6VQ6

Mammalian V-ATPase from rat brain - composite model of rotational state 1 bound to ADP and SidK (built from focused refinement models)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report



Literature

Mammalian V-ATPase from rat brain - composite model of rotational state 1 bound to ADP and SidK (built from focused refinement models)

Abbas, Y.M.Rubinstein, J.L.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATPase H+-transporting V1 subunit AABC617Rattus norvegicusMutation(s): 0 
Gene Names: Atp6v1arCG_52629
EC: 7.1.2.2
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit B, brain isoformDEF511Rattus norvegicusMutation(s): 0 
Gene Names: Atp6v1b2Atp6b2Vat2
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
V-ATPase, composite model rotational state 1 bound to ADP & SidK
Find proteins for P62815 (Rattus norvegicus)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit C 1G382Rattus norvegicusMutation(s): 0 
Gene Names: Atp6v1c1
Find proteins for Q5FVI6 (Rattus norvegicus)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
ATPase H+-transporting V1 subunit DH247Rattus norvegicusMutation(s): 0 
Gene Names: Atp6v1drCG_61537
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit E 1IJK226Rattus norvegicusMutation(s): 0 
Gene Names: Atp6v1e1
Find proteins for Q6PCU2 (Rattus norvegicus)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit FL119Rattus norvegicusMutation(s): 0 
Gene Names: Atp6v1fAtp6s14Vatf
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit GMNO118Rattus norvegicusMutation(s): 0 
Gene Names: 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Effector protein SidKQRS301Legionella pneumophila subsp. pneumophila str. Philadelphia 1Mutation(s): 0 
Gene Names: lpg0968
Find proteins for Q5ZWW6 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase 116 kDa subunit a isoform 1a838Rattus norvegicusMutation(s): 0 
Gene Names: Atp6v0a1Atp6n1Vpp1
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
V-ATPase, composite model rotational state 1 bound to ADP & SidK
Find proteins for P25286 (Rattus norvegicus)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_ab205Rattus norvegicusMutation(s): 0 
Gene Names: Atp6v0bAtp6v0b_predictedrCG_50448
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
V-ATPase, composite model rotational state 1 bound to ADP & SidK
Find proteins for B0K022 (Rattus norvegicus)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit S1c463Rattus norvegicusMutation(s): 0 
Gene Names: Atp6ap1Atp6ip1Atp6s1
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
V-ATPase, composite model rotational state 1 bound to ADP & SidK
Find proteins for O54715 (Rattus norvegicus)
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunitd351Rattus norvegicusMutation(s): 0 
Gene Names: Atp6v0d1rCG_51062
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit e 2e81Rattus norvegicusMutation(s): 0 
Gene Names: Atp6v0e2
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
V-ATPase, composite model rotational state 1 bound to ADP & SidK
Find proteins for Q5EB76 (Rattus norvegicus)
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonuclease Kf98Rattus norvegicusMutation(s): 0 
Gene Names: Rnasek
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
V-ATPase, composite model rotational state 1 bound to ADP & SidK
Find proteins for D3ZIM6 (Rattus norvegicus)
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase 16 kDa proteolipid subunitghijklmno155Rattus norvegicusMutation(s): 0 
Gene Names: Atp6v0cAtp6cAtp6lAtpl
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
V-ATPase, composite model rotational state 1 bound to ADP & SidK
Find proteins for P63081 (Rattus norvegicus)
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Renin receptorp350Rattus norvegicusMutation(s): 0 
Gene Names: Atp6ap2Atp6ip2
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
V-ATPase, composite model rotational state 1 bound to ADP & SidK
Find proteins for Q6AXS4 (Rattus norvegicus)
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download CCD File 
C
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada--

Revision History 

  • Version 1.0: 2020-03-18
    Type: Initial release