[English] 日本語
Yorodumi
- PDB-9bry: V0-only V-ATPase in synaptophysin gene knock-out mouse brain isol... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9bry
TitleV0-only V-ATPase in synaptophysin gene knock-out mouse brain isolated synaptic vesicles
Components
  • (V-type proton ATPase ...) x 6
  • Renin receptor cytoplasmic fragment
  • Ribonuclease kappa
KeywordsMEMBRANE PROTEIN / V0only V-ATPase / synaptic vesicle
Function / homology
Function and homology information


Ion channel transport / Amino acids regulate mTORC1 / Transferrin endocytosis and recycling / Insulin receptor recycling / Metabolism of Angiotensinogen to Angiotensins / eye pigmentation / central nervous system maturation / rostrocaudal neural tube patterning / ROS and RNS production in phagocytes / positive regulation of transforming growth factor beta1 production ...Ion channel transport / Amino acids regulate mTORC1 / Transferrin endocytosis and recycling / Insulin receptor recycling / Metabolism of Angiotensinogen to Angiotensins / eye pigmentation / central nervous system maturation / rostrocaudal neural tube patterning / ROS and RNS production in phagocytes / positive regulation of transforming growth factor beta1 production / RHOA GTPase cycle / synaptic vesicle lumen acidification / P-type proton-exporting transporter activity / proton-transporting V-type ATPase, V0 domain / cellular response to increased oxygen levels / endosome to plasma membrane protein transport / vacuolar proton-transporting V-type ATPase, V0 domain / clathrin-coated vesicle membrane / lysosomal lumen acidification / endosomal lumen acidification / proton-transporting V-type ATPase complex / head morphogenesis / vacuolar proton-transporting V-type ATPase complex / osteoclast development / vacuolar acidification / dendritic spine membrane / ATPase activator activity / regulation of MAPK cascade / autophagosome membrane / proton-transporting ATPase activity, rotational mechanism / cilium assembly / positive regulation of Wnt signaling pathway / regulation of macroautophagy / transporter activator activity / angiotensin maturation / receptor-mediated endocytosis of virus by host cell / Neutrophil degranulation / axon terminus / endoplasmic reticulum-Golgi intermediate compartment membrane / endomembrane system / RNA endonuclease activity / proton transmembrane transport / receptor-mediated endocytosis / small GTPase binding / synaptic vesicle membrane / melanosome / positive regulation of canonical Wnt signaling pathway / signaling receptor activity / ATPase binding / Hydrolases; Acting on ester bonds / postsynaptic membrane / intracellular iron ion homeostasis / early endosome / endosome membrane / endosome / nuclear speck / apical plasma membrane / axon / lysosomal membrane / external side of plasma membrane / ubiquitin protein ligase binding / centrosome / endoplasmic reticulum membrane / protein-containing complex binding / perinuclear region of cytoplasm / Golgi apparatus / membrane / plasma membrane / cytoplasm / cytosol
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 transmembrane spanning segment / Renin receptor N-terminal domain / : / V-type proton ATPase subunit f-like ...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 transmembrane spanning segment / Renin receptor N-terminal domain / : / V-type proton ATPase subunit f-like / 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
beta-D-mannopyranose / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsWang, C. / Jiang, W. / Yang, K. / Wang, X. / Guo, Q. / Brunger, A.T.
Funding support United States, 2items
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, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update
Revision 1.2Nov 20, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
c: V-type proton ATPase subunit S1
b: V-type proton ATPase 21 kDa proteolipid subunit c''
d: V-type proton ATPase subunit d 1
f: Ribonuclease kappa
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 cytoplasmic fragment
e: V-type proton ATPase subunit e 2
a: V-type proton ATPase 116 kDa subunit a 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)407,28724
Polymers404,74616
Non-polymers2,5418
Water00
1


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

-
Components

-
V-type proton ATPase ... , 6 types, 14 molecules cbdghijklmnoea

#1: Protein V-type proton ATPase subunit S1 / V-ATPase subunit S1 / Protein C7-1 / V-ATPase Ac45 subunit / V-ATPase S1 accessory protein / ...V-ATPase subunit S1 / Protein C7-1 / V-ATPase Ac45 subunit / V-ATPase S1 accessory protein / Vacuolar proton pump subunit S1


Mass: 51046.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: V-type proton ATPase subunit S1 / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9R1Q9
#2: Protein V-type proton ATPase 21 kDa proteolipid subunit c'' / V-ATPase 21 kDa proteolipid subunit c'' / 23 kDa subunit of V-ATPase / Vacuolar proton pump 21 kDa ...V-ATPase 21 kDa proteolipid subunit c'' / 23 kDa subunit of V-ATPase / Vacuolar proton pump 21 kDa proteolipid subunit c''


Mass: 21618.553 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: V-type proton ATPase 21 kDa proteolipid subunit / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q91V37
#3: Protein V-type proton ATPase subunit d 1 / V-ATPase subunit d 1 / P39 / Physophilin / V-ATPase 40 kDa accessory protein / V-ATPase AC39 ...V-ATPase subunit d 1 / P39 / Physophilin / V-ATPase 40 kDa accessory protein / V-ATPase AC39 subunit / Vacuolar proton pump subunit d 1


Mass: 40341.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: V-type proton ATPase subunit d 1 / Source: (natural) Mus musculus (house mouse) / References: UniProt: P51863
#5: Protein
V-type proton ATPase 16 kDa proteolipid subunit c / V-ATPase 16 kDa proteolipid subunit c / PL16 / Vacuolar proton pump 16 kDa proteolipid subunit c


Mass: 15815.833 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Details: V-type proton ATPase 16 kDa proteolipid subunit / Source: (natural) Mus musculus (house mouse) / References: UniProt: P63082
#7: 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 / Details: V-type proton ATPase subunit e 2 / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q91XE7
#8: Protein V-type proton ATPase 116 kDa subunit a 1 / V-ATPase 116 kDa subunit a 1 / Clathrin-coated vesicle/synaptic vesicle proton pump 116 kDa subunit ...V-ATPase 116 kDa subunit a 1 / 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: 96442.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: V-type proton ATPase 116 kDa subunit a isoform 1 / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9Z1G4

-
Protein , 2 types, 2 molecules fp

#4: Protein Ribonuclease kappa / RNase K / RNase kappa / V-type proton ATPase subunit f / V-ATPase subunit f


Mass: 11000.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribonuclease kappa / Source: (natural) Mus musculus (house mouse)
References: UniProt: Q8K3C0, Hydrolases; Acting on ester bonds
#6: Protein Renin receptor cytoplasmic fragment


Mass: 32751.381 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Renin receptor / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CYN9

-
Sugars , 4 types, 8 molecules

#9: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 627.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE
#10: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#11: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#12: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Syptophysin gene knock-out mouse brain isolated glutamatergic synaptic vesicles
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#8 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The specimen state should be an intact subcellular component.
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: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.21_5207: / Classification: refinement
EM software
IDNameCategory
7Cootmodel fitting
19PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53390 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
Details: The 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.
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00424030
ELECTRON MICROSCOPYf_angle_d0.83532572
ELECTRON MICROSCOPYf_dihedral_angle_d8.3283540
ELECTRON MICROSCOPYf_chiral_restr0.0443837
ELECTRON MICROSCOPYf_plane_restr0.0064040

+
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://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