7KHR

Cryo-EM structure of bafilomycin A1-bound intact V-ATPase from bovine brain


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.62 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular basis of V-ATPase inhibition by bafilomycin A1.

Wang, R.Wang, J.Hassan, A.Lee, C.H.Xie, X.S.Li, X.

(2021) Nat Commun 12: 1782-1782

  • DOI: 10.1038/s41467-021-22111-5
  • Primary Citation of Related Structures:  
    7KHR

  • PubMed Abstract: 
  • Pharmacological inhibition of vacuolar-type H + -ATPase (V-ATPase) by its specific inhibitor can abrogate tumor metastasis, prevent autophagy, and reduce cellular signaling responses. Bafilomycin A1, a member of macrolide antibiotics and an autophagy inhibitor, serves as a specific and potent V-ATPases inhibitor ...

    Pharmacological inhibition of vacuolar-type H + -ATPase (V-ATPase) by its specific inhibitor can abrogate tumor metastasis, prevent autophagy, and reduce cellular signaling responses. Bafilomycin A1, a member of macrolide antibiotics and an autophagy inhibitor, serves as a specific and potent V-ATPases inhibitor. Although there are many V-ATPase structures reported, the molecular basis of specific inhibitors on V-ATPase remains unknown. Here, we report the cryo-EM structure of bafilomycin A1 bound intact bovine V-ATPase at an overall resolution of 3.6-Å. The structure reveals six bafilomycin A1 molecules bound to the c-ring. One bafilomycin A1 molecule engages with two c subunits and disrupts the interactions between the c-ring and subunit a, thereby preventing proton translocation. Structural and sequence analyses demonstrate that the bafilomycin A1-binding residues are conserved in yeast and mammalian species and the 7'-hydroxyl group of bafilomycin A1 acts as a unique feature recognized by subunit c.


    Organizational Affiliation

    Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 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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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 
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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 
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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 subunit e 2T [auth e]81Bos taurusMutation(s): 0 
Gene Names: ATP6V0E2
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit S1U [auth s]468Bos taurusMutation(s): 0 
Gene Names: ATP6AP1ATP6IP1ATP6S1
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Renin receptorV [auth r]351Bos taurusMutation(s): 0 
Gene Names: ATP6AP2ATP6IP2
Membrane Entity: Yes 
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Entity ID: 15
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: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonuclease kappaFA [auth f]98Bos taurusMutation(s): 0 
Gene Names: RNASEK
EC: 3.1
Membrane Entity: Yes 
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Oligosaccharides

Help

Entity ID: 17
MoleculeChainsChain Length2D DiagramGlycosylation3D 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)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseGA [auth t]9N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G44289EY
GlyCosmos:  G44289EY
Entity ID: 18
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranoseHA [auth Q]2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G77384RA
GlyCosmos:  G77384RA
GlyGen:  G77384RA
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
POV
Query on POV

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CB [auth l],
LA [auth b],
MA [auth b],
NA [auth s],
OA [auth s],
CB [auth l],
LA [auth b],
MA [auth b],
NA [auth s],
OA [auth s],
WA [auth r],
XA [auth r],
YA [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
WEV (Subject of Investigation/LOI)
Query on WEV

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AB [auth g],
BB [auth g],
DB [auth l],
EB [auth m],
FB [auth o],
AB [auth g],
BB [auth g],
DB [auth l],
EB [auth m],
FB [auth o],
GB [auth p]
(5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S,4E,6E,9R,10S,11R,12E,14Z)-10-hydroxy-3,15-dimethoxy-7,9,11,13-tetramethyl-16-oxo-1-oxacyclohexadeca-4,6,12,14-tetraen-2-yl]pentan-2-yl}-4-methyl-5-propan-2-yl-alpha-D-threo-pentopyranose
C35 H58 O9
XDHNQDDQEHDUTM-XJKSCTEHSA-N
 Ligand Interaction
WJP
Query on WJP

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KA [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
 Ligand Interaction
ADP
Query on ADP

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JA [auth C]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
OLA
Query on OLA

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ZA [auth r]OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
 Ligand Interaction
NAG
Query on NAG

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PA [auth s],
QA [auth s],
RA [auth s],
SA [auth s],
TA [auth s],
PA [auth s],
QA [auth s],
RA [auth s],
SA [auth s],
TA [auth s],
UA [auth s],
VA [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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IA [auth C]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.62 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: 2021-03-17
    Type: Initial release
  • Version 1.1: 2021-09-29
    Changes: Database references