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- EMDB-44845: V0-only V-ATPase in synaptophysin gene knock-out mouse brain isol... -

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Basic information

Entry
Database: EMDB / ID: EMD-44845
TitleV0-only V-ATPase in synaptophysin gene knock-out mouse brain isolated synaptic vesicles
Map dataFull map of V0-only V-ATPase in SYP-KO ISVs.
Sample
  • Organelle or cellular component: Syptophysin gene knock-out mouse brain isolated glutamatergic synaptic vesicles
    • Protein or peptide: V-type proton ATPase subunit S1
    • Protein or peptide: V-type proton ATPase 21 kDa proteolipid subunit c''
    • Protein or peptide: V-type proton ATPase subunit d 1
    • Protein or peptide: Ribonuclease kappa
    • Protein or peptide: V-type proton ATPase 16 kDa proteolipid subunit c
    • Protein or peptide: Renin receptor cytoplasmic fragment
    • Protein or peptide: V-type proton ATPase subunit e 2
    • Protein or peptide: V-type proton ATPase 116 kDa subunit a 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: beta-D-mannopyranose
KeywordsV0only V-ATPase / synaptic vesicle / MEMBRANE PROTEIN
Function / homology
Function and homology information


Ion channel transport / Amino acids regulate mTORC1 / Transferrin endocytosis and recycling / eye pigmentation / Insulin receptor recycling / central nervous system maturation / transporter activator activity / negative regulation of autophagic cell death / RHOA GTPase cycle / rostrocaudal neural tube patterning ...Ion channel transport / Amino acids regulate mTORC1 / Transferrin endocytosis and recycling / eye pigmentation / Insulin receptor recycling / central nervous system maturation / transporter activator activity / negative regulation of autophagic cell death / RHOA GTPase cycle / rostrocaudal neural tube patterning / Metabolism of Angiotensinogen to Angiotensins / cellular response to increased oxygen levels / positive regulation of transforming growth factor beta1 production / synaptic vesicle lumen acidification / endosome to plasma membrane protein transport / proton-transporting V-type ATPase, V0 domain / P-type proton-exporting transporter activity / ROS and RNS production in phagocytes / intracellular organelle / plasma membrane proton-transporting V-type ATPase complex / lysosomal lumen acidification / clathrin-coated vesicle membrane / vacuolar proton-transporting V-type ATPase, V0 domain / endosomal lumen acidification / vacuolar transport / proton-transporting V-type ATPase complex / head morphogenesis / vacuolar proton-transporting V-type ATPase complex / vacuolar acidification / dendritic spine membrane / regulation of cellular pH / osteoclast development / ATPase activator activity / autophagosome membrane / regulation of MAPK cascade / transmembrane transporter complex / cilium assembly / positive regulation of Wnt signaling pathway / angiotensin maturation / regulation of macroautophagy / endomembrane system / axon terminus / proton transmembrane transport / RNA endonuclease activity / proton-transporting ATPase activity, rotational mechanism / Neutrophil degranulation / endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis / transmembrane transport / synaptic vesicle membrane / small GTPase binding / melanosome / positive regulation of canonical Wnt signaling pathway / synaptic vesicle / signaling receptor activity / cell body / ATPase binding / postsynaptic membrane / intracellular iron ion homeostasis / receptor-mediated endocytosis of virus by host cell / Hydrolases; Acting on ester bonds / early endosome / positive regulation of ERK1 and ERK2 cascade / endosome membrane / endosome / nuclear speck / apical plasma membrane / lysosomal membrane / axon / external side of plasma membrane / centrosome / ubiquitin protein ligase binding / protein-containing complex binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / protein-containing complex / extracellular space / 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 / Ribonuclease kappa / V-type proton ATPase subunit S1/VOA1, transmembrane domain / V0 complex accessory subunit Ac45/VOA1 transmembrane domain / ATPase, V0 complex, subunit e1/e2 ...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 / Ribonuclease kappa / V-type proton ATPase subunit S1/VOA1, transmembrane domain / V0 complex accessory subunit Ac45/VOA1 transmembrane domain / 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 / V-ATPase proteolipid subunit / 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-type ATPase, V0 complex, 116kDa subunit family / V-type ATPase 116kDa subunit family / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C
Similarity search - Domain/homology
V-type proton ATPase subunit d 1 / V-type proton ATPase 16 kDa proteolipid subunit c / 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 S1 / V-type proton ATPase 116 kDa subunit a 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 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 Held / Daniel J Adams / Tamara Basta / Lucas Hampton / Ruiqi Jian / Lihua Jiang ...Authors: Chuchu Wang / Wenhong Jiang / Jeremy Leitz / Kailu Yang / Luis Esquivies / Xing Wang / Xiaotao Shen / Richard 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 protein gradient across the synaptic vesicle, which in turn drives the uptake of neurotransmitters. Synaptophysin and its paralogs 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 12, 2024-
Header (metadata) releaseJun 19, 2024-
Map releaseJun 19, 2024-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44845.png

Downloads & links

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Map

FileDownload / File: emd_44845.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull map of V0-only V-ATPase in SYP-KO ISVs.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 288 pix.
= 318.643 Å		1.11 Å/pix.
x 288 pix.
= 318.643 Å		1.11 Å/pix.
x 288 pix.
= 318.643 Å

Surface

Projections

Slices (1/3)

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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: 0.18
Minimum - Maximum-0.8106693 - 1.107025
Average (Standard dev.)0.005312702 (±0.043816835)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 318.6432 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: EMhancer full map of V0-only V-ATPase in SYP-KO ISVs.

Fileemd_44845_additional_1.map
AnnotationEMhancer full map of V0-only V-ATPase in SYP-KO ISVs.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: Unsharpened map

Fileemd_44845_additional_2.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of V0-only V-ATPase in SYP-KO ISVs.

Fileemd_44845_half_map_1.map
AnnotationHalf map B of V0-only V-ATPase in SYP-KO ISVs.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of V0-only V-ATPase in SYP-KO ISVs.

Fileemd_44845_half_map_2.map
AnnotationHalf map A of V0-only V-ATPase in SYP-KO ISVs.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Syptophysin gene knock-out mouse brain isolated glutamatergic syn...

EntireName: Syptophysin gene knock-out mouse brain isolated glutamatergic synaptic vesicles
Components
  • Organelle or cellular component: Syptophysin gene knock-out mouse brain isolated glutamatergic synaptic vesicles
    • Protein or peptide: V-type proton ATPase subunit S1
    • Protein or peptide: V-type proton ATPase 21 kDa proteolipid subunit c''
    • Protein or peptide: V-type proton ATPase subunit d 1
    • Protein or peptide: Ribonuclease kappa
    • Protein or peptide: V-type proton ATPase 16 kDa proteolipid subunit c
    • Protein or peptide: Renin receptor cytoplasmic fragment
    • Protein or peptide: V-type proton ATPase subunit e 2
    • Protein or peptide: V-type proton ATPase 116 kDa subunit a 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: beta-D-mannopyranose

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Supramolecule #1: Syptophysin gene knock-out mouse brain isolated glutamatergic syn...

SupramoleculeName: Syptophysin gene knock-out mouse brain isolated glutamatergic synaptic vesicles
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: V-type proton ATPase subunit S1

MacromoleculeName: V-type proton ATPase subunit S1 / type: protein_or_peptide / ID: 1 / Details: 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 #2: V-type proton ATPase 21 kDa proteolipid subunit c''

MacromoleculeName: V-type proton ATPase 21 kDa proteolipid subunit c'' / type: protein_or_peptide / ID: 2 / Details: 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 #3: V-type proton ATPase subunit d 1

MacromoleculeName: V-type proton ATPase subunit d 1 / type: protein_or_peptide / ID: 3 / Details: 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 #4: Ribonuclease kappa

MacromoleculeName: Ribonuclease kappa / type: protein_or_peptide / ID: 4 / Details: 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 #5: V-type proton ATPase 16 kDa proteolipid subunit c

MacromoleculeName: V-type proton ATPase 16 kDa proteolipid subunit c / type: protein_or_peptide / ID: 5 / Details: 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 #6: Renin receptor cytoplasmic fragment

MacromoleculeName: Renin receptor cytoplasmic fragment / type: protein_or_peptide / ID: 6 / Details: Renin receptor / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 32.751381 KDa
SequenceString: WPGLAVGNLF HRPRATIMVM VKGVDKLALP AGSVISYPLE NAVPFSLDSV ANSIHSLFSE ETPVVLQLAP SEERVYMVGK ANSVFEDLS VTLRQLRNRL FQENSLLNSL PLNSLSRNNE VDLLFLSELQ VLHDISSLLS RHKHLAKDHS PDLYSLELAG L DELGKRYG ...String:
WPGLAVGNLF HRPRATIMVM VKGVDKLALP AGSVISYPLE NAVPFSLDSV ANSIHSLFSE ETPVVLQLAP SEERVYMVGK ANSVFEDLS VTLRQLRNRL FQENSLLNSL PLNSLSRNNE VDLLFLSELQ VLHDISSLLS RHKHLAKDHS PDLYSLELAG L DELGKRYG EDSEQFRDAS KILVDALQKF ADDMYSLYGG NAVVELVTVK SFDTSLVRKS RTILEAKQEN TQSPYNLAYK YN LEYSVVF NLVLWIMIGL ALAVIITSYN IWNMDPGYDS IIYRMTNQKI RID

UniProtKB: Renin receptor

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Macromolecule #7: V-type proton ATPase subunit e 2

MacromoleculeName: V-type proton ATPase subunit e 2 / type: protein_or_peptide / ID: 7 / Details: 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 #8: V-type proton ATPase 116 kDa subunit a 1

MacromoleculeName: V-type proton ATPase 116 kDa subunit a 1 / type: protein_or_peptide / ID: 8 / Details: 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 #11: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 11 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Macromolecule #12: beta-D-mannopyranose

MacromoleculeName: beta-D-mannopyranose / type: ligand / ID: 12 / Number of copies: 1 / Formula: BMA
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-BMA:
beta-D-mannopyranose / Mannose

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

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 53390

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Atomic model buiding 1

DetailsThe initial model is the model of wild-type V0-only V-ATPase. For fitting and refinement details, see https://doi.org/10.1038/s41586-024-07610-x.
RefinementProtocol: FLEXIBLE FIT
Output model

PDB-9bry:
V0-only V-ATPase in synaptophysin gene knock-out mouse brain isolated synaptic vesicles

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