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- EMDB-21353: Mammalian V-ATPase from rat brain collar and peripheral stalks ro... -

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Basic information

Entry
Database: EMDB / ID: EMD-21353
TitleMammalian V-ATPase from rat brain collar and peripheral stalks rotational state 3 (from focused refinement)
Map dataMammalian rat brain V-ATPase with SidK bound, focused refinement of the collar and membrane proximal regions conformational state 3
Sample
  • Complex: Peripheral stalk and collar region of mammalian V-ATPase composed of subunits E1, G2, N-terminal domain of a1, and C1.
    • Protein or peptide: V-type proton ATPase subunit C 1
    • Protein or peptide: V-type proton ATPase subunit E 1
    • Protein or peptide: V-type proton ATPase subunit G
    • Protein or peptide: V-type proton ATPase 116 kDa subunit a isoform 1
Keywordsmembrane protein complex / rotary atpase / PROTON TRANSPORT
Function / homology
Function and homology information


Transferrin endocytosis and recycling / Ion channel transport / Amino acids regulate mTORC1 / Insulin receptor recycling / proton-transporting V-type ATPase, V1 domain / synaptic vesicle lumen acidification / P-type proton-exporting transporter activity / extrinsic component of synaptic vesicle membrane / intracellular organelle / vacuolar proton-transporting V-type ATPase, V1 domain ...Transferrin endocytosis and recycling / Ion channel transport / Amino acids regulate mTORC1 / Insulin receptor recycling / proton-transporting V-type ATPase, V1 domain / synaptic vesicle lumen acidification / P-type proton-exporting transporter activity / extrinsic component of synaptic vesicle membrane / intracellular organelle / vacuolar proton-transporting V-type ATPase, V1 domain / clathrin-coated vesicle membrane / vacuolar proton-transporting V-type ATPase, V0 domain / proton-transporting V-type ATPase complex / vacuolar proton-transporting V-type ATPase complex / vacuolar acidification / transmembrane transporter complex / ROS and RNS production in phagocytes / Neutrophil degranulation / ATPase complex / microvillus / regulation of macroautophagy / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / terminal bouton / synaptic vesicle membrane / melanosome / synaptic vesicle / apical part of cell / ATPase binding / endosome / apical plasma membrane / perinuclear region of cytoplasm / ATP hydrolysis activity / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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, V0 complex, subunit 116kDa, eukaryotic / 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
Similarity search - Domain/homology
V-type proton ATPase 116 kDa subunit a 1 / V-type proton ATPase subunit C 1 / 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: 5.7 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 5, 2020-
Header (metadata) releaseFeb 19, 2020-
Map releaseMar 18, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6vqk
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6vqk
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21353.png

Downloads & links

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Map

FileDownload / File: emd_21353.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, focused refinement of the collar and membrane proximal regions conformational state 3
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.3 / Movie #1: 0.3
Minimum - Maximum-1.0123566 - 2.4945457
Average (Standard dev.)-0.00046290064 (±0.06429877)
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
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS340340340
D min/max/mean-1.0122.495-0.000

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Supplemental data

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Sample components

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Entire : Peripheral stalk and collar region of mammalian V-ATPase composed...

EntireName: Peripheral stalk and collar region of mammalian V-ATPase composed of subunits E1, G2, N-terminal domain of a1, and C1.
Components
  • Complex: Peripheral stalk and collar region of mammalian V-ATPase composed of subunits E1, G2, N-terminal domain of a1, and C1.
    • Protein or peptide: V-type proton ATPase subunit C 1
    • Protein or peptide: V-type proton ATPase subunit E 1
    • Protein or peptide: V-type proton ATPase subunit G
    • Protein or peptide: V-type proton ATPase 116 kDa subunit a isoform 1

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Supramolecule #1: Peripheral stalk and collar region of mammalian V-ATPase composed...

SupramoleculeName: Peripheral stalk and collar region of mammalian V-ATPase composed of subunits E1, G2, N-terminal domain of a1, and C1.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Macromolecule #1: V-type proton ATPase subunit C 1

MacromoleculeName: V-type proton ATPase subunit C 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 43.958453 KDa
SequenceString: MTEFWLISAP GEKTCQQTWE KLHAATTKNN NLAVSSKFNI PDLKVGTLDV LVGLSDELAK LDAFVEGVVK KVAQYMADVL EDSKDKVQE NLLASGVDLV TYITRFQWDM AKYPIKQSLK NISEIIAKGV TQIDNDLKSR ASAYNNLKGN LQNLERKNAG S LLTRSLAE ...String:
MTEFWLISAP GEKTCQQTWE KLHAATTKNN NLAVSSKFNI PDLKVGTLDV LVGLSDELAK LDAFVEGVVK KVAQYMADVL EDSKDKVQE NLLASGVDLV TYITRFQWDM AKYPIKQSLK NISEIIAKGV TQIDNDLKSR ASAYNNLKGN LQNLERKNAG S LLTRSLAE IVKKDDFVLD SEYLVTLLVV VPKLNHNDWI KQYETLAEMV VPRSSNVLSE DQDSYLCNVT LFKKAVDDFR HK ARENKFI VRDFQYNEEE MRADKEEMNR LSTDKKKQFG PLVRWLKVNF SEAFIAWIHI KALRVFVESV LRYGLPVNFQ AML LQPNKK SVKKLREVLH ELYKHLDSSA AAIIDAPMDI PGLNLSQQEY YPYVYYKIDC NLLEFK

UniProtKB: V-type proton ATPase subunit C 1

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Macromolecule #2: V-type proton ATPase subunit E 1

MacromoleculeName: V-type proton ATPase subunit E 1 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 26.167453 KDa
SequenceString: MALSDADVQK QIKHMMAFIE QEANEKAEEI DAKAEEEFNI EKGRLVQTQR LKIMEYYEKK EKQIEQQKKI QMSNLMNQAR LKVLRARDD LITDLLNEAK QRLSKVVKDT TRYQVLLDGL VLQGLYQLLE PRMIVRCRKQ DFPLVKAAVQ KAIPMYKIAT K KDVDVQID ...String:
MALSDADVQK QIKHMMAFIE QEANEKAEEI DAKAEEEFNI EKGRLVQTQR LKIMEYYEKK EKQIEQQKKI QMSNLMNQAR LKVLRARDD LITDLLNEAK QRLSKVVKDT TRYQVLLDGL VLQGLYQLLE PRMIVRCRKQ DFPLVKAAVQ KAIPMYKIAT K KDVDVQID LEAYLPEDIA GGVEIYNGDR KIKVSNTLES RLDLIAQQMM PEVRGALFGA NANRKFLD

UniProtKB: V-type proton ATPase subunit E 1

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Macromolecule #3: V-type proton ATPase subunit G

MacromoleculeName: V-type proton ATPase subunit G / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 13.690476 KDa
SequenceString:
MASQSQGIQQ LLQAEKRAAE KVADARKRKA RRLKQAKEEA QMEVEQYRRE REQEFQSKQQ AAMGSQGNLS AEVEQATRRQ VQGMQSSQQ RNRERVLTQL LGMVCDVRPQ VHPNYRITV

UniProtKB: V-type proton ATPase subunit G

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Macromolecule #4: V-type proton ATPase 116 kDa subunit a isoform 1

MacromoleculeName: V-type proton ATPase 116 kDa subunit a isoform 1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 96.429438 KDa
SequenceString: MGELFRSEEM TLAQLFLQSE AAYCCVSELE ELGKVQFRDL NPDVNVFQRK FVNEVRRCEE MDRKLRFVEK EIRKANIPIM DTGENPEVP FPRDMIDLEA NFEKIENELK EINTNQEALK RNFLELTELK FILRKTQQFF DEMADPDLLE ESSSLLEPNE M GRGAPLRL ...String:
MGELFRSEEM TLAQLFLQSE AAYCCVSELE ELGKVQFRDL NPDVNVFQRK FVNEVRRCEE MDRKLRFVEK EIRKANIPIM DTGENPEVP FPRDMIDLEA NFEKIENELK EINTNQEALK RNFLELTELK FILRKTQQFF DEMADPDLLE ESSSLLEPNE M GRGAPLRL GFVAGVINRE RIPTFERMLW RVCRGNVFLR QAEIENPLED PVTGDYVHKS VFIIFFQGDQ LKNRVKKICE GF RASLYPC PETPQERKEM ASGVNTRIDD LQMVLNQTED HRQRVLQAAA KNIRVWFIKV RKMKAIYHTL NLCNIDVTQK CLI AEVWCP VTDLDSIQFA LRRGTEHSGS TVPSILNRMQ TNQTPPTYNK TNKFTHGFQN IVDAYGIGTY REINPAPYTV ITFP FLFAV MFGDFGHGIL MTLFAVWMVL RESRILSQKN ENEMFSMVFS GRYIILLMGL FSIYTGLIYN DCFSKSLNIF GSSWS VRPM FTIGNWTEET LLGSSVLQLN PAIPGVFGGP YPFGIDPIWN IATNKLTFLN SFKMKMSVIL GIIHMLFGVS LSLFNH IYF KKPLNIYFGF IPEIIFMSSL FGYLVILIFY KWTAYDAHSS RNAPSLLIHF INMFLFSYPE SGNAMLYSGQ KGIQCFL IV VAMLCVPWML LFKPLILRHQ YLRKKHLGTL NFGGIRVGNG PTEEDAEIIQ HDQLSTHSED AEEPTEDEVF DFGDTMVH Q AIHTIEYCLG CISNTASYLR LWALSLAHAQ LSEVLWTMVI HIGLHVRSLA GGLGLFFIFA AFATLTVAIL LIMEGLSAF LHALRLHWVE FQNKFYTGTG FKFLPFSFEH IREGKFDE

UniProtKB: V-type proton ATPase 116 kDa subunit a 1

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

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 5.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 79654

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