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- EMDB-21317: Mammalian V-ATPase from rat brain with the Legionella pneumophila... -

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Basic information

Entry
Database: EMDB / ID: EMD-21317
TitleMammalian V-ATPase from rat brain with the Legionella pneumophila effector protein SidK - rotational state 1 non-uniform refinement
Map dataMammalian rat brain V-ATPase with SidK bound, non-uniform refinement conformational state 1
Sample
  • Complex: Mammalian rat brain V-ATPase collar and peripheral stalks state 1 - from focused refinement
Function / homology
Function and homology information


Metabolism of Angiotensinogen to Angiotensins / Ion channel transport / Transferrin endocytosis and recycling / Amino acids regulate mTORC1 / symbiont-mediated suppression of host phagosome acidification / negative regulation of autophagic cell death / Insulin receptor recycling / RHOA GTPase cycle / plasma membrane proton-transporting V-type ATPase complex / eye pigmentation ...Metabolism of Angiotensinogen to Angiotensins / Ion channel transport / Transferrin endocytosis and recycling / Amino acids regulate mTORC1 / symbiont-mediated suppression of host phagosome acidification / negative regulation of autophagic cell death / Insulin receptor recycling / RHOA GTPase cycle / plasma membrane proton-transporting V-type ATPase complex / eye pigmentation / central nervous system maturation / rostrocaudal neural tube patterning / proton-transporting V-type ATPase, V1 domain / positive regulation of transforming growth factor beta1 production / synaptic vesicle lumen acidification / P-type proton-exporting transporter activity / proton-transporting V-type ATPase, V0 domain / extrinsic component of synaptic vesicle membrane / cellular response to increased oxygen levels / vacuolar proton-transporting V-type ATPase, V1 domain / 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 / NURF complex / proton-transporting V-type ATPase complex / head morphogenesis / protein localization to cilium / vacuolar proton-transporting V-type ATPase complex / osteoclast development / vacuolar acidification / regulation of cellular pH / dendritic spine membrane / ROS and RNS production in phagocytes / Neutrophil degranulation / ATPase complex / microvillus / ATPase activator activity / regulation of MAPK cascade / MLL1 complex / autophagosome membrane / proton-transporting ATPase activity, rotational mechanism / cilium assembly / positive regulation of Wnt signaling pathway / regulation of macroautophagy / transporter activator activity / H+-transporting two-sector ATPase / ATP metabolic process / angiotensin maturation / ruffle / receptor-mediated endocytosis of virus by host cell / axon terminus / endoplasmic reticulum-Golgi intermediate compartment membrane / RNA endonuclease activity / proton transmembrane transport / receptor-mediated endocytosis / secretory granule / small GTPase binding / transmembrane transport / terminal bouton / apical part of cell / synaptic vesicle / synaptic vesicle membrane / melanosome / positive regulation of canonical Wnt signaling pathway / signaling receptor activity / cell body / ATPase binding / intracellular iron ion homeostasis / postsynaptic membrane / early endosome / positive regulation of ERK1 and ERK2 cascade / lysosome / endosome membrane / endosome / cilium / apical plasma membrane / axon / lysosomal membrane / external side of plasma membrane / ubiquitin protein ligase binding / centrosome / endoplasmic reticulum membrane / protein-containing complex binding / perinuclear region of cytoplasm / protein-containing complex / ATP hydrolysis activity / extracellular space / ATP binding / identical protein binding / membrane / plasma membrane / cytoplasm / cytosol
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 / ATPase, V1 complex, subunit A / ATPase, V1 complex, subunit C ...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 / ATPase, V1 complex, subunit A / ATPase, V1 complex, subunit C / Vacuolar ATP synthase subunit C superfamily / V-ATPase subunit C / Ribonuclease kappa / Vacuolar (H+)-ATPase G subunit / V-type proton ATPase subunit S1/VOA1, transmembrane domain / Vacuolar (H+)-ATPase G subunit / V0 complex accessory subunit Ac45/VOA1 transmembrane domain / 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 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
V-type proton ATPase 21 kDa proteolipid subunit c'' / Ribonuclease K / V-type proton ATPase catalytic subunit A / 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 21 kDa proteolipid subunit c'' / Ribonuclease K / V-type proton ATPase catalytic subunit A / 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 / V-type proton ATPase subunit G
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsAbbas YM / Rubinstein JL
Funding support Canada, 1 items
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, 2020-
Header (metadata) releaseFeb 19, 2020-
Map releaseMar 25, 2020-
UpdateSep 30, 2020-
Current statusSep 30, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6vq6
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6vq6
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21317.png

Downloads & links

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Map

FileDownload / File: emd_21317.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMammalian rat brain V-ATPase with SidK bound, non-uniform refinement conformational state 1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 340 pix.
= 360.4 Å		1.06 Å/pix.
x 340 pix.
= 360.4 Å		1.06 Å/pix.
x 340 pix.
= 360.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25 / Movie #1: 0.25
Minimum - Maximum-0.71948665 - 1.5117537
Average (Standard dev.)0.0062898365 (±0.0717019)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 360.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z340340340
origin x/y/z0.0000.0000.000
length x/y/z360.400360.400360.400
α/β/γ90.00090.00090.000
start NX/NY/NZ212211153
NX/NY/NZ80102186
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS340340340
D min/max/mean-0.7191.5120.006

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Supplemental data

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Sample components

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Entire : Mammalian rat brain V-ATPase collar and peripheral stalks state 1...

EntireName: Mammalian rat brain V-ATPase collar and peripheral stalks state 1 - from focused refinement
Components
  • Complex: Mammalian rat brain V-ATPase collar and peripheral stalks state 1 - from focused refinement

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Supramolecule #1: Mammalian rat brain V-ATPase collar and peripheral stalks state 1...

SupramoleculeName: Mammalian rat brain V-ATPase collar and peripheral stalks state 1 - from focused refinement
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 43.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 90648
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING

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