+Open data
-Basic information
Entry | Database: PDB / ID: 7uwc | ||||||
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Title | Citrus V-ATPase State 2, H in contact with subunit a | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / V-ATPase / rotary ATPase / complex | ||||||
Function / homology | Function and homology information proton-transporting V-type ATPase, V1 domain / proton-transporting V-type ATPase, V0 domain / proton-transporting two-sector ATPase complex, catalytic domain / plasma membrane proton-transporting V-type ATPase complex / vacuolar proton-transporting V-type ATPase, V0 domain / vacuolar proton-transporting V-type ATPase, V1 domain / vacuolar transport / plant-type vacuole / proton-transporting V-type ATPase complex / vacuolar proton-transporting V-type ATPase complex ...proton-transporting V-type ATPase, V1 domain / proton-transporting V-type ATPase, V0 domain / proton-transporting two-sector ATPase complex, catalytic domain / plasma membrane proton-transporting V-type ATPase complex / vacuolar proton-transporting V-type ATPase, V0 domain / vacuolar proton-transporting V-type ATPase, V1 domain / vacuolar transport / plant-type vacuole / proton-transporting V-type ATPase complex / vacuolar proton-transporting V-type ATPase complex / vacuole / vacuolar acidification / vacuolar membrane / ATP metabolic process / H+-transporting two-sector ATPase / phagocytic vesicle / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / transmembrane transport / ATPase binding / early endosome / lysosomal membrane / ATP hydrolysis activity / ATP binding / membrane Similarity search - Function | ||||||
Biological species | Citrus limon (lemon) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å | ||||||
Authors | Keon, K.A. / Abdelaziz, R.A. / Schulze, W.X. / Schumacher, K. / Rubinstein, J.L. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Structure / Year: 2022 Title: Structure of V-ATPase from citrus fruit. Authors: Yong Zi Tan / Kristine A Keon / Rana Abdelaziz / Peter Imming / Waltraud Schulze / Karin Schumacher / John L Rubinstein / Abstract: We used the Legionella pneumophila effector SidK to affinity purify the endogenous vacuolar-type ATPases (V-ATPases) from lemon fruit. The preparation was sufficient for cryoelectron microscopy, ...We used the Legionella pneumophila effector SidK to affinity purify the endogenous vacuolar-type ATPases (V-ATPases) from lemon fruit. The preparation was sufficient for cryoelectron microscopy, allowing structure determination of the enzyme in two rotational states. The structure defines the ATP:H ratio of the enzyme, demonstrating that it can establish a maximum ΔpH of ∼3, which is insufficient to maintain the low pH observed in the vacuoles of juice sac cells in lemons and other citrus fruit. Compared with yeast and mammalian enzymes, the membrane region of the plant V-ATPase lacks subunit f and possesses an unusual configuration of transmembrane α helices. Subunit H, which inhibits ATP hydrolysis in the isolated catalytic region of V-ATPase, adopts two different conformations in the intact complex, hinting at a role in modulating activity in the intact enzyme. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7uwc.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7uwc.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7uwc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7uwc_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7uwc_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7uwc_validation.xml.gz | 163.2 KB | Display | |
Data in CIF | 7uwc_validation.cif.gz | 279 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uw/7uwc ftp://data.pdbj.org/pub/pdb/validation_reports/uw/7uwc | HTTPS FTP |
-Related structure data
Related structure data | 26828MC 7uw9C 7uwaC 7uwbC 7uwdC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-V-type proton ATPase subunit ... , 14 types, 28 molecules PBDFGIKHJLMNOabcdeghijklmnor
#1: Protein | Mass: 51609.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Citrus limon (lemon) | ||||||||||||||||||||||||
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#3: Protein | Mass: 54417.594 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Citrus limon (lemon) / References: UniProt: A0A067FXK2 #4: Protein | Mass: 26331.332 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Citrus limon (lemon) / References: UniProt: Q9MB46 #5: Protein | Mass: 12354.938 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Citrus limon (lemon) / References: UniProt: A0A067DRZ4 #6: Protein | | Mass: 29235.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Citrus limon (lemon) / References: UniProt: A0A067FFQ8 #7: Protein | | Mass: 14301.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Citrus limon (lemon) / References: UniProt: A0A067E4V9 #8: Protein | | Mass: 42498.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Citrus limon (lemon) / References: UniProt: A0A2H5Q4L7 #9: Protein | | Mass: 92939.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Citrus limon (lemon) / References: UniProt: V4UBK8 #10: Protein/peptide | | Mass: 2741.370 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Citrus limon (lemon) #11: Protein | | Mass: 18581.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Citrus limon (lemon) / References: UniProt: Q84V02 #12: Protein | | Mass: 40693.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Citrus limon (lemon) / References: UniProt: A0A067G267 #13: Protein | | Mass: 7757.460 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Citrus limon (lemon) / References: UniProt: A0A067F7P5 #14: Protein | Mass: 16581.588 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Citrus limon (lemon) / References: UniProt: P0DH92 #15: Protein/peptide | | Mass: 2060.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Citrus limon (lemon) |
-Protein , 1 types, 3 molecules ACE
#2: Protein | Mass: 68755.219 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Citrus limon (lemon) References: UniProt: Q9SM09, H+-transporting two-sector ATPase |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Citrus V-ATPase / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Citrus limon (lemon) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3414.211 nm / Nominal defocus min: 677.558 nm |
Image recording | Electron dose: 31 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53303 / Symmetry type: POINT |