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- PDB-5voy: Yeast V-ATPase in complex with Legionella pneumophila effector Si... -
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Basic information
Entry | Database: PDB / ID: 5voy | ||||||||||||||||||
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Title | Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 2) | ||||||||||||||||||
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![]() | HYDROLASE / V-ATPase / SidK / rotational state 2 | ||||||||||||||||||
Function / homology | ![]() vacuole-mitochondrion membrane contact site / cell wall mannoprotein biosynthetic process / ATPase-coupled ion transmembrane transporter activity / cellular response to alkaline pH / Insulin receptor recycling / Transferrin endocytosis and recycling / polyphosphate metabolic process / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification ...vacuole-mitochondrion membrane contact site / cell wall mannoprotein biosynthetic process / ATPase-coupled ion transmembrane transporter activity / cellular response to alkaline pH / Insulin receptor recycling / Transferrin endocytosis and recycling / polyphosphate metabolic process / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / proteasome storage granule assembly / P-type proton-exporting transporter activity / plasma membrane proton-transporting V-type ATPase complex / pexophagy / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V0 domain / vacuolar proton-transporting V-type ATPase, V1 domain / vacuolar transport / vacuole organization / protein targeting to vacuole / proton-transporting V-type ATPase complex / fungal-type vacuole / protein metabolic process / intein-mediated protein splicing / intron homing / cellular hyperosmotic response / fungal-type vacuole membrane / vacuolar proton-transporting V-type ATPase complex / phosphatidylinositol-3,5-bisphosphate binding / vacuolar acidification / proton transmembrane transporter activity / intracellular copper ion homeostasis / ATP metabolic process / H+-transporting two-sector ATPase / proton transmembrane transport / Neutrophil degranulation / phagocytic vesicle / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / cell periphery / transmembrane transport / cytoplasmic stress granule / intracellular calcium ion homeostasis / endocytosis / ATPase binding / protein-containing complex assembly / endonuclease activity / intracellular iron ion homeostasis / Hydrolases; Acting on ester bonds / early endosome / Golgi membrane / mRNA binding / ATP hydrolysis activity / DNA binding / ATP binding / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.9 Å | ||||||||||||||||||
![]() | Zhao, J. | ||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Molecular basis for the binding and modulation of V-ATPase by a bacterial effector protein. Authors: Jianhua Zhao / Ksenia Beyrakhova / Yao Liu / Claudia P Alvarez / Stephanie A Bueler / Li Xu / Caishuang Xu / Michal T Boniecki / Voula Kanelis / Zhao-Qing Luo / Miroslaw Cygler / John L Rubinstein / ![]() ![]() Abstract: Intracellular pathogenic bacteria evade the immune response by replicating within host cells. Legionella pneumophila, the causative agent of Legionnaires' Disease, makes use of numerous effector ...Intracellular pathogenic bacteria evade the immune response by replicating within host cells. Legionella pneumophila, the causative agent of Legionnaires' Disease, makes use of numerous effector proteins to construct a niche supportive of its replication within phagocytic cells. The L. pneumophila effector SidK was identified in a screen for proteins that reduce the activity of the proton pumping vacuolar-type ATPases (V-ATPases) when expressed in the yeast Saccharomyces cerevisae. SidK is secreted by L. pneumophila in the early stages of infection and by binding to and inhibiting the V-ATPase, SidK reduces phagosomal acidification and promotes survival of the bacterium inside macrophages. We determined crystal structures of the N-terminal region of SidK at 2.3 Å resolution and used single particle electron cryomicroscopy (cryo-EM) to determine structures of V-ATPase:SidK complexes at ~6.8 Å resolution. SidK is a flexible and elongated protein composed of an α-helical region that interacts with subunit A of the V-ATPase and a second region of unknown function that is flexibly-tethered to the first. SidK binds V-ATPase strongly by interacting via two α-helical bundles at its N terminus with subunit A. In vitro activity assays show that SidK does not inhibit the V-ATPase completely, but reduces its activity by ~40%, consistent with the partial V-ATPase deficiency phenotype its expression causes in yeast. The cryo-EM analysis shows that SidK reduces the flexibility of the A-subunit that is in the 'open' conformation. Fluorescence experiments indicate that SidK binding decreases the affinity of V-ATPase for a fluorescent analogue of ATP. Together, these results reveal the structural basis for the fine-tuning of V-ATPase activity by SidK. | ||||||||||||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 1.1 MB | Display | ![]() |
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PDB format | ![]() | 708.5 KB | Display | ![]() |
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-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 147.9 KB | Display | |
Data in CIF | ![]() | 264.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8725MC ![]() 8724C ![]() 8726C ![]() 5uf5C ![]() 5ufkC ![]() 5voxC ![]() 5vozC C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 2 types, 6 molecules ACEefg
#1: Protein | Mass: 67796.508 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c References: UniProt: P17255, H+-transporting two-sector ATPase, Hydrolases; Acting on ester bonds #16: Protein | Mass: 65490.320 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: lp12_0990 / Production host: ![]() ![]() |
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-V-type proton ATPase subunit ... , 14 types, 27 molecules BDFGIKHJLMNOPQRSTUVWXYZabcd
#2: Protein | Mass: 57815.023 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P16140 #3: Protein | Mass: 26508.393 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P22203 #4: Protein | Mass: 12738.706 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P48836 #5: Protein | | Mass: 29235.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P32610 #6: Protein | | Mass: 13479.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P39111 #7: Protein | | Mass: 44241.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P31412 #8: Protein | | Mass: 54482.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P41807 #9: Protein | | Mass: 39822.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P32366 #10: Protein | | Mass: 22610.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P23968 #11: Protein | | Mass: 17046.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P32842 #12: Protein | Mass: 16357.501 Da / Num. of mol.: 8 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P25515 #13: Protein | | Mass: 95625.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P32563 #14: Protein | | Mass: 8387.065 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q3E7B6 #15: Protein | | Mass: 4613.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c |
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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 |
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Sample preparation
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Source (natural) |
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Source (recombinant) | Organism: ![]() ![]() Strain: ATCC 204508 / S288c | ||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 1.2 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.11.1_2575: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 7.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11125 / Symmetry type: POINT | ||||||||||||||||||||||||
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