[English] 日本語
Yorodumi
- PDB-9brb: Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9brb
TitleSynaptic Vesicle V-ATPase with synaptophysin and SidK, State 1
Components
  • (V-type proton ATPase ...) x 11
  • ATPase H+-transporting V1 subunit D
  • ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a
  • H(+)-transporting two-sector ATPase
  • Renin receptor
  • Rnasek protein
  • Synaptophysin
  • Type IV secretion protein Dot
KeywordsPROTON TRANSPORT / Vesicle / synaptic / membrane
Function / homology
Function and homology information


regulation of opioid receptor signaling pathway / Metabolism of Angiotensinogen to Angiotensins / Transferrin endocytosis and recycling / Ion channel transport / Amino acids regulate mTORC1 / Insulin receptor recycling / RHOA GTPase cycle / eye pigmentation / central nervous system maturation / transporter activator activity ...regulation of opioid receptor signaling pathway / Metabolism of Angiotensinogen to Angiotensins / Transferrin endocytosis and recycling / Ion channel transport / Amino acids regulate mTORC1 / Insulin receptor recycling / RHOA GTPase cycle / eye pigmentation / central nervous system maturation / transporter activator activity / negative regulation of autophagic cell death / rostrocaudal neural tube patterning / cellular response to increased oxygen levels / positive regulation of transforming growth factor beta1 production / proton-transporting V-type ATPase, V1 domain / synaptic vesicle lumen acidification / endosome to plasma membrane protein transport / intracellular organelle / proton-transporting V-type ATPase, V0 domain / extrinsic component of synaptic vesicle membrane / P-type proton-exporting transporter activity / plasma membrane proton-transporting V-type ATPase complex / lysosomal lumen acidification / clathrin-coated vesicle membrane / vacuolar proton-transporting V-type ATPase, V1 domain / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V0 domain / vacuolar transport / proton-transporting V-type ATPase complex / neuron spine / head morphogenesis / protein localization to cilium / regulation of short-term neuronal synaptic plasticity / neuron projection terminus / vacuolar proton-transporting V-type ATPase complex / dendritic spine membrane / regulation of cellular pH / vacuolar acidification / syntaxin-1 binding / ROS and RNS production in phagocytes / osteoclast development / Neutrophil degranulation / regulation of synaptic vesicle exocytosis / : / cholesterol binding / ATPase complex / presynaptic active zone / regulation of neuronal synaptic plasticity / autophagosome membrane / response to amyloid-beta / microvillus / regulation of MAPK cascade / ATPase activator activity / synaptic vesicle endocytosis / excitatory synapse / cilium assembly / positive regulation of Wnt signaling pathway / transmembrane transporter complex / angiotensin maturation / regulation of macroautophagy / axon terminus / ATP metabolic process / H+-transporting two-sector ATPase / proton transmembrane transport / ruffle / RNA endonuclease activity / phagocytic vesicle / proton-transporting ATPase activity, rotational mechanism / endoplasmic reticulum-Golgi intermediate compartment membrane / SH2 domain binding / proton-transporting ATP synthase activity, rotational mechanism / SNARE binding / receptor-mediated endocytosis / secretory granule / regulation of long-term neuronal synaptic plasticity / Schaffer collateral - CA1 synapse / neuromuscular junction / terminal bouton / transmembrane transport / cilium / synaptic vesicle membrane / small GTPase binding / endocytosis / melanosome / positive regulation of canonical Wnt signaling pathway / synaptic vesicle / presynapse / apical part of cell / presynaptic membrane / signaling receptor activity / cell body / ATPase binding / postsynaptic membrane / intracellular iron ion homeostasis / receptor-mediated endocytosis of virus by host cell / postsynaptic density / lysosome / positive regulation of ERK1 and ERK2 cascade / early endosome / endosome 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 / 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 / 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-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 / 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 subunit H / Rnasek protein / ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a / H(+)-transporting two-sector ATPase / V-type proton ATPase subunit S1 / Synaptophysin / V-type proton ATPase 116 kDa subunit a 1 / V-type proton ATPase subunit F / V-type proton ATPase subunit B, brain isoform / V-type proton ATPase 16 kDa proteolipid subunit c ...V-type proton ATPase subunit H / Rnasek protein / ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a / H(+)-transporting two-sector ATPase / V-type proton ATPase subunit S1 / Synaptophysin / V-type proton ATPase 116 kDa subunit a 1 / V-type proton ATPase subunit F / V-type proton ATPase subunit B, brain isoform / V-type proton ATPase 16 kDa proteolipid subunit c / V-type proton ATPase subunit e 2 / V-type proton ATPase subunit C 1 / V-type proton ATPase subunit / Type IV secretion protein Dot / Renin receptor / V-type proton ATPase subunit D / V-type proton ATPase subunit E 1 / V-type proton ATPase subunit G
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
Rattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsCoupland, C.E. / Rubinstein, J.L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Science / Year: 2024
Title: High-resolution electron cryomicroscopy of V-ATPase in native synaptic vesiclesAuthors: Coupland, C.E. / Karimi, R. / Bueler, S.A. / Liang, Y. / Courbon, G.M. / Di Trani, J.M. / Wong, C.J. / Saghian, R. / Youn, J.Y. / Wang, L.Y. / Rubinstein, J.L.
History
DepositionMay 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: H(+)-transporting two-sector ATPase
B: H(+)-transporting two-sector ATPase
C: H(+)-transporting two-sector ATPase
D: V-type proton ATPase subunit B, brain isoform
E: V-type proton ATPase subunit B, brain isoform
F: V-type proton ATPase subunit B, brain isoform
G: V-type proton ATPase subunit C 1
H: ATPase H+-transporting V1 subunit D
I: V-type proton ATPase subunit E 1
J: V-type proton ATPase subunit E 1
K: V-type proton ATPase subunit E 1
L: V-type proton ATPase subunit F
M: V-type proton ATPase subunit G
N: V-type proton ATPase subunit G
O: V-type proton ATPase subunit G
P: V-type proton ATPase subunit S1
Q: Type IV secretion protein Dot
R: Type IV secretion protein Dot
S: Type IV secretion protein Dot
T: V-type proton ATPase subunit H
U: Synaptophysin
a: V-type proton ATPase 116 kDa subunit a isoform 1
b: ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a
d: V-type proton ATPase subunit
e: V-type proton ATPase subunit e 2
f: Rnasek protein
g: V-type proton ATPase 16 kDa proteolipid subunit c
h: V-type proton ATPase 16 kDa proteolipid subunit c
i: V-type proton ATPase 16 kDa proteolipid subunit c
j: V-type proton ATPase 16 kDa proteolipid subunit c
k: V-type proton ATPase 16 kDa proteolipid subunit c
l: V-type proton ATPase 16 kDa proteolipid subunit c
m: V-type proton ATPase 16 kDa proteolipid subunit c
n: V-type proton ATPase 16 kDa proteolipid subunit c
o: V-type proton ATPase 16 kDa proteolipid subunit c
p: Renin receptor


Theoretical massNumber of molelcules
Total (without water)1,283,88636
Polymers1,283,88636
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Protein , 7 types, 11 molecules ABCHQRSUbfp

#1: Protein H(+)-transporting two-sector ATPase


Mass: 71483.438 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat)
References: UniProt: D4A133, H+-transporting two-sector ATPase
#4: Protein ATPase H+-transporting V1 subunit D / ATPase / H+ transporting / V1 subunit D / isoform CRA_c / lysosomal V1 subunit D


Mass: 28359.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q6P503
#9: Protein Type IV secretion protein Dot


Mass: 65505.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Gene: lpg0968 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZWW6
#11: Protein Synaptophysin / Major synaptic vesicle protein p38


Mass: 33331.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P07825
#13: Protein ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a / ATPase / H+ transporting / lysosomal V0 subunit B / Atp6v0b protein


Mass: 21618.553 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: B0K022
#16: Protein Rnasek protein


Mass: 10597.495 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: A0A8J8YMT9
#18: Protein Renin receptor / ATPase H(+)-transporting lysosomal accessory protein 2 / ATPase H(+)-transporting lysosomal- ...ATPase H(+)-transporting lysosomal accessory protein 2 / ATPase H(+)-transporting lysosomal-interacting protein 2 / Renin/prorenin receptor


Mass: 39118.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q6AXS4

-
V-type proton ATPase ... , 11 types, 25 molecules DEFGIJKLMNOPTadeghijklmno

#2: Protein V-type proton ATPase subunit B, brain isoform / V-ATPase subunit B 2 / Endomembrane proton pump 58 kDa subunit / Vacuolar proton pump subunit B 2


Mass: 56611.570 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P62815
#3: Protein V-type proton ATPase subunit C 1 / V-ATPase subunit C 1 / Vacuolar proton pump subunit C 1


Mass: 43958.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q5FVI6
#5: Protein V-type proton ATPase subunit E 1 / V-ATPase subunit E 1 / Vacuolar proton pump subunit E 1


Mass: 26167.453 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q6PCU2
#6: Protein V-type proton ATPase subunit F / V-ATPase subunit F / V-ATPase 14 kDa subunit / Vacuolar proton pump subunit F


Mass: 13389.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P50408
#7: Protein V-type proton ATPase subunit G


Mass: 13690.476 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q8R2H0
#8: Protein V-type proton ATPase subunit S1 / V-ATPase subunit S1 / C7-1 protein / V-ATPase Ac45 subunit / V-ATPase S1 accessory protein / ...V-ATPase subunit S1 / C7-1 protein / V-ATPase Ac45 subunit / V-ATPase S1 accessory protein / Vacuolar proton pump subunit S1


Mass: 51160.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: O54715
#10: Protein V-type proton ATPase subunit H


Mass: 53661.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: A0A8I5ZQ24
#12: Protein V-type proton ATPase 116 kDa subunit a isoform 1 / V-ATPase 116 kDa isoform a1 / Clathrin-coated vesicle/synaptic vesicle proton pump 116 kDa subunit ...V-ATPase 116 kDa isoform a1 / Clathrin-coated vesicle/synaptic vesicle proton pump 116 kDa subunit / Vacuolar adenosine triphosphatase subunit Ac116 / Vacuolar proton pump subunit 1 / Vacuolar proton translocating ATPase 116 kDa subunit a isoform 1


Mass: 96429.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P25286
#14: Protein V-type proton ATPase subunit


Mass: 40341.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q5M7T6
#15: Protein V-type proton ATPase subunit e 2 / V-ATPase subunit e 2 / Vacuolar proton pump subunit e 2


Mass: 9203.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q5EB76
#17: Protein
V-type proton ATPase 16 kDa proteolipid subunit c / V-ATPase 16 kDa proteolipid subunit c / Vacuolar proton pump 16 kDa proteolipid subunit c


Mass: 15815.833 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P63081

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: V-type proton ATPase / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1900 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 37.5 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

-
Processing

EM softwareName: PHENIX / Version: 1.21_5207: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 123220 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00575247
ELECTRON MICROSCOPYf_angle_d0.601101672
ELECTRON MICROSCOPYf_dihedral_angle_d5.85210227
ELECTRON MICROSCOPYf_chiral_restr0.04111529
ELECTRON MICROSCOPYf_plane_restr0.00513006

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • 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

Read more