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- PDB-7uzf: Rat Kidney V-ATPase with SidK, State 1 -

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Basic information

Entry
Database: PDB / ID: 7uzf
TitleRat Kidney V-ATPase with SidK, State 1
Components
  • (ATPase H+-transporting V1 subunit ...) x 2
  • (V-type proton ATPase ...) x 11
  • ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a
  • Effector SidK
  • Renin receptor
  • Ribonuclease K
KeywordsPROTON TRANSPORT / V-ATPase / Complex / Membrane protein
Function / homology
Function and homology information


Metabolism of Angiotensinogen to Angiotensins / Ion channel transport / Transferrin endocytosis and recycling / Amino acids regulate mTORC1 / Insulin receptor recycling / RHOA GTPase cycle / eye pigmentation / central nervous system maturation / transporter activator activity / negative regulation of autophagic cell death ...Metabolism of Angiotensinogen to Angiotensins / Ion channel transport / Transferrin endocytosis and recycling / Amino acids regulate mTORC1 / Insulin receptor recycling / RHOA GTPase cycle / eye pigmentation / central nervous system maturation / transporter activator activity / negative regulation of autophagic cell death / plasma membrane proton-transporting V-type ATPase complex / rostrocaudal neural tube patterning / positive regulation of transforming growth factor beta1 production / cellular response to increased oxygen levels / proton-transporting V-type ATPase, V1 domain / proton-transporting V-type ATPase, V0 domain / synaptic vesicle lumen acidification / extrinsic component of synaptic vesicle membrane / intracellular organelle / clathrin-coated vesicle membrane / lysosomal lumen acidification / NURF complex / endosome to plasma membrane protein transport / vacuolar transport / vacuolar proton-transporting V-type ATPase, V0 domain / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V1 domain / vacuolar proton-transporting V-type ATPase complex / proton-transporting V-type ATPase complex / head morphogenesis / vacuolar acidification / osteoclast development / protein localization to cilium / dendritic spine membrane / regulation of cellular pH / ROS and RNS production in phagocytes / Neutrophil degranulation / ATPase complex / microvillus / ATPase activator activity / regulation of MAPK cascade / autophagosome membrane / MLL1 complex / positive regulation of Wnt signaling pathway / cilium assembly / transmembrane transporter complex / regulation of macroautophagy / angiotensin maturation / ATP metabolic process / H+-transporting two-sector ATPase / axon terminus / ruffle / proton-transporting ATPase activity, rotational mechanism / RNA endonuclease activity / proton-transporting ATP synthase activity, rotational mechanism / endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis / proton transmembrane transport / secretory granule / terminal bouton / cilium / transmembrane transport / small GTPase binding / synaptic vesicle membrane / endocytosis / positive regulation of canonical Wnt signaling pathway / melanosome / synaptic vesicle / apical part of cell / signaling receptor activity / ATPase binding / cell body / postsynaptic membrane / intracellular iron ion homeostasis / receptor-mediated endocytosis of virus by host cell / positive regulation of ERK1 and ERK2 cascade / early endosome / lysosome / endosome membrane / endosome / apical plasma membrane / axon / external side of plasma membrane / lysosomal membrane / centrosome / ubiquitin protein ligase binding / endoplasmic reticulum membrane / protein-containing complex binding / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex / extracellular space / nucleoplasm / ATP binding / identical protein 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, V0 complex, subunit e1/e2 / ATP synthase subunit H / ATPase, V1 complex, subunit F, eukaryotic / 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 H / ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a / V-type proton ATPase subunit G / Similar to RIKEN cDNA 1110020A23 / H(+)-transporting two-sector ATPase / 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 subunit B, brain isoform ...ADENOSINE-5'-DIPHOSPHATE / V-type proton ATPase subunit H / ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a / V-type proton ATPase subunit G / Similar to RIKEN cDNA 1110020A23 / H(+)-transporting two-sector ATPase / 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 subunit B, brain isoform / V-type proton ATPase 16 kDa proteolipid subunit c / V-type proton ATPase subunit e 2 / V-type proton ATPase subunit C 1 / V-type proton ATPase subunit / Type IV secretion protein Dot / Renin receptor / V-type proton ATPase subunit D / V-type proton ATPase subunit E 1
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
Rattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsRubinstein, J.L. / Abbas, Y.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: To Be Published
Title: Structure of V-ATPase with NCOA7B
Authors: Abbas, Y.M. / Rubinstein, J.L.
History
DepositionMay 9, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATPase H+-transporting V1 subunit A
B: ATPase H+-transporting V1 subunit A
C: ATPase H+-transporting V1 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: ATPase H+-transporting V1 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
Q: Effector SidK
R: Effector SidK
S: Effector SidK
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,144,28736
Polymers1,143,85935
Non-polymers4271
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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ATPase H+-transporting V1 subunit ... , 2 types, 4 molecules ABCH

#1: Protein ATPase H+-transporting V1 subunit A / RCG52629


Mass: 68341.836 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Organ: kidney / References: UniProt: D4A133
#4: 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) / Organ: kidney / References: UniProt: Q6P503

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V-type proton ATPase ... , 11 types, 25 molecules DEFGIJKLMNOPacdeghijklmno

#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: 56611.570 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Organ: kidney / References: UniProt: P62815
#3: Protein V-type proton ATPase subunit C 1 / V-ATPase subunit C 1 / Vacuolar proton pump subunit C 1


Mass: 43958.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Organ: kidney / References: UniProt: Q5FVI6
#5: Protein V-type proton ATPase subunit E 1 / V-ATPase subunit E 1 / Vacuolar proton pump subunit E 1


Mass: 26167.453 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Organ: kidney / References: UniProt: Q6PCU2
#6: 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) / Organ: kidney / References: UniProt: P50408
#7: Protein V-type proton ATPase subunit G


Mass: 13733.393 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Organ: kidney / References: UniProt: B2GUV5
#8: Protein V-type proton ATPase subunit H


Mass: 55936.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Organ: kidney / References: UniProt: A0A0G2K9J2
#10: 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
#12: 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
#13: 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
#14: 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
#16: 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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Protein , 4 types, 6 molecules QRSbfp

#9: Protein Effector SidK


Mass: 32146.178 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: lpg0968 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZWW6
#11: 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
#15: 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
#17: 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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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: Rat Kidney V-ATPase with SidK / Type: COMPLEX / Entity ID: #1-#17 / Source: MULTIPLE SOURCES
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 / Nominal defocus max: 3800 nm / Nominal defocus min: 100 nm
Image recordingElectron dose: 44.825 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: OTHER / Num. of particles: 45083
Details: Model-map FSC (threshold 0.5) calculated in phenix.validation_cryoem
Symmetry type: POINT

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