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- EMDB-44846: V0-only V-ATPase and synaptophysin complex in mouse brain isolate... -

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Entry
Database: EMDB / ID: EMD-44846
TitleV0-only V-ATPase and synaptophysin complex in mouse brain isolated synaptic vesicles
Map dataHalf map A of V0-only V-ATPasesynaptophysin complex in wild-type ISVs.
Sample
  • Organelle or cellular component: 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: Synaptophysin
    • 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
KeywordsV0only V-ATPase / synaptic vesicle / MEMBRANE PROTEIN
Function / homology
Function and homology information


Ion channel transport / regulation of opioid receptor signaling pathway / Amino acids regulate mTORC1 / clathrin-sculpted glutamate transport vesicle membrane / Transferrin endocytosis and recycling / Insulin receptor recycling / eye pigmentation / central nervous system maturation / Metabolism of Angiotensinogen to Angiotensins / transporter activator activity ...Ion channel transport / regulation of opioid receptor signaling pathway / Amino acids regulate mTORC1 / clathrin-sculpted glutamate transport vesicle membrane / 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 / RHOA GTPase cycle / rostrocaudal neural tube patterning / positive regulation of transforming growth factor beta1 production / cellular response to increased oxygen levels / regulation of synaptic vesicle priming / ROS and RNS production in phagocytes / proton-transporting V-type ATPase, V0 domain / synaptic vesicle lumen acidification / P-type proton-exporting transporter activity / intracellular organelle / clathrin-coated vesicle membrane / lysosomal lumen acidification / endosome to plasma membrane protein transport / vacuolar transport / vacuolar proton-transporting V-type ATPase, V0 domain / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase complex / proton-transporting V-type ATPase complex / neuron spine / head morphogenesis / vacuolar acidification / osteoclast development / regulation of short-term neuronal synaptic plasticity / neuron projection terminus / dendritic spine membrane / regulation of cellular pH / syntaxin-1 binding / cholesterol binding / presynaptic active zone / regulation of neuronal synaptic plasticity / ATPase activator activity / regulation of MAPK cascade / autophagosome membrane / synaptic vesicle endocytosis / excitatory synapse / positive regulation of Wnt signaling pathway / cilium assembly / transmembrane transporter complex / regulation of macroautophagy / angiotensin maturation / endomembrane system / axon terminus / proton-transporting ATPase activity, rotational mechanism / RNA endonuclease activity / endoplasmic reticulum-Golgi intermediate compartment membrane / Neutrophil degranulation / SH2 domain binding / receptor-mediated endocytosis / proton transmembrane transport / SNARE binding / regulation of long-term neuronal synaptic plasticity / modulation of chemical synaptic transmission / neuromuscular junction / Schaffer collateral - CA1 synapse / terminal bouton / transmembrane transport / small GTPase binding / synaptic vesicle membrane / endocytosis / positive regulation of canonical Wnt signaling pathway / melanosome / synaptic vesicle / presynapse / signaling receptor activity / presynaptic membrane / ATPase binding / cell body / chemical synaptic transmission / postsynaptic membrane / intracellular iron ion homeostasis / receptor-mediated endocytosis of virus by host cell / Hydrolases; Acting on ester bonds / positive regulation of ERK1 and ERK2 cascade / postsynaptic density / early endosome / endosome membrane / endosome / nuclear speck / neuron projection / apical plasma membrane / protein domain specific binding / axon / external side of plasma membrane / lysosomal membrane / centrosome / ubiquitin protein ligase binding / synapse / endoplasmic reticulum membrane
Similarity search - Function
Synaptophysin/synaptoporin / Synaptophysin / synaptoporin signature. / Marvel domain / Membrane-associating domain / MARVEL domain profile. / 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 ...Synaptophysin/synaptoporin / Synaptophysin / synaptoporin signature. / Marvel domain / Membrane-associating domain / MARVEL domain profile. / 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 / 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-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 / Synaptophysin / 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: 3.8 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 12, 2024-
Header (metadata) releaseJun 19, 2024-
Map releaseJun 19, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44846.png

Downloads & links

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Map

FileDownload / File: emd_44846.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHalf map A of V0-only V-ATPasesynaptophysin complex in wild-type ISVs.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 288 pix.
= 319.968 Å		1.11 Å/pix.
x 288 pix.
= 319.968 Å		1.11 Å/pix.
x 288 pix.
= 319.968 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.111 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-1.5135226 - 1.9600891
Average (Standard dev.)0.009408272 (±0.08667885)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 319.968 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_44846_additional_1.map
Projections & Slices
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Additional map: Unsharpened map

Fileemd_44846_additional_2.map
AnnotationUnsharpened map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: Half map A of V0-only V-ATPasesynaptophysin complex in...

Fileemd_44846_half_map_1.map
AnnotationHalf map A of V0-only V-ATPasesynaptophysin complex in wild-type ISVs.
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-ATPasesynaptophysin complex in...

Fileemd_44846_half_map_2.map
AnnotationHalf map B of V0-only V-ATPasesynaptophysin complex in wild-type 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 : Mouse brain isolated glutamatergic synaptic vesicles

EntireName: Mouse brain isolated glutamatergic synaptic vesicles
Components
  • Organelle or cellular component: 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: Synaptophysin
    • 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

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Supramolecule #1: Mouse brain isolated glutamatergic synaptic vesicles

SupramoleculeName: Mouse brain isolated glutamatergic synaptic vesicles / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
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: 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 #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: 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 #3: V-type proton ATPase subunit d 1

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

MacromoleculeName: Ribonuclease kappa / type: protein_or_peptide / ID: 4 / 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 #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: 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 #6: Renin receptor cytoplasmic fragment

MacromoleculeName: Renin receptor cytoplasmic fragment / type: protein_or_peptide / ID: 6 / 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 #7: Synaptophysin

MacromoleculeName: Synaptophysin / type: protein_or_peptide / ID: 7 / Details: SYPH_MOUSE Synaptophysin / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 34.045406 KDa
SequenceString: MLLLADMDVV NQLVAGGQFR VVKEPLGFVK VLQWVFAIFA FATCGSYTGE LRLSVECANK TESALNIEVE FEYPFRLHQV YFDAPSCVK GGTTKIFLVG DYSSSAEFFV TVAVFAFLYS MGALATYIFL QNKYRENNKG PMMDFLATAV FAFMWLVSSS A WAKGLSDV ...String:
MLLLADMDVV NQLVAGGQFR VVKEPLGFVK VLQWVFAIFA FATCGSYTGE LRLSVECANK TESALNIEVE FEYPFRLHQV YFDAPSCVK GGTTKIFLVG DYSSSAEFFV TVAVFAFLYS MGALATYIFL QNKYRENNKG PMMDFLATAV FAFMWLVSSS A WAKGLSDV KMATDPENII KEMPMCRQTG NTCKELRDPV TSGLNTSVVF GFLNLVLWVG NLWFVFKETG WAAPFMRAPP GA PEKQPAP GDAYGDAGYG QGPGGYGPQD SYGPQGGYQP DYGQPASGGG GGYGPQGDYG QQGYGQQGAP TSFSNQM

UniProtKB: Synaptophysin

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Macromolecule #8: V-type proton ATPase subunit e 2

MacromoleculeName: V-type proton ATPase subunit e 2 / type: protein_or_peptide / ID: 8 / 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 #9: V-type proton ATPase 116 kDa subunit a 1

MacromoleculeName: V-type proton ATPase 116 kDa subunit a 1 / type: protein_or_peptide / ID: 9
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 #12: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 12 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 42137
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

DetailsInitial model: 6VQH, 6WLW, mouse synaptophysin from AlphaFold2 . For fitting and refinement details, see https://doi.org/10.1038/s41586-024-07610-x.
RefinementProtocol: FLEXIBLE FIT
Output model

PDB-9brz:
V0-only V-ATPase and synaptophysin complex in mouse brain isolated synaptic vesicles

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  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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