9BRD

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

PDB DOI: https://doi.org/10.2210/pdb9BRD/pdb
EM Map EMD-44353: EMDB EMDataResource

Classification: PROTON TRANSPORT
Organism(s): Rattus norvegicus, Legionella pneumophila subsp. pneumophila str. Philadelphia 1
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)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 1,310.92 kDa
Atom Count: 72,445
Modelled Residue Count: 9,421
Deposited Residue Count: 11,503
Unique protein chains: 18

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H(+)-transporting two-sector ATPase	A, B, C	646	Rattus norvegicus	Mutation(s): 0 EC: 7.1.2.2
UniProt
Find proteins for D4A133 (Rattus norvegicus) Explore D4A133 Go to UniProtKB: D4A133
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UniProt Group	D4A133
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Reference Sequence

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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
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UniProt Group	P62815
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Reference Sequence

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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
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UniProt Group	Q5FVI6
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Reference Sequence

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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
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UniProt Group	Q6P503
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Reference Sequence

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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
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UniProt Group	Q6PCU2
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Reference Sequence

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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
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UniProt Group	P50408
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Reference Sequence

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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
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UniProt Group	Q8R2H0
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Reference Sequence

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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
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UniProt Group	O54715
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Type IV secretion protein Dot	Q, R, S	573	Legionella pneumophila subsp. pneumophila str. Philadelphia 1	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
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UniProt Group	Q5ZWW6
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Reference Sequence

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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
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UniProt Group	A0A8I5ZQ24
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Reference Sequence

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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
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UniProt Group	P07825
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase 116 kDa subunit a 1	V [auth a]	832	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for P25286 (Rattus norvegicus) Explore P25286 Go to UniProtKB: P25286
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UniProt Group	P25286
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Reference Sequence

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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
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UniProt Group	B0K022
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Reference Sequence

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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
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UniProt Group	Q5M7T6
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Reference Sequence

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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
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UniProt Group	Q5EB76
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Reference Sequence

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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Rnasek protein	Z [auth f]	86	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for A0A8J8YMT9 (Rattus norvegicus) Explore A0A8J8YMT9 Go to UniProtKB: A0A8J8YMT9
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UniProt Group	A0A8J8YMT9
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Reference Sequence

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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase 16 kDa proteolipid subunit	AA [auth g] BA [auth h] CA [auth i] DA [auth j] EA [auth k] 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
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UniProt Group	P63081
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Reference Sequence

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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
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UniProt Group	Q6AXS4
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Reference Sequence

Oligosaccharides

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Entity ID: 19
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	KA [auth V], LA [auth W], MA [auth X], NA [auth Y], OA [auth Z], KA [auth V], LA [auth W], MA [auth X], NA [auth Y], OA [auth Z], PA [auth c], QA [auth q], RA [auth r]	2		N-Glycosylation	Interactions Focus chain KA [auth V] Focus chain LA [auth W] Focus chain MA [auth X] Focus chain NA [auth Y] Focus chain OA [auth Z] Focus chain PA [auth c] Focus chain QA [auth q] Focus chain RA [auth r] Interactions & Density Focus chain KA [auth V] Focus chain LA [auth W] Focus chain MA [auth X] Focus chain NA [auth Y] Focus chain OA [auth Z] Focus chain PA [auth c] Focus chain QA [auth q] Focus chain RA [auth r]

Entity ID: 20
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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-glucopyranose	SA [auth s]	11		N/A	Interactions Focus chain SA [auth s] Interactions & Density Focus chain SA [auth s]

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PC1 Query on PC1 Download Ideal Coordinates CCD File SDF format, chain DB [auth b] SDF format, chain UB [auth l] SDF format, chain VA [auth P] SDF format, chain WA [auth a] SDF format, chain UA [auth P] MOL2 format, chain DB [auth b] MOL2 format, chain UB [auth l] MOL2 format, chain VA [auth P] MOL2 format, chain WA [auth a] MOL2 format, chain UA [auth P]	DB [auth b], UA [auth P], UB [auth l], VA [auth P], WA [auth a]	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₈ N O₈ P NRJAVPSFFCBXDT-HUESYALOSA-N		Interactions Focus chain DB [auth b] Focus chain UA [auth P] Focus chain UB [auth l] Focus chain VA [auth P] Focus chain WA [auth a] Interactions & Density Focus chain DB [auth b] Focus chain UA [auth P] Focus chain UB [auth l] Focus chain VA [auth P] Focus chain WA [auth a]
PTY Query on PTY Download Ideal Coordinates CCD File SDF format, chain LC [auth p] SDF format, chain OC [auth p] SDF format, chain YA [auth a] SDF format, chain ZA [auth a] SDF format, chain EB [auth b] SDF format, chain FB [auth b] SDF format, chain MC [auth p] SDF format, chain NC [auth p] SDF format, chain XA [auth a] MOL2 format, chain LC [auth p] MOL2 format, chain OC [auth p] MOL2 format, chain YA [auth a] MOL2 format, chain ZA [auth a] MOL2 format, chain EB [auth b] MOL2 format, chain FB [auth b] MOL2 format, chain MC [auth p] MOL2 format, chain NC [auth p] MOL2 format, chain XA [auth a]	EB [auth b] FB [auth b] LC [auth p] MC [auth p] NC [auth p] EB [auth b], FB [auth b], LC [auth p], MC [auth p], NC [auth p], OC [auth p], XA [auth a], YA [auth a], ZA [auth a]	PHOSPHATIDYLETHANOLAMINE C₄₀ H₈₀ N O₈ P NJGIRBISCGPRPF-KXQOOQHDSA-N		Interactions Focus chain EB [auth b] Focus chain FB [auth b] Focus chain LC [auth p] Focus chain MC [auth p] Focus chain NC [auth p] Focus chain OC [auth p] Focus chain XA [auth a] Focus chain YA [auth a] Focus chain ZA [auth a] Interactions & Density Focus chain EB [auth b] Focus chain FB [auth b] Focus chain LC [auth p] Focus chain MC [auth p] Focus chain NC [auth p] Focus chain OC [auth p] Focus chain XA [auth a] Focus chain YA [auth a] Focus chain ZA [auth a]
WJP Query on WJP Download Ideal Coordinates CCD File SDF format, chain AB [auth a] MOL2 format, chain AB [auth a]	AB [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		Interactions Focus chain AB [auth a] Interactions & Density Focus chain AB [auth a]
LP3 Query on LP3 Download Ideal Coordinates CCD File SDF format, chain CB [auth a] MOL2 format, chain CB [auth a]	CB [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		Interactions Focus chain CB [auth a] Interactions & Density Focus chain CB [auth a]
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain TA [auth A] MOL2 format, chain TA [auth A]	TA [auth A]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain TA [auth A] Interactions & Density Focus chain TA [auth A]
CLR Query on CLR Download Ideal Coordinates CCD File SDF format, chain AC [auth m] SDF format, chain BC [auth m] SDF format, chain CC [auth m] SDF format, chain DC [auth n] SDF format, chain EC [auth n] SDF format, chain FC [auth n] SDF format, chain GB [auth b] SDF format, chain GC [auth n] SDF format, chain HB [auth h] SDF format, chain HC [auth n] SDF format, chain IB [auth h] SDF format, chain IC [auth o] SDF format, chain JB [auth i] SDF format, chain JC [auth o] SDF format, chain KB [auth i] SDF format, chain KC [auth o] SDF format, chain LB [auth i] SDF format, chain MB [auth i] SDF format, chain NB [auth j] SDF format, chain OB [auth j] SDF format, chain PB [auth j] SDF format, chain SB [auth k] SDF format, chain TB [auth k] SDF format, chain VB [auth l] SDF format, chain WB [auth l] SDF format, chain XB [auth l] SDF format, chain YB [auth l] SDF format, chain QB [auth j] SDF format, chain RB [auth k] SDF format, chain ZB [auth l] MOL2 format, chain AC [auth m] MOL2 format, chain BC [auth m] MOL2 format, chain CC [auth m] MOL2 format, chain DC [auth n] MOL2 format, chain EC [auth n] MOL2 format, chain FC [auth n] MOL2 format, chain GB [auth b] MOL2 format, chain GC [auth n] MOL2 format, chain HB [auth h] MOL2 format, chain HC [auth n] MOL2 format, chain IB [auth h] MOL2 format, chain IC [auth o] MOL2 format, chain JB [auth i] MOL2 format, chain JC [auth o] MOL2 format, chain KB [auth i] MOL2 format, chain KC [auth o] MOL2 format, chain LB [auth i] MOL2 format, chain MB [auth i] MOL2 format, chain NB [auth j] MOL2 format, chain OB [auth j] MOL2 format, chain PB [auth j] MOL2 format, chain SB [auth k] MOL2 format, chain TB [auth k] MOL2 format, chain VB [auth l] MOL2 format, chain WB [auth l] MOL2 format, chain XB [auth l] MOL2 format, chain YB [auth l] MOL2 format, chain QB [auth j] MOL2 format, chain RB [auth k] MOL2 format, chain ZB [auth l]	AC [auth m] BC [auth m] CC [auth m] DC [auth n] EC [auth n] AC [auth m], BC [auth m], CC [auth m], DC [auth n], EC [auth n], FC [auth n], GB [auth b], GC [auth n], HB [auth h], HC [auth n], IB [auth h], IC [auth o], JB [auth i], JC [auth o], KB [auth i], KC [auth o], LB [auth i], MB [auth i], NB [auth j], OB [auth j], PB [auth j], QB [auth j], RB [auth k], SB [auth k], TB [auth k], VB [auth l], WB [auth l], XB [auth l], YB [auth l], ZB [auth l]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain AC [auth m] Focus chain BC [auth m] Focus chain CC [auth m] Focus chain DC [auth n] Focus chain EC [auth n] Focus chain FC [auth n] Focus chain GB [auth b] Focus chain GC [auth n] Focus chain HB [auth h] Focus chain HC [auth n] Focus chain IB [auth h] Focus chain IC [auth o] Focus chain JB [auth i] Focus chain JC [auth o] Focus chain KB [auth i] Focus chain KC [auth o] Focus chain LB [auth i] Focus chain MB [auth i] Focus chain NB [auth j] Focus chain OB [auth j] Focus chain PB [auth j] Focus chain QB [auth j] Focus chain RB [auth k] Focus chain SB [auth k] Focus chain TB [auth k] Focus chain VB [auth l] Focus chain WB [auth l] Focus chain XB [auth l] Focus chain YB [auth l] Focus chain ZB [auth l] Interactions & Density Focus chain AC [auth m] Focus chain BC [auth m] Focus chain CC [auth m] Focus chain DC [auth n] Focus chain EC [auth n] Focus chain FC [auth n] Focus chain GB [auth b] Focus chain GC [auth n] Focus chain HB [auth h] Focus chain HC [auth n] Focus chain IB [auth h] Focus chain IC [auth o] Focus chain JB [auth i] Focus chain JC [auth o] Focus chain KB [auth i] Focus chain KC [auth o] Focus chain LB [auth i] Focus chain MB [auth i] Focus chain NB [auth j] Focus chain OB [auth j] Focus chain PB [auth j] Focus chain QB [auth j] Focus chain RB [auth k] Focus chain SB [auth k] Focus chain TB [auth k] Focus chain VB [auth l] Focus chain WB [auth l] Focus chain XB [auth l] Focus chain YB [auth l] Focus chain ZB [auth l]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain BB [auth a] MOL2 format, chain BB [auth a]	BB [auth a]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain BB [auth a] Interactions & Density Focus chain BB [auth a]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21_5207:

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-06-26

Deposition Author(s):

Coupland, C.E.

Rubinstein, J.L.

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

Revision History (Full details and data files)

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

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Validate Data

Deposit Data

Help and Resources

9BRD

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

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

Entity ID: 1

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Entity ID: 2

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Entity ID: 11

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Entity ID: 12

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Entity ID: 17

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Entity ID: 18

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Entity ID: 19

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