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- EMDB-44842: Intact V-ATPase State 2 in synaptophysin knock-out isolated synap... -

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Basic information

Entry
Database: EMDB / ID: EMD-44842
TitleIntact V-ATPase State 2 in synaptophysin knock-out isolated synaptic vesicles
Map dataFull map of V-ATPase State 2 in synaptophysin knock-out ISVs.
Sample
  • Organelle or cellular component: Synaptophysin knock-out mouse brain isolated glutamatergic synaptic vesicles
    • Protein or peptide: x 16 types
KeywordsV-ATPase / synaptic vesicle / MEMBRANE PROTEIN
Function / homology
Function and homology information


Ion channel transport / Amino acids regulate mTORC1 / Transferrin endocytosis and recycling / Insulin receptor recycling / eye pigmentation / central nervous system maturation / Metabolism of Angiotensinogen to Angiotensins / transporter activator activity / negative regulation of autophagic cell death / plasma membrane proton-transporting V-type ATPase complex ...Ion channel transport / Amino acids regulate mTORC1 / Transferrin endocytosis and recycling / Insulin receptor recycling / eye pigmentation / central nervous system maturation / Metabolism of Angiotensinogen to Angiotensins / transporter activator activity / negative regulation of autophagic cell death / plasma membrane proton-transporting V-type ATPase complex / rostrocaudal neural tube patterning / RHOA GTPase cycle / positive regulation of transforming growth factor beta1 production / cellular response to increased oxygen levels / proton-transporting V-type ATPase, V1 domain / ROS and RNS production in phagocytes / proton-transporting V-type ATPase, V0 domain / synaptic vesicle lumen acidification / extrinsic component of synaptic vesicle membrane / P-type proton-exporting transporter activity / intracellular organelle / endosome to plasma membrane protein transport / lysosomal lumen acidification / clathrin-coated vesicle membrane / vacuolar transport / endosomal lumen acidification / 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 / head morphogenesis / vacuolar acidification / osteoclast development / protein localization to cilium / dendritic spine membrane / regulation of cellular pH / ATPase complex / regulation of MAPK cascade / microvillus / ATPase activator activity / autophagosome membrane / positive regulation of Wnt signaling pathway / cilium assembly / transmembrane transporter complex / endomembrane system / regulation of macroautophagy / angiotensin maturation / ATP metabolic process / H+-transporting two-sector ATPase / axon terminus / ruffle / endoplasmic reticulum-Golgi intermediate compartment membrane / proton-transporting ATPase activity, rotational mechanism / RNA endonuclease activity / proton-transporting ATP synthase activity, rotational mechanism / Neutrophil degranulation / receptor-mediated endocytosis / proton transmembrane transport / secretory granule / transmembrane transport / cilium / small GTPase binding / synaptic vesicle membrane / endocytosis / positive regulation of canonical Wnt signaling pathway / melanosome / synaptic vesicle / apical part of cell / myelin sheath / signaling receptor activity / ATPase binding / cell body / postsynaptic membrane / intracellular iron ion homeostasis / Hydrolases; Acting on ester bonds / receptor-mediated endocytosis of virus by host cell / lysosome / positive regulation of ERK1 and ERK2 cascade / early endosome / endosome membrane / endosome / nuclear speck / apical plasma membrane / lysosomal membrane / axon / external side of plasma membrane / centrosome / ubiquitin protein ligase binding / endoplasmic reticulum membrane / protein-containing complex binding / perinuclear region of cytoplasm / Golgi apparatus / ATP hydrolysis activity / protein-containing complex / mitochondrion / extracellular space / nucleoplasm / ATP binding / membrane / plasma membrane
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
V-type proton ATPase catalytic subunit A / V-type proton ATPase subunit E 1 / V-type proton ATPase subunit d 1 / V-type proton ATPase subunit D / V-type proton ATPase subunit B, brain isoform / V-type proton ATPase 16 kDa proteolipid subunit c / V-type proton ATPase subunit H / Ribonuclease kappa / V-type proton ATPase 21 kDa proteolipid subunit c'' / V-type proton ATPase subunit e 2 ...V-type proton ATPase catalytic subunit A / V-type proton ATPase subunit E 1 / V-type proton ATPase subunit d 1 / V-type proton ATPase subunit D / V-type proton ATPase subunit B, brain isoform / V-type proton ATPase 16 kDa proteolipid subunit c / V-type proton ATPase subunit H / Ribonuclease kappa / V-type proton ATPase 21 kDa proteolipid subunit c'' / V-type proton ATPase subunit e 2 / Renin receptor / V-type proton ATPase subunit F / V-type proton ATPase subunit S1 / V-type proton ATPase subunit G 2 / V-type proton ATPase subunit C 1 / V-type proton ATPase 116 kDa subunit a 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsWang C / Jiang W / Yang K / Wang X / Guo Q / Brunger AT
Funding support United States, 2 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)RO1MH63105 United States
CitationJournal: Nature / Year: 2024
Title: Structure and topography of the synaptic V-ATPase-synaptophysin complex.
Authors: Chuchu Wang / Wenhong Jiang / Jeremy Leitz / Kailu Yang / Luis Esquivies / Xing Wang / Xiaotao Shen / Richard G Held / Daniel J Adams / Tamara Basta / Lucas Hampton / Ruiqi Jian / Lihua ...Authors: Chuchu Wang / Wenhong Jiang / Jeremy Leitz / Kailu Yang / Luis Esquivies / Xing Wang / Xiaotao Shen / Richard G Held / Daniel J Adams / Tamara Basta / Lucas Hampton / Ruiqi Jian / Lihua Jiang / Michael H B Stowell / Wolfgang Baumeister / Qiang Guo / Axel T Brunger /
Abstract: Synaptic vesicles are organelles with a precisely defined protein and lipid composition, yet the molecular mechanisms for the biogenesis of synaptic vesicles are mainly unknown. Here we discovered a ...Synaptic vesicles are organelles with a precisely defined protein and lipid composition, yet the molecular mechanisms for the biogenesis of synaptic vesicles are mainly unknown. Here we discovered a well-defined interface between the synaptic vesicle V-ATPase and synaptophysin by in situ cryo-electron tomography and single-particle cryo-electron microscopy of functional synaptic vesicles isolated from mouse brains. The synaptic vesicle V-ATPase is an ATP-dependent proton pump that establishes the proton gradient across the synaptic vesicle, which in turn drives the uptake of neurotransmitters. Synaptophysin and its paralogues synaptoporin and synaptogyrin belong to a family of abundant synaptic vesicle proteins whose function is still unclear. We performed structural and functional studies of synaptophysin-knockout mice, confirming the identity of synaptophysin as an interaction partner with the V-ATPase. Although there is little change in the conformation of the V-ATPase upon interaction with synaptophysin, the presence of synaptophysin in synaptic vesicles profoundly affects the copy number of V-ATPases. This effect on the topography of synaptic vesicles suggests that synaptophysin assists in their biogenesis. In support of this model, we observed that synaptophysin-knockout mice exhibit severe seizure susceptibility, suggesting an imbalance of neurotransmitter release as a physiological consequence of the absence of synaptophysin.
History
DepositionMay 11, 2024-
Header (metadata) releaseJun 19, 2024-
Map releaseJun 19, 2024-
UpdateAug 7, 2024-
Current statusAug 7, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44842.png

Downloads & links

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Map

FileDownload / File: emd_44842.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull map of V-ATPase State 2 in synaptophysin knock-out ISVs.
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 448 pix.
= 495.667 Å		1.11 Å/pix.
x 448 pix.
= 495.667 Å		1.11 Å/pix.
x 448 pix.
= 495.667 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1064 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.003
Minimum - Maximum-0.01996166 - 0.028340058
Average (Standard dev.)0.000001896608 (±0.0010832566)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 495.6672 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: EMhancer map of V-ATPase State 2 in synaptophysin knock-out ISVs.

Fileemd_44842_additional_1.map
AnnotationEMhancer map of V-ATPase State 2 in synaptophysin knock-out ISVs.
Projections & Slices
AxesZYX

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Additional map: Unsharpened map

Fileemd_44842_additional_2.map
AnnotationUnsharpened map
Projections & Slices
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Half map: Half map of V-ATPase State 2 in synaptophysin knock-out ISVs.

Fileemd_44842_half_map_1.map
AnnotationHalf map of V-ATPase State 2 in synaptophysin knock-out ISVs.
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half map of V-ATPase State 2 in synaptophysin knock-out ISVs.

Fileemd_44842_half_map_2.map
AnnotationHalf map of V-ATPase State 2 in synaptophysin knock-out ISVs.
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AxesZYX

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Sample components

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Entire : Synaptophysin knock-out mouse brain isolated glutamatergic synapt...

EntireName: Synaptophysin knock-out mouse brain isolated glutamatergic synaptic vesicles
Components
  • Organelle or cellular component: Synaptophysin knock-out mouse brain isolated glutamatergic synaptic vesicles
    • Protein or peptide: V-type proton ATPase subunit E 1
    • Protein or peptide: V-type proton ATPase subunit G 2
    • Protein or peptide: V-type proton ATPase subunit C 1
    • Protein or peptide: V-type proton ATPase subunit H
    • Protein or peptide: V-type proton ATPase 116 kDa subunit a 1
    • Protein or peptide: V-type proton ATPase subunit e 2
    • Protein or peptide: Ribonuclease kappa
    • Protein or peptide: V-type proton ATPase subunit F
    • Protein or peptide: V-type proton ATPase subunit d 1
    • Protein or peptide: V-type proton ATPase subunit S1
    • Protein or peptide: Renin receptor cytoplasmic fragment
    • Protein or peptide: V-type proton ATPase 21 kDa proteolipid subunit c''
    • Protein or peptide: V-type proton ATPase 16 kDa proteolipid subunit c
    • Protein or peptide: V-type proton ATPase catalytic subunit A
    • Protein or peptide: V-type proton ATPase subunit B, brain isoform
    • Protein or peptide: V-type proton ATPase subunit D

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Supramolecule #1: Synaptophysin knock-out mouse brain isolated glutamatergic synapt...

SupramoleculeName: Synaptophysin knock-out mouse brain isolated glutamatergic synaptic vesicles
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

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

MacromoleculeName: V-type proton ATPase subunit E 1 / type: protein_or_peptide / ID: 1 / Details: VATE1_MOUSE V-type proton ATPase subunit E 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 26.196449 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 QEAYLPEEIA GGVEIYNGDR KIKVSNTLES RLDLIAQQMM PEVRGALFGA NANRKFLD

UniProtKB: V-type proton ATPase subunit E 1

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Macromolecule #2: V-type proton ATPase subunit G 2

MacromoleculeName: V-type proton ATPase subunit G 2 / type: protein_or_peptide / ID: 2 / Details: VATG2_MOUSE V-type proton ATPase subunit G 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.674476 KDa
SequenceString:
MASQTQGIQQ LLQAEKRAAE KVADARKRKA RRLKQAKEEA QMEVEQYRRE REQEFQSKQQ AAMGSQGNLS AEVEQATRRQ VQGMQSSQQ RNRERVLAQL LGMVCEVRPQ VHPNYRVTV

UniProtKB: V-type proton ATPase subunit G 2

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Macromolecule #3: V-type proton ATPase subunit C 1

MacromoleculeName: V-type proton ATPase subunit C 1 / type: protein_or_peptide / ID: 3 / Details: VATC1_MOUSE V-type proton ATPase subunit C 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 43.945449 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 LFRKAVDDFR HK ARENKFI VRDFQYNEEE MKADKEEMTR 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 #4: V-type proton ATPase subunit H

MacromoleculeName: V-type proton ATPase subunit H / type: protein_or_peptide / ID: 4 / Details: VATH_MOUSE V-type proton ATPase subunit H / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 55.922859 KDa
SequenceString: MTKMDIRGAV DAAVPTNIIA AKAAEVRANK VNWQSYLQGQ MISAEDCEFI QRFEMKRSSE DKQEMLQTEG SQCAKTFINL MTHISKEQT VQYILTMVDD MLQENHQRVS IFFDYAKRSK STAWPYFLPM LNRQDPFTVH MAARIIAKLA AWGKELMEGS D LNYYFNWI ...String:
MTKMDIRGAV DAAVPTNIIA AKAAEVRANK VNWQSYLQGQ MISAEDCEFI QRFEMKRSSE DKQEMLQTEG SQCAKTFINL MTHISKEQT VQYILTMVDD MLQENHQRVS IFFDYAKRSK STAWPYFLPM LNRQDPFTVH MAARIIAKLA AWGKELMEGS D LNYYFNWI KTQLSSQKLR GSGVAVETGT ISSSDSSQYV QCVAGCLQLM LRVNEYRFAW VEADGVNCIM GVLSNKCGFQ LQ YQMIFSI WLLAFSPQMC EHLRRYNIIP VLSDILQESV KEKVTRIILA AFRNFLEKST ERETRQEYAL AMIQCKVLKQ LEN LEQQKY DDEDISEDIK FLLEKLGESV QDLSSFDEYS SELKSGRLEW SPVHKSEKFW RENAVRLNEK NYELLKILTK LLEV SDDPQ VLAVAAHDVG EYVRHYPRGK RVIEQLGGKQ LVMNHMHHED QQVRYNALLA VQKLMVHNWE YLGKQLQSEQ PQTAA ARS

UniProtKB: V-type proton ATPase subunit H

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Macromolecule #5: V-type proton ATPase 116 kDa subunit a 1

MacromoleculeName: V-type proton ATPase 116 kDa subunit a 1 / type: protein_or_peptide / ID: 5
Details: VPP1_MOUSE V-type proton ATPase 116 kDa subunit a isoform 1
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 96.4425 KDa
SequenceString: MGELFRSEEM TLAQLFLQSE AAYCCVSELG ELGKVQFRDL NPDVNVFQRK FVNEVRRCEE MDRKLRFVEK EIRKANIPIM DTGENPEVP FPRDMIDLEA NFEKIENELK EINTNQEALK RNFLELTELK FILRKTQQFF DEAELHHQQM ADPDLLEESS S LLEPNEMG ...String:
MGELFRSEEM TLAQLFLQSE AAYCCVSELG ELGKVQFRDL NPDVNVFQRK FVNEVRRCEE MDRKLRFVEK EIRKANIPIM DTGENPEVP FPRDMIDLEA NFEKIENELK EINTNQEALK RNFLELTELK FILRKTQQFF DEAELHHQQM ADPDLLEESS S LLEPNEMG RGAPLRLGFV AGVINRERIP TFERMLWRVC RGNVFLRQAE IENPLEDPVT GDYVHKSVFI IFFQGDQLKN RV KKICEGF RASLYPCPET PQERKEMASG VNTRIDDLQM VLNQTEDHRQ RVLQAAAKNI RVWFIKVRKM KAIYHTLNLC NID VTQKCL IAEVWCPVTD LDSIQFALRR GTEHSGSTVP SILNRMQTNQ TPPTYNKTNK FTHGFQNIVD AYGIGTYREI NPAP YTVIT FPFLFAVMFG DFGHGILMTL FAVWMVLRES RILSQKHENE MFSMVFSGRY IILLMGLFSI YTGLIYNDCF SKSLN IFGS SWSVRPMFTQ GNWTEETLLG SSVLQLNPAI PGVFGGPYPF GIDPIWNIAT NKLTFLNSFK MKMSVILGII HMLFGV SLS LFNHIYFKKP LNIYFGFIPE IIFMSSLFGY LVILIFYKWT AYDAHSSRNA PSLLIHFINM FLFSYPESGN AMLYSGQ KG IQCFLIVVAM LCVPWMLLFK PLILRHQYLR KKHLGTLNFG GIRVGNGPTE EDAEIIQHDQ LSTHSEDAEE FDFGDTMV H QAIHTIEYCL GCISNTASYL RLWALSLAHA QLSEVLWTMV IHIGLHVRSL AGGLGLFFIF AAFATLTVAI LLIMEGLSA FLHALRLHWV EFQNKFYTGT GFKFLPFSFE HIREGKFD

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

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Macromolecule #6: V-type proton ATPase subunit e 2

MacromoleculeName: V-type proton ATPase subunit e 2 / type: protein_or_peptide / ID: 6 / Details: VA0E2_MOUSE V-type proton ATPase subunit e 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 9.20302 KDa
SequenceString:
MTAHSFALPV IIFTTFWGLI GIAGPWFVPK GPNRGVIITM LVATAVCCYL FWLIAILAQL NPLFGPQLKN ETIWYVRFLW E

UniProtKB: V-type proton ATPase subunit e 2

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Macromolecule #7: Ribonuclease kappa

MacromoleculeName: Ribonuclease kappa / type: protein_or_peptide / ID: 7 / Details: RNK_MOUSE Ribonuclease kappa / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.000004 KDa
SequenceString:
MASLLCCGPK LAACGIVLSA WGVIMLIMLG IFFNVHSAVL IEDVPFTEKD FENGPQNIYN LYEQVSYNCF IAAGLYLLLG GFSFCQVRL NKRKEYMVR

UniProtKB: Ribonuclease kappa

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Macromolecule #8: V-type proton ATPase subunit F

MacromoleculeName: V-type proton ATPase subunit F / type: protein_or_peptide / ID: 8 / Details: VATF_MOUSE V-type proton ATPase subunit F / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.389262 KDa
SequenceString:
MAGRGKLIAV IGDEDTVTGF LLGGIGELNK NRHPNFLVVE KDTTINEIED TFRQFLNRDD IGIILINQYI AEMVRHALDA HQRSIPAVL EIPSKEHPYD AAKDSILRRA KGMFTAEDLR

UniProtKB: V-type proton ATPase subunit F

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Macromolecule #9: V-type proton ATPase subunit d 1

MacromoleculeName: V-type proton ATPase subunit d 1 / type: protein_or_peptide / ID: 9 / Details: VA0D1_MOUSE V-type proton ATPase subunit d 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 40.341934 KDa
SequenceString: MSFFPELYFN VDNGYLEGLV RGLKAGVLSQ ADYLNLVQCE TLEDLKLHLQ STDYGNFLAN EASPLTVSVI DDKLKEKMVV EFRHMRNHA YEPLASFLDF ITYSYMIDNV ILLITGTLHQ RSIAELVPKC HPLGSFEQME AVNIAQTPAE LYNAILVDTP L AAFFQDCI ...String:
MSFFPELYFN VDNGYLEGLV RGLKAGVLSQ ADYLNLVQCE TLEDLKLHLQ STDYGNFLAN EASPLTVSVI DDKLKEKMVV EFRHMRNHA YEPLASFLDF ITYSYMIDNV ILLITGTLHQ RSIAELVPKC HPLGSFEQME AVNIAQTPAE LYNAILVDTP L AAFFQDCI SEQDLDEMNI EIIRNTLYKA YLESFYKFCT LLGGTTADAM CPILEFEADR RAFIITINSF GTELSKEDRA KL FPHCGRL YPEGLAQLAR ADDYEQVKNV ADYYPEYKLL FEGAGSNPGD KTLEDRFFEH EVKLNKLAFL NQFHFGVFYA FVK LKEQEC RNIVWIAECI AQRHRAKIDN YIPIF

UniProtKB: V-type proton ATPase subunit d 1

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Macromolecule #10: V-type proton ATPase subunit S1

MacromoleculeName: V-type proton ATPase subunit S1 / type: protein_or_peptide / ID: 10 / Details: VAS1_MOUSE V-type proton ATPase subunit S1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 51.046215 KDa
SequenceString: MMAATVVSRI RTGTGRAPVM WLSLSLVAVA AAVATEQQVP LVLWSSDRNL WAPVADTHEG HITSDMQLST YLDPALELGP RNVLLFLQD KLSIEDFTAY GGVFGNKQDS AFSNLENALD LAPSSLVLPA VDWYAISTLT TYLQEKLGAS PLHVDLATLK E LKLNASLP ...String:
MMAATVVSRI RTGTGRAPVM WLSLSLVAVA AAVATEQQVP LVLWSSDRNL WAPVADTHEG HITSDMQLST YLDPALELGP RNVLLFLQD KLSIEDFTAY GGVFGNKQDS AFSNLENALD LAPSSLVLPA VDWYAISTLT TYLQEKLGAS PLHVDLATLK E LKLNASLP ALLLIRLPYT ASSGLMAPRE VLTGNDEVIG QVLSTLKSED VPYTAALTAV RPSRVARDIT MVAGGLGRQL LQ TQVASPA IHPPVSYNDT APRILFWAQN FSVAYKDEWK DLTSLTFGVE NLNLTGSFWN DSFAMLSLTY EPLFGATVTF KFI LASRFY PVSARYWFAM ERLEIHSNGS VAHFNVSQVT GPSIYSFHCE YVSSVSKKGN LLVTNVPSVW QMTLHNFQIQ AFNV TGEQF SYASDCAGFF SPGIWMGLLT TLFMLFIFTY GLHMILSLKT MDRFDDHKGP TITLTQIV

UniProtKB: V-type proton ATPase subunit S1

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Macromolecule #11: Renin receptor cytoplasmic fragment

MacromoleculeName: Renin receptor cytoplasmic fragment / type: protein_or_peptide / ID: 11 / Details: RENR_MOUSE Renin receptor / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 39.128789 KDa
SequenceString: MAVLVVLLFF LVAGALGNEF SILRSPGSVV FRNGNWPIPG DRIPDVAALS MGFSVKEDLS WPGLAVGNLF HRPRATIMVM VKGVDKLAL PAGSVISYPL ENAVPFSLDS VANSIHSLFS EETPVVLQLA PSEERVYMVG KANSVFEDLS VTLRQLRNRL F QENSLLNS ...String:
MAVLVVLLFF LVAGALGNEF SILRSPGSVV FRNGNWPIPG DRIPDVAALS MGFSVKEDLS WPGLAVGNLF HRPRATIMVM VKGVDKLAL PAGSVISYPL ENAVPFSLDS VANSIHSLFS EETPVVLQLA PSEERVYMVG KANSVFEDLS VTLRQLRNRL F QENSLLNS LPLNSLSRNN EVDLLFLSEL QVLHDISSLL SRHKHLAKDH SPDLYSLELA GLDELGKRYG EDSEQFRDAS KI LVDALQK FADDMYSLYG GNAVVELVTV KSFDTSLVRK SRTILEAKQE NTQSPYNLAY KYNLEYSVVF NLVLWIMIGL ALA VIITSY NIWNMDPGYD SIIYRMTNQK IRID

UniProtKB: Renin receptor

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Macromolecule #12: V-type proton ATPase 21 kDa proteolipid subunit c''

MacromoleculeName: V-type proton ATPase 21 kDa proteolipid subunit c'' / type: protein_or_peptide / ID: 12
Details: VATO_MOUSE V-type proton ATPase 21 kDa proteolipid subunit
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 21.618553 KDa
SequenceString: MTGLELLYLG IFVAFWACMV VVGICYTIFD LGFRFDVAWF LTETSPFMWS NLGIGLAISL SVVGAAWGIY ITGSSIIGGG VKAPRIKTK NLVSIIFCEA VAIYGIIMAI VISNMAEPFS ATEPKAIGHR NYHAGYSMFG AGLTVGLSNL FCGVCVGIVG S GAALADAQ ...String:
MTGLELLYLG IFVAFWACMV VVGICYTIFD LGFRFDVAWF LTETSPFMWS NLGIGLAISL SVVGAAWGIY ITGSSIIGGG VKAPRIKTK NLVSIIFCEA VAIYGIIMAI VISNMAEPFS ATEPKAIGHR NYHAGYSMFG AGLTVGLSNL FCGVCVGIVG S GAALADAQ NPSLFVKILI VEIFGSAIGL FGVIVAILQT SRVKMGD

UniProtKB: V-type proton ATPase 21 kDa proteolipid subunit c''

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Macromolecule #13: V-type proton ATPase 16 kDa proteolipid subunit c

MacromoleculeName: V-type proton ATPase 16 kDa proteolipid subunit c / type: protein_or_peptide / ID: 13
Details: VATL_MOUSE V-type proton ATPase 16 kDa proteolipid subunit
Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 15.815833 KDa
SequenceString:
MADIKNNPEY SSFFGVMGAS SAMVFSAMGA AYGTAKSGTG IAAMSVMRPE LIMKSIIPVV MAGIIAIYGL VVAVLIANSL TDGITLYRS FLQLGAGLSV GLSGLAAGFA IGIVGDAGVR GTAQQPRLFV GMILILIFAE VLGLYGLIVA LILSTK

UniProtKB: V-type proton ATPase 16 kDa proteolipid subunit c

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Macromolecule #14: V-type proton ATPase catalytic subunit A

MacromoleculeName: V-type proton ATPase catalytic subunit A / type: protein_or_peptide / ID: 14
Details: VATA_MOUSE V-type proton ATPase catalytic subunit A
Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 68.402875 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 PPRNRGSVTY IAPPGNYDAS DVVLELEFEG VKEKFSMVQV 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: V-type proton ATPase catalytic subunit A

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Macromolecule #15: V-type proton ATPase subunit B, brain isoform

MacromoleculeName: V-type proton ATPase subunit B, brain isoform / type: protein_or_peptide / ID: 15 / Details: VATB2_MOUSE V-type proton ATPase subunit B / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
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 #16: V-type proton ATPase subunit D

MacromoleculeName: V-type proton ATPase subunit D / type: protein_or_peptide / ID: 16 / Details: VATD_MOUSE V-type proton ATPase subunit D / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 28.419117 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 KKIIKEKFEK DLERRRAAGE VMEPANLLAE EK DEDLLFE

UniProtKB: V-type proton ATPase subunit D

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE
DetailsThe specimen state should be an intact subcellular component.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 30487
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-9brs:
Intact V-ATPase State 2 in synaptophysin knock-out isolated synaptic vesicles

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