[English] 日本語
Yorodumi- PDB-8zi0: Cryo-EM reveals transition states of the Acinetobacter baumannii ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8zi0 | ||||||
---|---|---|---|---|---|---|---|
Title | Cryo-EM reveals transition states of the Acinetobacter baumannii F1-ATPase rotary subunits gamma and epsilon and novel compound targets - Conformation 1 | ||||||
Components | (ATP synthase ...) x 4 | ||||||
Keywords | HYDROLASE / ATP hydrolysis / F1-ATPase | ||||||
Function / homology | Function and homology information proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / hydrolase activity / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Acinetobacter baumannii AB5075 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.18 Å | ||||||
Authors | Le, K.C.M. / Wong, C.F. / Gruber, G. | ||||||
Funding support | Singapore, 1items
| ||||||
Citation | Journal: FASEB J / Year: 2024 Title: Cryo-EM reveals transition states of the Acinetobacter baumannii F-ATPase rotary subunits γ and ε, unveiling novel compound targets. Authors: Khoa Cong Minh Le / Chui Fann Wong / Volker Müller / Gerhard Grüber / Abstract: Priority 1: critical WHO pathogen Acinetobacter baumannii depends on ATP synthesis and ATP:ADP homeostasis and its bifunctional FF-ATP synthase. While synthesizing ATP, it regulates ATP cleavage by ...Priority 1: critical WHO pathogen Acinetobacter baumannii depends on ATP synthesis and ATP:ADP homeostasis and its bifunctional FF-ATP synthase. While synthesizing ATP, it regulates ATP cleavage by its inhibitory ε subunit to prevent wasteful ATP consumption. We determined cryo-electron microscopy structures of the ATPase active A. baumannii F-αßγε mutant in four distinct conformational states, revealing four transition states and structural transformation of the ε's C-terminal domain, forming the switch of an ATP hydrolysis off- and an ATP synthesis on-state based. These alterations go in concert with altered motions and interactions in the catalytic- and rotary subunits of this engine. These A. baumannii interacting sites provide novel pathogen-specific targets for inhibitors, with the aim of ATP depletion and/or ATP synthesis and growth inhibition. Furthermore, the presented diversity to other bacterial F-ATP synthases extends the view of structural elements regulating such a catalyst. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8zi0.cif.gz | 613.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8zi0.ent.gz | 501.9 KB | Display | PDB format |
PDBx/mmJSON format | 8zi0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8zi0_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8zi0_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 8zi0_validation.xml.gz | 91.8 KB | Display | |
Data in CIF | 8zi0_validation.cif.gz | 143.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zi/8zi0 ftp://data.pdbj.org/pub/pdb/validation_reports/zi/8zi0 | HTTPS FTP |
-Related structure data
Related structure data | 60117MC 8zi1C 8zi2C 8zi3C M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-ATP synthase ... , 4 types, 8 molecules ABCDEFeg
#1: Protein | Mass: 55452.906 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii AB5075 (bacteria) Gene: atpA, A1S_0153 / Plasmid: pET29b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 References: UniProt: A3M142, H+-transporting two-sector ATPase #2: Protein | Mass: 50327.180 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii AB5075 (bacteria) Gene: atpD, A0141_RS12845, A0141_RS20960, A7M90_08515, Aba7835_18750, ABCAM1_0171, ABR2091_0172, ABUW_3732, ACX61_17955, APD17_18800, AUO97_06425, AYR68_18055, B7L45_18625, B9W25_04445, B9X95_01225, ...Gene: atpD, A0141_RS12845, A0141_RS20960, A7M90_08515, Aba7835_18750, ABCAM1_0171, ABR2091_0172, ABUW_3732, ACX61_17955, APD17_18800, AUO97_06425, AYR68_18055, B7L45_18625, B9W25_04445, B9X95_01225, C2U32_15270, CAS83_08025, CBE85_14440, CBL15_17790, CSB70_3894, CTZ19_18505, CV954_019160, D8O08_000340, DLI71_10780, DOL94_02915, E1A86_02070, E1A87_05115, EA706_05505, EA720_009770, EA722_10620, EGM95_19710, F2P40_12655, F4T85_15180, FDN00_02380, FE003_18670, FJU42_13260, FJV09_08800, FR761_02120, G3N53_14495, GNY86_14295, GSE42_00720, HB367_12615, HBK86_18980, HIN86_18910, IAG11_01885, IMO23_00745, ITE13_08765, JHZ39_002240, P9867_05895, SAMEA104305318_03329, SAMEA4394745_01410 Plasmid: pET29b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 References: UniProt: V5VHQ6, H+-transporting two-sector ATPase #3: Protein | | Mass: 13838.840 Da / Num. of mol.: 1 / Mutation: deletion 134-139 Source method: isolated from a genetically manipulated source Details: Subunit epsilon with truncated C-terminus domain, deletion I134-Q139 Source: (gene. exp.) Acinetobacter baumannii AB5075 (bacteria) Gene: atpC, A0141_RS12850, A0141_RS20965, A7M90_08520, Aba7835_18745, ABCAM1_0172, ABR2091_0173, ABUW_3731, ACX61_17950, APD17_18795, AUO97_06420, AYR68_18050, B7L45_18620, B9W25_04440, B9X95_01230, ...Gene: atpC, A0141_RS12850, A0141_RS20965, A7M90_08520, Aba7835_18745, ABCAM1_0172, ABR2091_0173, ABUW_3731, ACX61_17950, APD17_18795, AUO97_06420, AYR68_18050, B7L45_18620, B9W25_04440, B9X95_01230, C2U32_15275, CAS83_08020, CBE85_14435, CBL15_17785, CSB70_3895, CTZ19_18500, CV954_019155, D8O08_000335, DLI71_10775, DOL94_02920, E1A86_02075, E1A87_05110, EA686_08570, EA706_05510, EA720_009765, EA722_10625, EGM95_19705, F2P40_12650, F4T85_15175, FDN00_02385, FE003_18665, FJU42_13255, FJV09_08795, FR761_02125, G3N53_14500, GNY86_14290, GSE42_00725, HB367_12610, HBK86_18985, HIN86_18905, IMO23_00750, JHZ39_002241, P9867_05900, SAMEA104305318_03328, SAMEA4394745_01411 Plasmid: pET29b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: V5VHG0 #4: Protein | | Mass: 32135.037 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii AB5075 (bacteria) Gene: atpG, A1S_0154 / Plasmid: pET29b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: A3M143 |
---|
-Non-polymers , 4 types, 9 molecules
#5: Chemical | #6: Chemical | ChemComp-MG / #7: Chemical | ChemComp-ADP / | #8: Chemical | ChemComp-PO4 / | |
---|
-Details
Has ligand of interest | Y |
---|---|
Has protein modification | N |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Acinetobacter baumannii F1-ATPase recombinant protein with truncation mutation at subunit epsilon CTD, 134-139 Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Value: 0.37 MDa / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: Acinetobacter baumannii AB5075 (bacteria) | |||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) / Strain: C41 | |||||||||||||||
Buffer solution | pH: 7.5 / Details: 50 mM Tris-HCl, 150 mM NaCl | |||||||||||||||
Buffer component |
| |||||||||||||||
Specimen | Conc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 160000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 6.02 sec. / Electron dose: 68.6 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8635 |
-Processing
EM software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 829861 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 47078 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 7YRY Accession code: 7YRY Details: The initial model is from the CryoEM structure of AbF1-ATPase Wild Type form. Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|