 / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C
Similarity search - Domain/homology
: / CHOLESTEROL / Chem-POV / Chem-WJP / V-type proton ATPase subunit e 1 / Renin receptor / V-type proton ATPase 16 kDa proteolipid subunit c / V-type proton ATPase subunit d 1 / V-type proton ATPase subunit S1 / Ribonuclease kappa ...: / CHOLESTEROL / Chem-POV / Chem-WJP / V-type proton ATPase subunit e 1 / Renin receptor / V-type proton ATPase 16 kDa proteolipid subunit c / V-type proton ATPase subunit d 1 / V-type proton ATPase subunit S1 / Ribonuclease kappa / V-type proton ATPase 21 kDa proteolipid subunit c'' / V-type proton ATPase 116 kDa subunit a 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsOot, R.A. / Park, J.B. / Roh, S.-H. / Wilkens, S.
Funding support United States, Korea, Republic Of, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM141908 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA228340 United States
Other private73258
National Research Foundation (NRF, Korea)2020R1A6C101A183 Korea, Republic Of
National Research Foundation (NRF, Korea)2021M3A9I4021220 Korea, Republic Of
CitationJournal: To Be Published
Title: Inhibitor bound Vo subcomplex from human V-ATPase
Authors: Oot, R.A. / Park, J.B. / Roh, S.-H. / Wilkens, S.
History
DepositionAug 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 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
e: V-type proton ATPase subunit e 1
f: Ribonuclease kappa
o: V-type proton ATPase subunit S1
p: Renin receptor
b: V-type proton ATPase 21 kDa proteolipid subunit
c: V-type proton ATPase 16 kDa proteolipid subunit
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
d: V-type proton ATPase subunit d 1
a: V-type proton ATPase 116 kDa subunit a 4
q: Anti V-ATPase Nanobody 2CAS66
hetero molecules


Theoretical massNumber of molelcules
Total (without water)442,63339
Polymers433,72117
Non-polymers8,91222
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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

#1: Protein V-type proton ATPase subunit e 1 / V-ATPase subunit e 1 / V-ATPase 9.2 kDa membrane accessory protein / V-ATPase M9.2 subunit / ...V-ATPase subunit e 1 / V-ATPase 9.2 kDa membrane accessory protein / V-ATPase M9.2 subunit / Vacuolar proton pump subunit e 1


Mass: 9380.329 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: O15342
#3: Protein V-type proton ATPase subunit S1 / V-ATPase subunit S1 / Protein XAP-3 / V-ATPase Ac45 subunit / V-ATPase S1 accessory protein / ...V-ATPase subunit S1 / Protein XAP-3 / V-ATPase Ac45 subunit / V-ATPase S1 accessory protein / Vacuolar proton pump subunit S1


Mass: 52067.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q15904
#5: Protein V-type proton ATPase 21 kDa proteolipid subunit / V-ATPase 21 kDa proteolipid subunit / Vacuolar proton pump 21 kDa proteolipid subunit / hATPL


Mass: 21418.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q99437
#6: Protein
V-type proton ATPase 16 kDa proteolipid subunit / V-ATPase 16 kDa proteolipid subunit / Vacuolar proton pump 16 kDa proteolipid subunit


Mass: 15743.655 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: P27449
#7: Protein V-type proton ATPase subunit d 1 / V-ATPase subunit d 1 / 32 kDa accessory protein / V-ATPase 40 kDa accessory protein / V-ATPase AC39 ...V-ATPase subunit d 1 / 32 kDa accessory protein / V-ATPase 40 kDa accessory protein / V-ATPase AC39 subunit / p39 / Vacuolar proton pump subunit d 1


Mass: 40369.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: P61421
#8: Protein V-type proton ATPase 116 kDa subunit a 4 / V-ATPase 116 kDa isoform a 4 / Vacuolar proton translocating ATPase 116 kDa subunit a isoform 4 / ...V-ATPase 116 kDa isoform a 4 / Vacuolar proton translocating ATPase 116 kDa subunit a isoform 4 / Vacuolar proton translocating ATPase 116 kDa subunit a kidney isoform


Mass: 99168.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-terminal 2 x FLAG tag / Source: (gene. exp.) Homo sapiens (human) / Gene: ATP6V0A4, ATP6N1B, ATP6N2 / Plasmid: pCDNA3 / Details (production host): C-terminal 2x FLAG tag / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q9HBG4

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Protein , 2 types, 2 molecules fp

#2: Protein Ribonuclease kappa / RNase kappa


Mass: 15435.220 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F
References: UniProt: Q6P5S7, Hydrolases; Acting on ester bonds
#4: 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 / ER-localized type I transmembrane adapter / Embryonic liver differentiation factor 10 / N14F / Renin/prorenin receptor / Vacuolar ATP synthase membrane sector-associated protein M8-9 / V-ATPase M8.9 subunit


Mass: 39045.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: O75787

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Antibody / Sugars , 2 types, 9 molecules q

#10: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#9: Antibody Anti V-ATPase Nanobody 2CAS66


Mass: 15142.920 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 4 types, 14 molecules

#11: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
#12: Chemical ChemComp-POV / (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / POPC


Mass: 760.076 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C42H82NO8P / Comment: phospholipid*YM
#13: Chemical
ChemComp-A1A4Q / Cladoniamide A


Mass: 437.833 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C22H16ClN3O5 / Feature type: SUBJECT OF INVESTIGATION
#14: Chemical ChemComp-WJP / methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate / dolichol-pp


Mass: 534.603 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H48O7P2

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Details

Has ligand of interestY
Has protein modificationY

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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: Vo subcomplex from human V-ATPase bound to Nanobody and inhibitor
Type: COMPLEX
Details: Subunit a, isoform 4 (a4) carrying a C-terminal 2x FLAG tag was stably expressed in HEK293F cells. All other subunits present in the complex are endogenously expressed and have formed a ...Details: Subunit a, isoform 4 (a4) carrying a C-terminal 2x FLAG tag was stably expressed in HEK293F cells. All other subunits present in the complex are endogenously expressed and have formed a complex with the FLAG tagged a4. The Nanobody was raised against a4 and used for concentrating the sample for EM. A small molecule inhibitor is also bound to the complex.
Entity ID: #1-#9 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human) / Cellular location: Membranes
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293F / Plasmid: pCDNA3
Buffer solutionpH: 7.2
Details: 20 mM Tris, 150 mM NaCl, 0.5 mM EDTA, 2 mM DTT, pH 7.2
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMSodium ChlorideNaCl1
220 mMTrisC4H11NO31
30.5 mMEthylenediaminetetraacetic acidC10H14N2Na2O81
42 mMDithiothreitolC4H10O2S21
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1300 nm
Image recordingElectron dose: 39.96 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 144439 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00325649
ELECTRON MICROSCOPYf_angle_d0.45434857
ELECTRON MICROSCOPYf_dihedral_angle_d7.3534076
ELECTRON MICROSCOPYf_chiral_restr0.0364016
ELECTRON MICROSCOPYf_plane_restr0.0034414

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