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- EMDB-21346: Mammalian V-ATPase from rat brain soluble V1 region rotational st... -

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Entry
Database: EMDB / ID: EMD-21346
TitleMammalian V-ATPase from rat brain soluble V1 region rotational state 2 with SidK and ADP (from focused refinement)
Map dataMammalian rat brain V-ATPase with SidK bound, focused refinement of the soluble V1 region conformational state 2
Sample
  • Complex: Soluble region of rat brain V-ATPase composed of subunits A, B2, D, E1, G2, and the Legionella pneumophila effector protein SidK
    • Protein or peptide: ATPase H+-transporting V1 subunit A
    • Protein or peptide: V-type proton ATPase subunit B, brain isoform
    • Protein or peptide: ATPase H+-transporting V1 subunit D
    • Protein or peptide: V-type proton ATPase subunit E 1
    • Protein or peptide: V-type proton ATPase subunit G
    • Protein or peptide: Effector protein SidK
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
Keywordsmembrane protein complex / rotary atpase / PROTON TRANSPORT
Function / homology
Function and homology information


Ion channel transport / Transferrin endocytosis and recycling / Amino acids regulate mTORC1 / Insulin receptor recycling / cellular response to increased oxygen levels / proton-transporting V-type ATPase, V1 domain / synaptic vesicle lumen acidification / extrinsic component of synaptic vesicle membrane / P-type proton-exporting transporter activity / clathrin-coated vesicle membrane ...Ion channel transport / Transferrin endocytosis and recycling / Amino acids regulate mTORC1 / Insulin receptor recycling / cellular response to increased oxygen levels / proton-transporting V-type ATPase, V1 domain / synaptic vesicle lumen acidification / extrinsic component of synaptic vesicle membrane / P-type proton-exporting transporter activity / clathrin-coated vesicle membrane / vacuolar proton-transporting V-type ATPase, V1 domain / vacuolar proton-transporting V-type ATPase complex / proton-transporting V-type ATPase complex / vacuolar acidification / protein localization to cilium / regulation of cellular pH / ROS and RNS production in phagocytes / Neutrophil degranulation / ATPase complex / microvillus / cilium assembly / transmembrane transporter complex / ATP metabolic process / H+-transporting two-sector ATPase / ruffle / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / secretory granule / cilium / synaptic vesicle membrane / melanosome / ATPase binding / intracellular iron ion homeostasis / endosome / apical plasma membrane / centrosome / ATP hydrolysis activity / nucleoplasm / ATP binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
ATPase, V1 complex, subunit A / Vacuolar (H+)-ATPase G subunit / Vacuolar (H+)-ATPase G subunit / ATPase, V1 complex, subunit B / 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 / ATP synthase subunit D / V-type ATP synthase regulatory subunit B/beta ...ATPase, V1 complex, subunit A / Vacuolar (H+)-ATPase G subunit / Vacuolar (H+)-ATPase G subunit / ATPase, V1 complex, subunit B / 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 / ATP synthase subunit D / 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 / 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
H(+)-transporting two-sector ATPase / V-type proton ATPase subunit B, brain isoform / Type IV secretion protein Dot / 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) / Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 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 4, 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: 0.5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6vqa
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21346.png

Downloads & links

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Map

FileDownload / File: emd_21346.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 soluble V1 region conformational state 2
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: 0.5 / Movie #1: 0.5
Minimum - Maximum-1.2950116 - 2.651067
Average (Standard dev.)0.0003567371 (±0.0917385)
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-1.2952.6510.000

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Supplemental data

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Sample components

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Entire : Soluble region of rat brain V-ATPase composed of subunits A, B2, ...

EntireName: Soluble region of rat brain V-ATPase composed of subunits A, B2, D, E1, G2, and the Legionella pneumophila effector protein SidK
Components
  • Complex: Soluble region of rat brain V-ATPase composed of subunits A, B2, D, E1, G2, and the Legionella pneumophila effector protein SidK
    • Protein or peptide: ATPase H+-transporting V1 subunit A
    • Protein or peptide: V-type proton ATPase subunit B, brain isoform
    • Protein or peptide: ATPase H+-transporting V1 subunit D
    • Protein or peptide: V-type proton ATPase subunit E 1
    • Protein or peptide: V-type proton ATPase subunit G
    • Protein or peptide: Effector protein SidK
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Soluble region of rat brain V-ATPase composed of subunits A, B2, ...

SupramoleculeName: Soluble region of rat brain V-ATPase composed of subunits A, B2, D, E1, G2, and the Legionella pneumophila effector protein SidK
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Macromolecule #1: ATPase H+-transporting V1 subunit A

MacromoleculeName: ATPase H+-transporting V1 subunit A / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 68.341836 KDa
SequenceString: MDFSKLPKIR DEDKESTFGY VHGVSGPVVT ACDMAGAAMY ELVRVGHSEL VGEIIRLEGD MATIQVYEET SGVSVGDPVL RTGKPLSVE LGPGIMGAIF DGIQRPLSDI SSQTQSIYIP RGVNVSALSR DIKWEFIPSK NLRVGSHITG GDIYGIVNEN S LIKHKIML ...String:
MDFSKLPKIR DEDKESTFGY VHGVSGPVVT ACDMAGAAMY ELVRVGHSEL VGEIIRLEGD MATIQVYEET SGVSVGDPVL RTGKPLSVE LGPGIMGAIF DGIQRPLSDI SSQTQSIYIP RGVNVSALSR DIKWEFIPSK NLRVGSHITG GDIYGIVNEN S LIKHKIML PPRSRGSVTY IAPPGNYDAS DVVLELEFEG VKEKLSMVQV WPVRQVRPVT EKLPANHPLL TGQRVLDALF PC VQGGTTA IPGAFGCGKT VISQSLSKYS NSDVIIYVGC GERGNEMSEV LRDFPELTME VDGKVESIMK RTALVANTSN MPV AAREAS IYTGITLSEY FRDMGYHVSM MADSTSRWAE ALREISGRLA EMPADSGYPA YLGARLASFY ERAGRVKCLG NPER EGSVS IVGAVSPPGG DFSDPVTSAT LGIVQVFWGL DKKLAQRKHF PSVNWLISYS KYMRALDEYY DKHFTEFVPL RTKAK EILQ EEEDLAEIVQ LVGKASLAET DKITLEVAKL IKDDFLQQNG YTPYDRFCPF YKTVGMLSNM ISFYDMARRA VETTAQ SDN KITWSIIREH MGEILYKLSS MKFKDPVKDG EAKIKADYAQ LLEDMQNAFR SLED

UniProtKB: H(+)-transporting two-sector ATPase

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Macromolecule #2: V-type proton ATPase subunit B, brain isoform

MacromoleculeName: V-type proton ATPase subunit B, brain isoform / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 56.61157 KDa
SequenceString: MALRAMRGIV NGAAPELPVP TGGPMAGARE QALAVSRNYL SQPRLTYKTV SGVNGPLVIL DHVKFPRYAE IVHLTLPDGT KRSGQVLEV SGSKAVVQVF EGTSGIDAKK TSCEFTGDIL RTPVSEDMLG RVFNGSGKPI DRGPVVLAED FLDIMGQPIN P QCRIYPEE ...String:
MALRAMRGIV NGAAPELPVP TGGPMAGARE QALAVSRNYL SQPRLTYKTV SGVNGPLVIL DHVKFPRYAE IVHLTLPDGT KRSGQVLEV SGSKAVVQVF EGTSGIDAKK TSCEFTGDIL RTPVSEDMLG RVFNGSGKPI DRGPVVLAED FLDIMGQPIN P QCRIYPEE MIQTGISAID GMNSIARGQK IPIFSAAGLP HNEIAAQICR QAGLVKKSKD VVDYSEENFA IVFAAMGVNM ET ARFFKSD FEENGSMDNV CLFLNLANDP TIERIITPRL ALTTAEFLAY QCEKHVLVIL TDMSSYAEAL REVSAAREEV PGR RGFPGY MYTDLATIYE RAGRVEGRNG SITQIPILTM PNDDITHPIP DLTGYITEGQ IYVDRQLHNR QIYPPINVLP SLSR LMKSA IGEGMTRKDH ADVSNQLYAC YAIGKDVQAM KAVVGEEALT SDDLLYLEFL QKFEKNFITQ GPYENRTVYE TLDIG WQLL RIFPKEMLKR IPQSTLSEFY PRDSAKH

UniProtKB: V-type proton ATPase subunit B, brain isoform

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Macromolecule #3: ATPase H+-transporting V1 subunit D

MacromoleculeName: ATPase H+-transporting V1 subunit D / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 28.35902 KDa
SequenceString: MSGKDRIEIF PSRMAQTIMK ARLKGAQTGR NLLKKKSDAL TLRFRQILKK IIETKMLMGE VMREAAFSLA EAKFTAGDFS TTVIQNVNK AQVKIRAKKD NVAGVTLPVF EHYHEGTDSY ELTGLARGGE QLAKLKRNYA KAVELLVELA SLQTSFVTLD E AIKITNRR ...String:
MSGKDRIEIF PSRMAQTIMK ARLKGAQTGR NLLKKKSDAL TLRFRQILKK IIETKMLMGE VMREAAFSLA EAKFTAGDFS TTVIQNVNK AQVKIRAKKD NVAGVTLPVF EHYHEGTDSY ELTGLARGGE QLAKLKRNYA KAVELLVELA SLQTSFVTLD E AIKITNRR VNAIEHVIIP RIERTLAYII TELDEREREE FYRLKKIQEK KKIIKEKSEK DLERRRAAGE VMEPANLLAE EK DEDLLFE

UniProtKB: V-type proton ATPase subunit D

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Macromolecule #4: V-type proton ATPase subunit E 1

MacromoleculeName: V-type proton ATPase subunit E 1 / type: protein_or_peptide / ID: 4 / 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 #5: V-type proton ATPase subunit G

MacromoleculeName: V-type proton ATPase subunit G / type: protein_or_peptide / ID: 5 / 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 #6: Effector protein SidK

MacromoleculeName: Effector protein SidK / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513
Molecular weightTheoretical: 34.693605 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GMSFIKVGIK MGGLTSEQYH SQVVGKIGYI ARCMQTIDPE NNLKKIREDY QDVLIWAEKN YRFEEILEAS KSGKCPNDLD ALSRRSLIL QELLRLVSSI SPFKMKLDLI ESQYEKMKQH VNLWKSDYHV KLNQLNQLTD YLKNAAPTPK NNFLRAMTSV L QMQIAQYG ...String:
GMSFIKVGIK MGGLTSEQYH SQVVGKIGYI ARCMQTIDPE NNLKKIREDY QDVLIWAEKN YRFEEILEAS KSGKCPNDLD ALSRRSLIL QELLRLVSSI SPFKMKLDLI ESQYEKMKQH VNLWKSDYHV KLNQLNQLTD YLKNAAPTPK NNFLRAMTSV L QMQIAQYG ITEDNEGINQ LFKLGLHLLA MANEKIDEQY HLFKGYVKDQ PEESPFEGIL PAEDQKILVK TMIDYAMPKL SS KVLQDKL SALSSSDVLT KTLLDSIDRI VKENEKLNAL SKDYKDHDGD YKDHDIDYKD DDDK

UniProtKB: Type IV secretion protein Dot

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Macromolecule #7: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 74789
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING

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