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- PDB-7u8r: Structure of porcine kidney V-ATPase with SidK, Rotary State 3 -

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Entry
Database: PDB / ID: 7u8r
TitleStructure of porcine kidney V-ATPase with SidK, Rotary State 3
Components
  • (V-type proton ATPase ...) x 12
  • ATPase H(+)-transporting lysosomal accessory protein 2
  • ATPase H+ transporting accessory protein 1
  • Bacterial effector protein SidK
  • Ribonuclease kappa
  • Vacuolar proton pump subunit B
KeywordsMEMBRANE PROTEIN / proton translocation / complex
Function / homology
Function and homology information


ROS and RNS production in phagocytes / RHOA GTPase cycle / Transferrin endocytosis and recycling / Amino acids regulate mTORC1 / Ion channel transport / Insulin receptor recycling / transporter activator activity / plasma membrane proton-transporting V-type ATPase complex / cellular response to increased oxygen levels / proton-transporting V-type ATPase, V1 domain ...ROS and RNS production in phagocytes / RHOA GTPase cycle / Transferrin endocytosis and recycling / Amino acids regulate mTORC1 / Ion channel transport / Insulin receptor recycling / transporter activator activity / plasma membrane proton-transporting V-type ATPase complex / cellular response to increased oxygen levels / proton-transporting V-type ATPase, V1 domain / proton-transporting V-type ATPase, V0 domain / synaptic vesicle lumen acidification / proton-transporting two-sector ATPase complex, catalytic domain / endosome to plasma membrane protein transport / clathrin-coated vesicle membrane / vacuolar transport / vacuolar proton-transporting V-type ATPase, V0 domain / vacuolar proton-transporting V-type ATPase, V1 domain / vacuolar proton-transporting V-type ATPase complex / proton-transporting V-type ATPase complex / cell projection organization / vacuolar acidification / osteoclast development / dendritic spine membrane / regulation of cellular pH / vacuolar membrane / microvillus / ATPase activator activity / autophagosome membrane / ATP metabolic process / H+-transporting two-sector ATPase / transport vesicle / proton-transporting ATPase activity, rotational mechanism / RNA endonuclease activity / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / small GTPase binding / synaptic vesicle membrane / melanosome / presynapse / signaling receptor activity / ATPase binding / intracellular iron ion homeostasis / lysosome / early endosome / endosome membrane / endosome / apical plasma membrane / lysosomal membrane / endoplasmic reticulum membrane / ATP hydrolysis activity / ATP binding / membrane / plasma membrane / cytosol / 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 protein / 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 ...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 protein / 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 / V-type proton ATPase subunit S1/VOA1, transmembrane domain / V0 complex accessory subunit Ac45/VOA1 transmembrane domain / ATPase, V1 complex, subunit C / Vacuolar ATP synthase subunit C superfamily / V-ATPase subunit C / 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 / V-type ATPase subunit E / V-type ATPase subunit E, C-terminal domain superfamily / ATP synthase (E/31 kDa) subunit / 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-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 N-term extension / 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 / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / V-type proton ATPase subunit D / Renin receptor / V-type proton ATPase 21 kDa proteolipid subunit isoform 1 / Ribonuclease kappa / V-type proton ATPase subunit a / V-type proton ATPase subunit / V-type proton ATPase subunit / V-type proton ATPase subunit G / V-type proton ATPase proteolipid subunit ...ADENOSINE-5'-DIPHOSPHATE / V-type proton ATPase subunit D / Renin receptor / V-type proton ATPase 21 kDa proteolipid subunit isoform 1 / Ribonuclease kappa / V-type proton ATPase subunit a / V-type proton ATPase subunit / V-type proton ATPase subunit / V-type proton ATPase subunit G / V-type proton ATPase proteolipid subunit / Vacuolar proton pump subunit B / V-type proton ATPase subunit C / V-type proton ATPase subunit F / ATPase H+ transporting accessory protein 1 / V-type proton ATPase subunit E 1 / V-type proton ATPase catalytic subunit A / Type IV secretion protein Dot / V-type proton ATPase subunit H
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsTan, Y.Z. / Keon, K.A.
Funding support Canada, Singapore, 4items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT166152 Canada
Canadian Institutes of Health Research (CIHR)FDN-143202 Canada
Canadian Institutes of Health Research (CIHR)FDN-143301 Canada
Ministry of Education (MoE, Singapore) Singapore
CitationJournal: Life Sci Alliance / Year: 2022
Title: CryoEM of endogenous mammalian V-ATPase interacting with the TLDc protein mEAK-7.
Authors: Yong Zi Tan / Yazan M Abbas / Jing Ze Wu / Di Wu / Kristine A Keon / Geoffrey G Hesketh / Stephanie A Bueler / Anne-Claude Gingras / Carol V Robinson / Sergio Grinstein / John L Rubinstein /
Abstract: V-ATPases are rotary proton pumps that serve as signaling hubs with numerous protein binding partners. CryoEM with exhaustive focused classification allowed detection of endogenous proteins ...V-ATPases are rotary proton pumps that serve as signaling hubs with numerous protein binding partners. CryoEM with exhaustive focused classification allowed detection of endogenous proteins associated with porcine kidney V-ATPase. An extra C subunit was found in ∼3% of complexes, whereas ∼1.6% of complexes bound mEAK-7, a protein with proposed roles in dauer formation in nematodes and mTOR signaling in mammals. High-resolution cryoEM of porcine kidney V-ATPase with recombinant mEAK-7 showed that mEAK-7's TLDc domain interacts with V-ATPase's stator, whereas its C-terminal α helix binds V-ATPase's rotor. This crosslink would be expected to inhibit rotary catalysis. However, unlike the yeast TLDc protein Oxr1p, exogenous mEAK-7 does not inhibit V-ATPase and mEAK-7 overexpression in cells does not alter lysosomal or phagosomal pH. Instead, cryoEM suggests that the mEAK-7:V-ATPase interaction is disrupted by ATP-induced rotation of the rotor. Comparison of Oxr1p and mEAK-7 binding explains this difference. These results show that V-ATPase binding by TLDc domain proteins can lead to effects ranging from strong inhibition to formation of labile interactions that are sensitive to the enzyme's activity.
History
DepositionMar 9, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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: Vacuolar proton pump subunit B
E: Vacuolar proton pump subunit B
F: Vacuolar proton pump subunit B
G: V-type proton ATPase subunit C
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
Q: Bacterial effector protein SidK
R: Bacterial effector protein SidK
S: Bacterial effector protein SidK
T: V-type proton ATPase subunit H
a: V-type proton ATPase subunit a
b: V-type proton ATPase 21 kDa proteolipid subunit isoform 1
c: ATPase H+ transporting accessory protein 1
d: V-type proton ATPase subunit
e: V-type proton ATPase subunit
f: Ribonuclease kappa
g: V-type proton ATPase proteolipid subunit
h: V-type proton ATPase proteolipid subunit
i: V-type proton ATPase proteolipid subunit
j: V-type proton ATPase proteolipid subunit
k: V-type proton ATPase proteolipid subunit
l: V-type proton ATPase proteolipid subunit
m: V-type proton ATPase proteolipid subunit
n: V-type proton ATPase proteolipid subunit
o: V-type proton ATPase proteolipid subunit
p: ATPase H(+)-transporting lysosomal accessory protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,164,26736
Polymers1,163,84035
Non-polymers4271
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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V-type proton ATPase ... , 12 types, 26 molecules ABCGHIJKLMNOTabdeghijklmno

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


Mass: 68393.844 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: Q29048, H+-transporting two-sector ATPase
#3: Protein V-type proton ATPase subunit C


Mass: 44066.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1S0R4
#4: Protein V-type proton ATPase subunit D / V-type proton ATPase subunit d / Vacuolar proton pump subunit D


Mass: 28301.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZJL5
#5: Protein V-type proton ATPase subunit E 1 / V-type proton ATPase subunit E 1 isoform a


Mass: 26162.373 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: K9J4U3
#6: Protein V-type proton ATPase subunit F


Mass: 13403.288 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SMN6
#7: Protein V-type proton ATPase subunit G


Mass: 13748.474 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1UZN2
#9: Protein V-type proton ATPase subunit H / V-ATPase subunit H / V-ATPase 50/57 kDa subunits / Vacuolar proton pump subunit H / Vacuolar proton ...V-ATPase subunit H / V-ATPase 50/57 kDa subunits / Vacuolar proton pump subunit H / Vacuolar proton pump subunit SFD


Mass: 55917.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q9TVC1
#10: Protein V-type proton ATPase subunit a


Mass: 96365.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1U3K4
#11: Protein V-type proton ATPase 21 kDa proteolipid subunit isoform 1


Mass: 21530.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A480L444
#13: Protein V-type proton ATPase subunit


Mass: 40369.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1UJS8
#14: Protein V-type proton ATPase subunit


Mass: 9343.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1U843
#16: Protein
V-type proton ATPase proteolipid subunit


Mass: 15639.677 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VUN6

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Protein , 5 types, 9 molecules DEFQRScfp

#2: Protein Vacuolar proton pump subunit B / V-ATPase subunit B / Vacuolar proton pump subunit B


Mass: 57162.859 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1W9K3
#8: Protein Bacterial effector protein SidK


Mass: 38539.371 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZWW6
#12: Protein ATPase H+ transporting accessory protein 1 / V-type proton ATPase subunit S1


Mass: 51547.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: K9IWA3
#15: Protein Ribonuclease kappa


Mass: 11016.065 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A480L8C4
#17: Protein ATPase H(+)-transporting lysosomal accessory protein 2 / ATPase H(+)-transporting lysosomal-interacting protein 2 / Renin receptor / Renin/prorenin receptor


Mass: 39200.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287AJK1

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Non-polymers , 1 types, 1 molecules

#18: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM

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Details

Has ligand of interestY

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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: Porcine kidney V-ATPase with SidK, Rotary State 3 / Type: COMPLEX / Entity ID: #1-#17 / Source: MULTIPLE SOURCES
Source (natural)Organism: Sus scrofa (pig)
Buffer solutionpH: 7.4
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: 3911.445 nm / Nominal defocus min: 100 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22866 / Symmetry type: POINT

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