9B8O

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


This is version 1.2 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 of 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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATPase H+-transporting V1 subunit DA [auth H]247Rattus norvegicusMutation(s): 0 
UniProt
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UniProt GroupQ6P503
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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)
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UniProt GroupO54715
Glycosylation
Glycosylation Sites: 5Go to GlyGen: O54715-1
Sequence Annotations
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
SynaptophysinC [auth U]307Rattus norvegicusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P07825 (Rattus norvegicus)
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UniProt GroupP07825
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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)
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UniProt GroupP25286
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P25286-1
Sequence Annotations
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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)
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UniProt GroupB0K022
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunitF [auth d]351Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for Q5M7T6 (Rattus norvegicus)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit e 2G [auth e]81Rattus norvegicusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Rnasek proteinH [auth f]86Rattus norvegicusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase 16 kDa proteolipid subunit c155Rattus norvegicusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Renin receptorR [auth p]350Rattus norvegicusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q6AXS4 (Rattus norvegicus)
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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)
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Oligosaccharides

Help

Entity ID: 12
MoleculeChains Length2D Diagram Glycosylation3D 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 Glycosylation3D 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
GlyGen:  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

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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