6XBY

Cryo-EM structure of V-ATPase from bovine brain, state 2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.79 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

Cryo-EM structures of intact V-ATPase from bovine brain.

Wang, R.Long, T.Hassan, A.Wang, J.Sun, Y.Xie, X.S.Li, X.

(2020) Nat Commun 11: 3921-3921

  • DOI: 10.1038/s41467-020-17762-9
  • Primary Citation of Related Structures:  
    6XBW, 6XBY

  • PubMed Abstract: 
  • The vacuolar-type H + -ATPases (V-ATPase) hydrolyze ATP to pump protons across the plasma or intracellular membrane, secreting acids to the lumen or acidifying intracellular compartments. It has been implicated in tumor metastasis, renal tubular acidosis, and osteoporosis ...

    The vacuolar-type H + -ATPases (V-ATPase) hydrolyze ATP to pump protons across the plasma or intracellular membrane, secreting acids to the lumen or acidifying intracellular compartments. It has been implicated in tumor metastasis, renal tubular acidosis, and osteoporosis. Here, we report two cryo-EM structures of the intact V-ATPase from bovine brain with all the subunits including the subunit H, which is essential for ATPase activity. Two type-I transmembrane proteins, Ac45 and (pro)renin receptor, along with subunit c", constitute the core of the c-ring. Three different conformations of A/B heterodimers suggest a mechanism for ATP hydrolysis that triggers a rotation of subunits DF, inducing spinning of subunit d with respect to the entire c-ring. Moreover, many lipid molecules have been observed in the Vo domain to mediate the interactions between subunit c, c", (pro)renin receptor, and Ac45. These two structures reveal unique features of mammalian V-ATPase and suggest a mechanism of V1-Vo torque transmission.


    Organizational Affiliation

    Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA. xiaochun.li@utsouthwestern.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase catalytic subunit AA, B, C617Bos taurusMutation(s): 0 
Gene Names: ATP6V1AATP6A1ATP6V1A1
EC: 7.1.2.2
Membrane Entity: Yes 
UniProt
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UniProt GroupP31404
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit B, brain isoformD, E, F511Bos taurusMutation(s): 0 
Gene Names: ATP6V1B2ATP6B2
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit C 1G382Bos taurusMutation(s): 0 
Gene Names: ATP6V1C1ATP6CVATC
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit DH247Bos taurusMutation(s): 0 
Gene Names: ATP6V1DATP6MVATD
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit E 1I, J, K226Bos taurusMutation(s): 0 
Gene Names: ATP6V1E1ATP6E
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit FL119Bos taurusMutation(s): 0 
Gene Names: ATP6V1FATP6S14VATF
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit GM, N, O118Bos taurusMutation(s): 0 
Gene Names: ATP6V1G2
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit HP465Bos taurusMutation(s): 0 
Gene Names: ATP6V1H
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit aQ [auth a]838Bos taurusMutation(s): 0 
Gene Names: ATP6V0A1ATP6N1VPP1
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase 21 kDa proteolipid subunitR [auth b]205Bos taurusMutation(s): 0 
Gene Names: ATP6V0B
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit d 1S [auth d]351Bos taurusMutation(s): 0 
Gene Names: ATP6V0D1ATP6DVPATPD
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase 16 kDa proteolipid subunit155Bos taurusMutation(s): 0 
Gene Names: ATP6V0CATP6CATP6L
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit S1CA [auth s]468Bos taurusMutation(s): 0 
Gene Names: ATP6AP1ATP6IP1ATP6S1
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Renin receptorDA [auth r]351Bos taurusMutation(s): 0 
Gene Names: ATP6AP2ATP6IP2
Membrane Entity: Yes 
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Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
POV
Query on POV

Download Ideal Coordinates CCD File 
GA [auth b],
HA [auth l],
IA [auth o],
JA [auth s],
QA [auth r],
GA [auth b],
HA [auth l],
IA [auth o],
JA [auth s],
QA [auth r],
RA [auth r],
SA [auth r]
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
C42 H82 N O8 P
WTJKGGKOPKCXLL-PFDVCBLKSA-N
 Ligand Interaction
ADP
Query on ADP

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FA [auth D]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
NAG
Query on NAG

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KA [auth s],
LA [auth s],
MA [auth s],
NA [auth s],
OA [auth s],
KA [auth s],
LA [auth s],
MA [auth s],
NA [auth s],
OA [auth s],
PA [auth s]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
MG
Query on MG

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EA [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.79 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-19
    Type: Initial release