9BRC

Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 2

• PDB DOI: https://doi.org/10.2210/pdb9BRC/pdb
• EM Map EMD-44354: EMDB EMDataResource

• Classification: PROTON TRANSPORT
• Organism(s): Rattus norvegicus, Legionella pneumophila subsp. pneumophila
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-05-11 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: 3.90 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 36-mer - A9B3C3D3E3F3G1H1I1J1K1L1M1N1O1P1Q1R1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 36-mer - A10B6C3D3E3F1G1H1I1J1K1L1M1N1O1P1 

Local Symmetry: Cyclic - C9  (Explore in 3D)
Local Stoichiometry: Homo 9-mer - A9 Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Hetero 15-mer - B3C3D3E3F3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 1,283.89 kDa 
• Atom Count: 46,442 
• Modelled Residue Count: 9,424 
• Deposited Residue Count: 11,520 
• Unique protein chains: 18

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H(+)-transporting two-sector ATPase	A, B, C	647	Rattus norvegicus	Mutation(s): 0  EC: 7.1.2.2
UniProt
Find proteins for D4A133 (Rattus norvegicus) Explore D4A133  Go to UniProtKB:  D4A133

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit B, brain isoform	D, E, F	511	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for P62815 (Rattus norvegicus) Explore P62815  Go to UniProtKB:  P62815

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit C 1	G	382	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for Q5FVI6 (Rattus norvegicus) Explore Q5FVI6  Go to UniProtKB:  Q5FVI6

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ATPase H+-transporting V1 subunit D	H	247	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for Q6P503 (Rattus norvegicus) Explore Q6P503  Go to UniProtKB:  Q6P503

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit E 1	I, J, K	226	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for Q6PCU2 (Rattus norvegicus) Explore Q6PCU2  Go to UniProtKB:  Q6PCU2

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit F	L	119	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for P50408 (Rattus norvegicus) Explore P50408  Go to UniProtKB:  P50408

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit G	M, N, O	118	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for Q8R2H0 (Rattus norvegicus) Explore Q8R2H0  Go to UniProtKB:  Q8R2H0

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit S1	P	463	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for O54715 (Rattus norvegicus) Explore O54715  Go to UniProtKB:  O54715

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Type IV secretion protein Dot	Q, R, S	573	Legionella pneumophila subsp. pneumophila	Mutation(s): 0  Gene Names: lpg0968
UniProt
Find proteins for Q5ZWW6 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZWW6  Go to UniProtKB:  Q5ZWW6

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit H	T	463	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for A0A8I5ZQ24 (Rattus norvegicus) Explore A0A8I5ZQ24  Go to UniProtKB:  A0A8I5ZQ24

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Synaptophysin	U	307	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for P07825 (Rattus norvegicus) Explore P07825  Go to UniProtKB:  P07825

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase 116 kDa subunit a isoform 1	V [auth a]	838	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for P25286 (Rattus norvegicus) Explore P25286  Go to UniProtKB:  P25286

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a	W [auth b]	205	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for B0K022 (Rattus norvegicus) Explore B0K022  Go to UniProtKB:  B0K022

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit	X [auth d]	351	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for Q5M7T6 (Rattus norvegicus) Explore Q5M7T6  Go to UniProtKB:  Q5M7T6

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit e 2	Y [auth e]	81	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for Q5EB76 (Rattus norvegicus) Explore Q5EB76  Go to UniProtKB:  Q5EB76

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Rnasek protein	Z [auth f]	94	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for A0A8J8YMT9 (Rattus norvegicus) Explore A0A8J8YMT9  Go to UniProtKB:  A0A8J8YMT9

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase 16 kDa proteolipid subunit c	AA [auth g], BA [auth h], CA [auth i], DA [auth j], EA [auth k], FA [auth l], GA [auth m], HA [auth n], IA [auth o]	155	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for P63081 (Rattus norvegicus) Explore P63081  Go to UniProtKB:  P63081

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Renin receptor	JA [auth p]	350	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for Q6AXS4 (Rattus norvegicus) Explore Q6AXS4  Go to UniProtKB:  Q6AXS4

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 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	--

Revision History  

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