7UZJ

Rat Kidney V1 complex with SidK and NCOA7B, State 1

• PDB DOI: https://doi.org/10.2210/pdb7UZJ/pdb
• EM Map EMD-26913: EMDB EMDataResource

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


• Deposited: 2022-05-09 Released: 2023-11-22 
• Deposition Author(s): Abbas, Y.M., Rubinstein, J.L.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of V-ATPase with NCOA7B

Abbas, Y.M., Rubinstein, J.L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 20-mer - A3B3C3D3E3F1G1H1I1J1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 20-mer - A5B3C3D3E1F1G1H1I1J1 Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Hetero 9-mer - A3B3E3 

Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Hetero 9-mer - A3B3E3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 758.69 kDa 
• Atom Count: 49,624 
• Modelled Residue Count: 6,232 
• Deposited Residue Count: 6,708 
• Unique protein chains: 10

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATPase H+-transporting V1 subunit A	A, B, C	617	Rattus norvegicus	Mutation(s): 0
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 B2GUV5 (Rattus norvegicus) Explore B2GUV5  Go to UniProtKB:  B2GUV5

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit H	P	483	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for A0A0G2K9J2 (Rattus norvegicus) Explore A0A0G2K9J2  Go to UniProtKB:  A0A0G2K9J2

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Effector SidK	Q, R, S	280	Legionella 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
Nuclear receptor coactivator 7B	T	221	Rattus norvegicus	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP (Subject of Investigation/LOI)	U [auth C]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)	V [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-11-22 
Deposition Author(s): Abbas, Y.M., Rubinstein, J.L.

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

Revision History  

• Version 1.0: 2023-11-22
  Type: Initial release