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- PDB-6xbw: Cryo-EM structure of V-ATPase from bovine brain, state 1 -

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Entry
Database: PDB / ID: 6xbw
TitleCryo-EM structure of V-ATPase from bovine brain, state 1
Components
  • (V-type proton ATPase ...) x 14
  • Renin receptor
  • Ribonuclease kappa
KeywordsPROTON TRANSPORT
Function / homology
Function and homology information


ROS and RNS production in phagocytes / Insulin receptor recycling / Transferrin endocytosis and recycling / Amino acids regulate mTORC1 / Ion channel transport / Metabolism of Angiotensinogen to Angiotensins / pH reduction / RHOA GTPase cycle / plasma membrane proton-transporting V-type ATPase complex / cellular response to increased oxygen levels ...ROS and RNS production in phagocytes / Insulin receptor recycling / Transferrin endocytosis and recycling / Amino acids regulate mTORC1 / Ion channel transport / Metabolism of Angiotensinogen to Angiotensins / pH reduction / RHOA GTPase cycle / plasma membrane proton-transporting V-type ATPase complex / cellular response to increased oxygen levels / synaptic vesicle lumen acidification / vacuolar 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 / cell projection organization / 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 / Neutrophil degranulation / ATPase activator activity / microvillus / autophagosome membrane / positive regulation of Wnt signaling pathway / cilium assembly / regulation of macroautophagy / ATP metabolic process / H+-transporting two-sector ATPase / transport vesicle / receptor-mediated endocytosis of virus by host cell / ruffle / proton-transporting ATPase activity, rotational mechanism / endoplasmic reticulum-Golgi intermediate compartment membrane / RNA endonuclease activity / proton-transporting ATP synthase activity, rotational mechanism / receptor-mediated endocytosis / endomembrane system / proton transmembrane transport / cilium / transmembrane transport / synaptic vesicle membrane / positive regulation of canonical Wnt signaling pathway / melanosome / signaling receptor activity / ATPase binding / intracellular iron ion homeostasis / postsynaptic membrane / Hydrolases; Acting on ester bonds / early endosome / lysosome / endosome / endosome membrane / nuclear speck / apical plasma membrane / axon / lysosomal membrane / external side of plasma membrane / centrosome / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / ATP hydrolysis activity / ATP binding / membrane / plasma membrane / cytosol
Similarity search - Function
Helix Hairpins - #3240 / ATP synthase, E subunit, C-terminal / hypothetical protein PF0899 fold / 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 / ATPase, V1 complex, subunit H ...Helix Hairpins - #3240 / ATP synthase, E subunit, C-terminal / hypothetical protein PF0899 fold / 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 / ATPase, V1 complex, subunit H / ATPase, V1 complex, subunit H, C-terminal / ATPase, V1 complex, subunit H, C-terminal domain superfamily / V-ATPase subunit H / V-ATPase subunit H / ATPase, V1 complex, subunit A / Ribonuclease kappa / ATPase, V1 complex, subunit C / Vacuolar ATP synthase subunit C superfamily / V-ATPase subunit C / V-type proton ATPase subunit S1/VOA1, transmembrane domain / V0 complex accessory subunit Ac45/VOA1 transmembrane domain / Vacuolar (H+)-ATPase G subunit / Vacuolar (H+)-ATPase G subunit / ATPase, V1 complex, subunit B / 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 / V-type ATPase subunit E / ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F superfamily / V-type ATPase subunit E, C-terminal domain superfamily / ATP synthase subunit D / ATP synthase (F/14-kDa) subunit / ATP synthase (E/31 kDa) subunit / V-type ATP synthase regulatory subunit B/beta / V-type ATP synthase catalytic alpha chain / ATPsynthase alpha/beta subunit, N-terminal extension / ATPsynthase alpha/beta subunit barrel-sandwich domain / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / : / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / Armadillo-like helical / Helix Hairpins / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / OLEIC ACID / Chem-POV / V-type proton ATPase subunit D / V-type proton ATPase subunit a / V-type proton ATPase subunit H / V-type proton ATPase subunit E 1 / V-type proton ATPase subunit C 1 / V-type proton ATPase 16 kDa proteolipid subunit c / V-type proton ATPase catalytic subunit A ...ADENOSINE-5'-DIPHOSPHATE / OLEIC ACID / Chem-POV / V-type proton ATPase subunit D / V-type proton ATPase subunit a / V-type proton ATPase subunit H / V-type proton ATPase subunit E 1 / V-type proton ATPase subunit C 1 / V-type proton ATPase 16 kDa proteolipid subunit c / V-type proton ATPase catalytic subunit A / V-type proton ATPase subunit B, brain isoform / V-type proton ATPase subunit D / V-type proton ATPase subunit S1 / V-type proton ATPase subunit d 1 / Renin receptor / V-type proton ATPase subunit G 2 / V-type proton ATPase subunit F / V-type proton ATPase 116 kDa subunit a 1 / V-type proton ATPase subunit e 2 / V-type proton ATPase 21 kDa proteolipid subunit c'' / Ribonuclease kappa
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsWang, R. / Li, X.
CitationJournal: Nat Commun / Year: 2020
Title: Cryo-EM structures of intact V-ATPase from bovine brain.
Authors: Rong Wang / Tao Long / Abdirahman Hassan / Jin Wang / Yingyuan Sun / Xiao-Song Xie / Xiaochun Li /
Abstract: The vacuolar-type H-ATPases (V-ATPase) hydrolyze ATP to pump protons across the plasma or intracellular membrane, secreting acids to the lumen or acidifying intracellular compartments. It has been ...The vacuolar-type H-ATPases (V-ATPase) hydrolyze ATP to pump protons across the plasma or intracellular membrane, secreting acids to the lumen or acidifying intracellular compartments. It has been implicated in tumor metastasis, renal tubular acidosis, and osteoporosis. Here, we report two cryo-EM structures of the intact V-ATPase from bovine brain with all the subunits including the subunit H, which is essential for ATPase activity. Two type-I transmembrane proteins, Ac45 and (pro)renin receptor, along with subunit c", constitute the core of the c-ring. Three different conformations of A/B heterodimers suggest a mechanism for ATP hydrolysis that triggers a rotation of subunits DF, inducing spinning of subunit d with respect to the entire c-ring. Moreover, many lipid molecules have been observed in the Vo domain to mediate the interactions between subunit c, c", (pro)renin receptor, and Ac45. These two structures reveal unique features of mammalian V-ATPase and suggest a mechanism of V1-Vo torque transmission.
History
DepositionJun 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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Assembly

Deposited unit
A: V-type proton ATPase catalytic subunit A
B: V-type proton ATPase catalytic subunit A
C: V-type proton ATPase catalytic subunit A
D: V-type proton ATPase subunit B, brain isoform
E: V-type proton ATPase subunit B, brain isoform
F: V-type proton ATPase subunit B, brain isoform
G: V-type proton ATPase subunit C 1
H: V-type proton ATPase subunit D
I: V-type proton ATPase subunit E 1
J: V-type proton ATPase subunit E 1
K: V-type proton ATPase subunit E 1
L: V-type proton ATPase subunit F
M: V-type proton ATPase subunit G
N: V-type proton ATPase subunit G
O: V-type proton ATPase subunit G
P: V-type proton ATPase subunit H
a: V-type proton ATPase subunit a
b: V-type proton ATPase 21 kDa proteolipid subunit
d: V-type proton ATPase subunit d 1
e: V-type proton ATPase subunit e 2
s: V-type proton ATPase subunit S1
r: Renin receptor
c: V-type proton ATPase 16 kDa proteolipid subunit
g: 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: V-type proton ATPase 16 kDa proteolipid subunit
q: V-type proton ATPase 16 kDa proteolipid subunit
f: Ribonuclease kappa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,054,73950
Polymers1,045,83832
Non-polymers8,90218
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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V-type proton ATPase ... , 14 types, 30 molecules ABCDEFGHIJKLMNOPabdescgklmnopq

#1: Protein V-type proton ATPase catalytic subunit A / V-ATPase subunit A / V-ATPase 69 kDa subunit / Vacuolar proton pump subunit alpha


Mass: 68420.914 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle)
References: UniProt: P31404, H+-transporting two-sector ATPase
#2: Protein V-type proton ATPase subunit B, brain isoform / V-ATPase subunit B 2 / Endomembrane proton pump 58 kDa subunit / Vacuolar proton pump subunit B 2


Mass: 56637.555 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P31408
#3: Protein V-type proton ATPase subunit C 1 / V-ATPase subunit C 1 / Vacuolar proton pump subunit C 1


Mass: 44042.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P21282
#4: Protein V-type proton ATPase subunit D


Mass: 28297.893 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: A0A3Q1M4W9, UniProt: P39942*PLUS
#5: Protein V-type proton ATPase subunit E 1 / V-ATPase subunit E 1 / V-ATPase 31 kDa subunit / P31 / Vacuolar proton pump subunit E 1


Mass: 26178.371 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P11019
#6: Protein V-type proton ATPase subunit F / V-ATPase subunit F / V-ATPase 14 kDa subunit / Vacuolar proton pump subunit F


Mass: 13417.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q28029
#7: Protein V-type proton ATPase subunit G


Mass: 13588.344 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q0VCV6
#8: Protein V-type proton ATPase subunit H


Mass: 54155.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: F1MZL6
#9: Protein V-type proton ATPase subunit a


Mass: 96431.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: F1MJV0, UniProt: Q29466*PLUS
#10: Protein V-type proton ATPase 21 kDa proteolipid subunit / V-ATPase 21 kDa proteolipid subunit / Vacuolar proton pump 21 kDa proteolipid subunit


Mass: 21530.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q2TA24
#11: Protein V-type proton ATPase subunit d 1 / V-ATPase subunit d 1 / 32 kDa accessory protein / P39 / V-ATPase 40 kDa accessory protein / V- ...V-ATPase subunit d 1 / 32 kDa accessory protein / P39 / V-ATPase 40 kDa accessory protein / V-ATPase AC39 subunit / Vacuolar proton pump subunit d 1


Mass: 40369.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P61420
#12: Protein V-type proton ATPase subunit e 2 / V-ATPase subunit e 2 / Vacuolar proton pump subunit e 2


Mass: 9188.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q2KIB5
#13: Protein V-type proton ATPase subunit S1 / V-ATPase subunit S1 / V-ATPase Ac45 subunit / V-ATPase S1 accessory protein / Vacuolar proton pump subunit S1


Mass: 51818.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P40682
#15: Protein
V-type proton ATPase 16 kDa proteolipid subunit / V-ATPase 16 kDa proteolipid subunit / Vacuolar proton pump 16 kDa proteolipid subunit


Mass: 15727.726 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P23956

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Protein , 2 types, 2 molecules rf

#14: 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 / Vacuolar ATP synthase membrane sector-associated protein M8-9 / V-ATPase M8.9 subunit


Mass: 39529.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P81134
#16: Protein Ribonuclease kappa / RNase kappa


Mass: 11030.029 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle)
References: UniProt: Q3ZC23, Hydrolases; Acting on ester bonds

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Sugars , 1 types, 6 molecules

#20: 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.: 6 / 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

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Non-polymers , 4 types, 12 molecules

#17: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#18: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#19: Chemical
ChemComp-POV / (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / POPC


Mass: 760.076 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C42H82NO8P / Comment: phospholipid*YM
#21: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2

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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: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of V-ATPase complex from bovine brain, state 1
Type: COMPLEX / Entity ID: #1-#16 / Source: NATURAL
Source (natural)Organism: Bos taurus (domestic cattle)
Buffer solutionpH: 7.5
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
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 84345 / Symmetry type: POINT

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