EMDB-44843: Intact V-ATPase State 1 and synaptophysin complex in mouse brain ...

Basic information

Entry

Database: EMDB / ID: EMD-44843

• Title: Intact V-ATPase State 1 and synaptophysin complex in mouse brain isolated synaptic vesicles
• Map data: Full map of V-ATPase State 1 synaptophysin complex in wild-type ISVs.

Sample

• Organelle or cellular component: Mouse brain isolated glutamatergic synaptic vesicles
  • Protein or peptide: x 17 types

• Keywords: V-ATPase / synaptic vesicle / MEMBRANE PROTEIN

Function / homology

Function:

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 / 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 / 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, V1 domain / vacuolar proton-transporting V-type ATPase complex / proton-transporting V-type ATPase complex / neuron spine / head morphogenesis / vacuolar acidification / osteoclast development / protein localization to cilium / regulation of short-term neuronal synaptic plasticity / neuron projection terminus / dendritic spine membrane / regulation of cellular pH / syntaxin-1 binding / cholesterol binding / ATPase complex / presynaptic active zone / regulation of neuronal synaptic plasticity / microvillus / 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 / ATP metabolic process / H+-transporting two-sector ATPase / axon terminus / ruffle / proton-transporting ATPase activity, rotational mechanism / RNA endonuclease activity / proton-transporting ATP synthase activity, rotational mechanism / endoplasmic reticulum-Golgi intermediate compartment membrane / Neutrophil degranulation / SH2 domain binding / receptor-mediated endocytosis / proton transmembrane transport / SNARE binding / secretory granule / regulation of long-term neuronal synaptic plasticity / modulation of chemical synaptic transmission / neuromuscular junction / Schaffer collateral - CA1 synapse / terminal bouton / cilium / transmembrane transport / small GTPase binding / synaptic vesicle membrane / endocytosis / positive regulation of canonical Wnt signaling pathway / melanosome / synaptic vesicle / apical part of cell / myelin sheath / 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

Domain/homology:

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 / 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, V0 complex, subunit e1/e2 / ATP synthase subunit H / ATPase, V1 complex, subunit F, eukaryotic / 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

Component:

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 / Synaptophysin / 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

• Biological species: Mus musculus (house mouse)
• Method: single particle reconstruction / cryo EM / Resolution: 4.3 Å
• Authors: Wang C / Jiang W / Yang K / Wang X / Guo Q / Brunger AT

Funding support

United States, 2 items

Organization	Grant number	Country
Howard Hughes Medical Institute (HHMI)		United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)	RO1MH63105	United States

• Citation: Journal: 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 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 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

Deposition	May 11, 2024	-
Header (metadata) release	Jun 19, 2024	-
Map release	Jun 19, 2024	-
Update	Aug 7, 2024	-
Current status	Aug 7, 2024	Processing site: RCSB / Status: Released

Map

• File: Download / File: emd_44843.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: Full map of V-ATPase State 1 synaptophysin complex in wild-type ISVs.
• Voxel size: X=Y=Z: 1.11138 Å

Density

Contour Level	By AUTHOR: 0.28
Minimum - Maximum	-0.69003093 - 1.4339924
Average (Standard dev.)	0.002278173 (±0.06169591)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 448 448 448 Spacing 448 448 448
Cell	A=B=C: 497.8969 Å α=β=γ: 90.0 °

Supplemental data

Additional map: EMhancer map of V-ATPase State 1 synaptophysin complex...

• File: emd_44843_additional_1.map
• Annotation: EMhancer map of V-ATPase State 1 synaptophysin complex in wild-type ISVs.

Additional map: Unsharpened map of V-ATPase State 1

• File: emd_44843_additional_2.map
• Annotation: Unsharpened map of V-ATPase State 1

Half map: Half map of V-ATPase State 1 synaptophysin complex in wild-type ISVs.

• File: emd_44843_half_map_1.map
• Annotation: Half map of V-ATPase State 1 synaptophysin complex in wild-type ISVs.

Half map: Half map of V-ATPase State 1 synaptophysin complex in wild-type ISVs.

• File: emd_44843_half_map_2.map
• Annotation: Half map of V-ATPase State 1 synaptophysin complex in wild-type ISVs.

Sample components

Entire : Mouse brain isolated glutamatergic synaptic vesicles

• Entire: Name: 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 E 1
  • Protein or peptide: V-type proton ATPase subunit G 2
  • 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 C 1
  • Protein or peptide: V-type proton ATPase subunit D
  • Protein or peptide: V-type proton ATPase subunit H
  • Protein or peptide: V-type proton ATPase subunit F
  • Protein or peptide: V-type proton ATPase 116 kDa subunit a 1
  • 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: V-type proton ATPase 16 kDa proteolipid subunit c
  • Protein or peptide: Renin receptor cytoplasmic fragment
  • Protein or peptide: V-type proton ATPase subunit S1
  • Protein or peptide: Ribonuclease kappa
  • Protein or peptide: Synaptophysin
  • Protein or peptide: V-type proton ATPase subunit e 2

Supramolecule #1: Mouse brain isolated glutamatergic synaptic vesicles

• Supramolecule: Name: 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)

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

• Macromolecule: Name: 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 weight: Theoretical: 26.196449 KDa

Sequence

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

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

• Macromolecule: Name: 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 weight: Theoretical: 13.674476 KDa

Sequence

String:

MASQTQGIQQ LLQAEKRAAE KVADARKRKA RRLKQAKEEA QMEVEQYRRE REQEFQSKQQ AAMGSQGNLS AEVEQATRRQ VQGMQSSQQ RNRERVLAQL LGMVCEVRPQ VHPNYRVTV

UniProtKB: V-type proton ATPase subunit G 2

Macromolecule #3: V-type proton ATPase catalytic subunit A

• Macromolecule: Name: V-type proton ATPase catalytic subunit A / type: protein_or_peptide / ID: 3 ; 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 weight: Theoretical: 68.402875 KDa

Sequence

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

Macromolecule #4: V-type proton ATPase subunit B, brain isoform

• Macromolecule: Name: V-type proton ATPase subunit B, brain isoform / type: protein_or_peptide / ID: 4 / Details: VATB2_MOUSE V-type proton ATPase subunit B / Number of copies: 3 / Enantiomer: LEVO
• Source (natural): Organism: Mus musculus (house mouse)
• Molecular weight: Theoretical: 56.61157 KDa

Sequence

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

Macromolecule #5: V-type proton ATPase subunit C 1

• Macromolecule: Name: V-type proton ATPase subunit C 1 / type: protein_or_peptide / ID: 5 / Details: VATC1_MOUSE V-type proton ATPase subunit C 1 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mus musculus (house mouse)
• Molecular weight: Theoretical: 43.945449 KDa

Sequence

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

Macromolecule #6: V-type proton ATPase subunit D

• Macromolecule: Name: V-type proton ATPase subunit D / type: protein_or_peptide / ID: 6 / Details: VATD_MOUSE V-type proton ATPase subunit D / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mus musculus (house mouse)
• Molecular weight: Theoretical: 28.419117 KDa

Sequence

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

Macromolecule #7: V-type proton ATPase subunit H

• Macromolecule: Name: V-type proton ATPase subunit H / type: protein_or_peptide / ID: 7 / Details: VATH_MOUSE V-type proton ATPase subunit H / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mus musculus (house mouse)
• Molecular weight: Theoretical: 55.922859 KDa

Sequence

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

Macromolecule #8: V-type proton ATPase subunit F

• Macromolecule: Name: 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 weight: Theoretical: 13.389262 KDa

Sequence

String:

MAGRGKLIAV IGDEDTVTGF LLGGIGELNK NRHPNFLVVE KDTTINEIED TFRQFLNRDD IGIILINQYI AEMVRHALDA HQRSIPAVL EIPSKEHPYD AAKDSILRRA KGMFTAEDLR

UniProtKB: V-type proton ATPase subunit F

Macromolecule #9: V-type proton ATPase 116 kDa subunit a 1

• Macromolecule: Name: 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 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mus musculus (house mouse)
• Molecular weight: Theoretical: 96.4425 KDa

Sequence

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

Macromolecule #10: V-type proton ATPase 21 kDa proteolipid subunit c''

• Macromolecule: Name: V-type proton ATPase 21 kDa proteolipid subunit c'' / type: protein_or_peptide / ID: 10 ; 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 weight: Theoretical: 21.618553 KDa

Sequence

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''

Macromolecule #11: V-type proton ATPase subunit d 1

• Macromolecule: Name: V-type proton ATPase subunit d 1 / type: protein_or_peptide / ID: 11 / Details: VA0D1_MOUSE V-type proton ATPase subunit d 1 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mus musculus (house mouse)
• Molecular weight: Theoretical: 40.341934 KDa

Sequence

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

Macromolecule #12: V-type proton ATPase 16 kDa proteolipid subunit c

• Macromolecule: Name: V-type proton ATPase 16 kDa proteolipid subunit c / type: protein_or_peptide / ID: 12 ; 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 weight: Theoretical: 15.815833 KDa

Sequence

String:

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

Macromolecule #13: Renin receptor cytoplasmic fragment

• Macromolecule: Name: Renin receptor cytoplasmic fragment / type: protein_or_peptide / ID: 13 / Details: RENR_MOUSE Renin receptor / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mus musculus (house mouse)
• Molecular weight: Theoretical: 39.128789 KDa

Sequence

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

Macromolecule #14: V-type proton ATPase subunit S1

• Macromolecule: Name: V-type proton ATPase subunit S1 / type: protein_or_peptide / ID: 14 / Details: VAS1_MOUSE V-type proton ATPase subunit S1 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mus musculus (house mouse)
• Molecular weight: Theoretical: 51.046215 KDa

Sequence

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

Macromolecule #15: Ribonuclease kappa

• Macromolecule: Name: Ribonuclease kappa / type: protein_or_peptide / ID: 15 / 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 weight: Theoretical: 11.000004 KDa

Sequence

String:

MASLLCCGPK LAACGIVLSA WGVIMLIMLG IFFNVHSAVL IEDVPFTEKD FENGPQNIYN LYEQVSYNCF IAAGLYLLLG GFSFCQVRL NKRKEYMVR

UniProtKB: Ribonuclease kappa

Macromolecule #16: Synaptophysin

• Macromolecule: Name: Synaptophysin / type: protein_or_peptide / ID: 16 / Details: SYPH_MOUSE Synaptophysin / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mus musculus (house mouse)
• Molecular weight: Theoretical: 34.045406 KDa

Sequence

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

Macromolecule #17: V-type proton ATPase subunit e 2

• Macromolecule: Name: V-type proton ATPase subunit e 2 / type: protein_or_peptide / ID: 17 / Details: VA0E2_MOUSE V-type proton ATPase subunit e 2 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mus musculus (house mouse)
• Molecular weight: Theoretical: 9.20302 KDa

Sequence

String:

MTAHSFALPV IIFTTFWGLI GIAGPWFVPK GPNRGVIITM LVATAVCCYL FWLIAILAQL NPLFGPQLKN ETIWYVRFLW E

UniProtKB: V-type proton ATPase subunit e 2

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: cell

Sample preparation

• Buffer: pH: 7.4
• Vitrification: Cryogen name: ETHANE
• Details: The specimen state should be an intact subcellular component.

Electron microscopy

• Microscope: TFS KRIOS
• Image recording: Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Startup model: Type of model: OTHER
• Final reconstruction: Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 17889
• Initial angle assignment: Type: RANDOM ASSIGNMENT
• Final angle assignment: Type: MAXIMUM LIKELIHOOD

Atomic model buiding 1

• Refinement: Protocol: FLEXIBLE FIT

Output model

PDB-9brt:
Intact V-ATPase State 1 and synaptophysin complex in mouse brain isolated synaptic vesicles