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Yorodumi- PDB-9ayc: Tetra-phosphorylated, E1435Q Ycf1 mutant in inward-facing wide co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9ayc | |||||||||
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Title | Tetra-phosphorylated, E1435Q Ycf1 mutant in inward-facing wide conformation | |||||||||
Components | Metal resistance protein YCF1 | |||||||||
Keywords | MEMBRANE PROTEIN / ABC-transporter / ycf1 / r-domain / phosphorylation / heavy metal | |||||||||
Function / homology | Function and homology information ABC-type Cd2+ transporter / ABC-type cadmium transporter activity / Recycling of bile acids and salts / Heme degradation / Aspirin ADME / Paracetamol ADME / Atorvastatin ADME / P-type cadmium transporter activity / bilirubin transmembrane transporter activity / bilirubin transport ...ABC-type Cd2+ transporter / ABC-type cadmium transporter activity / Recycling of bile acids and salts / Heme degradation / Aspirin ADME / Paracetamol ADME / Atorvastatin ADME / P-type cadmium transporter activity / bilirubin transmembrane transporter activity / bilirubin transport / ABC-family proteins mediated transport / vacuole fusion, non-autophagic / ABC-type glutathione-S-conjugate transporter / ABC-type glutathione S-conjugate transporter activity / response to metal ion / fungal-type vacuole membrane / ATPase-coupled transmembrane transporter activity / response to cadmium ion / glutathione metabolic process / cell redox homeostasis / transmembrane transport / membrane raft / ATP hydrolysis activity / ATP binding / membrane Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.23 Å | |||||||||
Authors | Carvalho, R.S.A. / Rasel, M.S.I. / Khandelwal, N.K. / Tomasiak, T.M. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published Title: Cryo-EM structure of the tetra-phosphorylated R-domain in Ycf1 reveals key interactions for transport regulation Authors: Carvalho, R.S.A. / Rasel, M.S.I. / Khandelwal, N.K. / Tomasiak, T.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9ayc.cif.gz | 565.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9ayc.ent.gz | 466.9 KB | Display | PDB format |
PDBx/mmJSON format | 9ayc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/9ayc ftp://data.pdbj.org/pub/pdb/validation_reports/ay/9ayc | HTTPS FTP |
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-Related structure data
Related structure data | 43985MC 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
#1: Protein | Mass: 176263.234 Da / Num. of mol.: 1 / Mutation: E1435Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: YCF1, YDR135C, YD9302.11C / Production host: Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P39109, ABC-type Cd2+ transporter, ABC-type glutathione-S-conjugate transporter |
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Has ligand of interest | Y |
-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: Phosphorylated, E1435Q Ycf1 mutant in inward-facing wide conformation Type: ORGANELLE OR CELLULAR COMPONENT / Details: c-AMP PKA treated E1435Q Ycf1 mutant / Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 176462 kDa/nm / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||||||||||
Source (recombinant) | Organism: Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||||||||||
Buffer solution | pH: 7 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 5.94 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse | ||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 283 K Details: 5 microliters of sample of concentrated E1435Q (5.94 mg/mL) PKA-treated Ycf1 sample was applied to QF-1.2/1,3 Au grid. Grids were place inside of a Leica EM GP2 equilibrated at 10 degress ...Details: 5 microliters of sample of concentrated E1435Q (5.94 mg/mL) PKA-treated Ycf1 sample was applied to QF-1.2/1,3 Au grid. Grids were place inside of a Leica EM GP2 equilibrated at 10 degress Celcius amd 80% humidity. Following 10 seconds incubation, the side of the grid to which the sample was applied was blotted on a Whatman 1 paper (3.5 seconds) then immediately plunge frrozen in liquid ethan equilibrated at -185 degree Celcius. |
-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: 2100 nm / Nominal defocus min: 900 nm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 0.9 sec. / Electron dose: 54 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8587 Details: Movies were collected at 22,500X magnification with automated super-resolution mode and defocus range of -0.9 to -2.1 micrometer. Moview frames cotained 60 frames with a per frame expousre ...Details: Movies were collected at 22,500X magnification with automated super-resolution mode and defocus range of -0.9 to -2.1 micrometer. Moview frames cotained 60 frames with a per frame expousre of 0.9 electrons per angstrom squared (54 electron/angstrom square total dose) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 4840688 Details: Manual and auto particle picking and extraction from 8380 curated micropgrahs | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 68169 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL | ||||||||||||||||||||||||||||
Atomic model building | Accession code: p39109 / Source name: AlphaFold / Type: in silico model | ||||||||||||||||||||||||||||
Refine LS restraints |
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