9B8O | pdb_00009b8o

Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, Vo


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9B8O

This is version 1.3 of the entry. See complete history

Literature

High-resolution electron cryomicroscopy of V-ATPase in native synaptic vesicles.

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.

(2024) Science 385: 168-174

  • DOI: https://doi.org/10.1126/science.adp5577
  • Primary Citation Related Structures: 
    9B8O, 9B8P, 9B8Q, 9BRB, 9BRC, 9BRD

  • PubMed Abstract: 

    Intercellular communication in the nervous system occurs through the release of neurotransmitters into the synaptic cleft between neurons. In the presynaptic neuron, the proton pumping vesicular- or vacuolar-type ATPase (V-ATPase) powers neurotransmitter loading into synaptic vesicles (SVs), with the V 1 complex dissociating from the membrane region of the enzyme before exocytosis. We isolated SVs from rat brain using SidK, a V-ATPase-binding bacterial effector protein. Single particle electron cryomicroscopy allowed high-resolution structure determination of V-ATPase within the native SV membrane. In the structure, regularly spaced cholesterol molecules decorate the enzyme's rotor and the abundant SV protein synaptophysin binds the complex stoichiometrically. ATP hydrolysis during vesicle loading results in loss of V 1 from the SV membrane, suggesting that loading is sufficient to induce dissociation of the enzyme.


  • Organizational Affiliation
    • Molecular Medicine Program, The Hospital for Sick Children, Toronto, Canada M5G 1X8.

Macromolecule Content 

  • Total Structure Weight: 512.03 kDa 
  • Atom Count: 24,407 
  • Modeled Residue Count: 3,028 
  • Deposited Residue Count: 4,430 
  • Unique protein chains: 11

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ATPase H+-transporting V1 subunit DA [auth H]247Rattus norvegicusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q6P503 (Rattus norvegicus)
Explore Q6P503 
Go to UniProtKB:  Q6P503
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6P503
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit S1B [auth P]463Rattus norvegicusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for O54715 (Rattus norvegicus)
Explore O54715 
Go to UniProtKB:  O54715
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO54715
Glycosylation
Glycosylation Sites: 5Go to GlyGen: O54715-1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
SynaptophysinC [auth U]307Rattus norvegicusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P07825 (Rattus norvegicus)
Explore P07825 
Go to UniProtKB:  P07825
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07825
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
V-type proton ATPase 116 kDa subunit a 1D [auth a]826Rattus norvegicusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P25286 (Rattus norvegicus)
Explore P25286 
Go to UniProtKB:  P25286
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25286
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P25286-1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_aE [auth b]205Rattus norvegicusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B0K022 (Rattus norvegicus)
Explore B0K022 
Go to UniProtKB:  B0K022
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0K022
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
V-type proton ATPase subunitF [auth d]351Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for Q5M7T6 (Rattus norvegicus)
Explore Q5M7T6 
Go to UniProtKB:  Q5M7T6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5M7T6
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit e 2G [auth e]81Rattus norvegicusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q5EB76 (Rattus norvegicus)
Explore Q5EB76 
Go to UniProtKB:  Q5EB76
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5EB76
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Rnasek proteinH [auth f]86Rattus norvegicusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D3ZIM6 (Rattus norvegicus)
Explore D3ZIM6 
Go to UniProtKB:  D3ZIM6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD3ZIM6
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
V-type proton ATPase 16 kDa proteolipid subunit c155Rattus norvegicusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P63081 (Rattus norvegicus)
Explore P63081 
Go to UniProtKB:  P63081
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63081
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Renin receptorR [auth p]350Rattus norvegicusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q6AXS4 (Rattus norvegicus)
Explore Q6AXS4 
Go to UniProtKB:  Q6AXS4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6AXS4
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit FS [auth L]119Rattus norvegicusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P50408 (Rattus norvegicus)
Explore P50408 
Go to UniProtKB:  P50408
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50408
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 12
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth I],
T [auth A],
U [auth B],
V [auth C],
W [auth D],
AA [auth I],
T [auth A],
U [auth B],
V [auth C],
W [auth D],
X [auth E],
Y [auth F],
Z [auth G]
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 13
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseBA [auth Z]11N/A
Glycosylation Resources
GlyTouCan: G71069MN
GlyCosmos: G71069MN

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PC1

Query on PC1



Download:Ideal Coordinates CCD File
CA [auth P],
EB [auth l],
GA [auth a],
JA [auth b],
KA [auth b]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
PTY

Query on PTY



Download:Ideal Coordinates CCD File
HA [auth a]
IA [auth a]
LA [auth b]
MA [auth b]
OA [auth e]
HA [auth a],
IA [auth a],
LA [auth b],
MA [auth b],
OA [auth e],
UB [auth p],
VA [auth j],
VB [auth p],
WB [auth p]
PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
WJP

Query on WJP



Download:Ideal Coordinates CCD File
DA [auth a]methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate
C26 H48 O7 P2
GDOCHZBDTMOKKR-FEJNUDJDSA-N
LP3

Query on LP3



Download:Ideal Coordinates CCD File
FA [auth a](7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE
C26 H55 N O7 P
IHNKQIMGVNPMTC-RUZDIDTESA-O
CLR

Query on CLR



Download:Ideal Coordinates CCD File
AB [auth k]
BB [auth k]
CB [auth k]
DB [auth k]
FB [auth l]
AB [auth k],
BB [auth k],
CB [auth k],
DB [auth k],
FB [auth l],
GB [auth l],
HB [auth l],
IB [auth m],
JB [auth m],
KB [auth m],
LB [auth m],
MB [auth m],
NA [auth b],
NB [auth n],
OB [auth n],
PA [auth h],
PB [auth n],
QA [auth h],
QB [auth n],
RA [auth i],
RB [auth o],
SA [auth i],
SB [auth o],
TA [auth i],
TB [auth o],
UA [auth i],
WA [auth j],
XA [auth j],
YA [auth j],
ZA [auth j]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
EA [auth a]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaPJT166152

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-26
    Type: Initial release
  • Version 1.1: 2024-07-03
    Changes: Data collection, Database references
  • Version 1.2: 2024-07-24
    Changes: Data collection, Database references
  • Version 1.3: 2024-10-23
    Changes: Data collection, Structure summary