9B8Q

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

• PDB DOI: https://doi.org/10.2210/pdb9B8Q/pdb
• EM Map EMD-44352: EMDB EMDataResource

• Classification: PROTON TRANSPORT
• Organism(s): Rattus norvegicus
• Mutation(s): No 


• Deposited: 2024-03-31 Released: 2024-06-26 
• Deposition Author(s): Coupland, C.E., Rubinstein, J.L.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

High-resolution electron cryomicroscopy of V-ATPase in native synaptic vesiclesCoupland, 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 

• DOI: https://doi.org/10.1126/science.adp5577

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 9-mer - A3B3C1D1E1 Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Hetero 6-mer - A3B3 

Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 315.9 kDa 
• Atom Count: 12,348 
• Modelled Residue Count: 1,886 
• Deposited Residue Count: 2,735 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit C 1	A [auth G]	382	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for Q5FVI6 (Rattus norvegicus) Explore Q5FVI6  Go to UniProtKB:  Q5FVI6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit E 1	B [auth I], C [auth J], D [auth K]	226	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for Q6PCU2 (Rattus norvegicus) Explore Q6PCU2  Go to UniProtKB:  Q6PCU2

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit G	E [auth M], F [auth N], G [auth O]	118	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for Q8R2H0 (Rattus norvegicus) Explore Q8R2H0  Go to UniProtKB:  Q8R2H0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit H	H [auth T]	483	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for A0A8I5ZQ24 (Rattus norvegicus) Explore A0A8I5ZQ24  Go to UniProtKB:  A0A8I5ZQ24

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase 116 kDa subunit a isoform 1	I [auth a]	838	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for P25286 (Rattus norvegicus) Explore P25286  Go to UniProtKB:  P25286

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21_5207

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-26 
Deposition Author(s): Coupland, C.E., Rubinstein, J.L.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	PJT166152

Revision History  

• Version 1.0: 2024-06-26
  Type: Initial release