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Yorodumi- PDB-8f6i: Cryo-EM structure of a Zinc-loaded symmetrical D70A mutant of the... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8f6i | |||||||||
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Title | Cryo-EM structure of a Zinc-loaded symmetrical D70A mutant of the YiiP-Fab complex | |||||||||
Components |
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Keywords | TRANSPORT PROTEIN / Zinc transporter / cation diffusion facilitator / membrane protein | |||||||||
Function / homology | Function and homology information zinc efflux active transmembrane transporter activity / cadmium ion transmembrane transporter activity / ferrous iron transmembrane transporter activity / intracellular zinc ion homeostasis / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Shewanella oneidensis MR-1 (bacteria) Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.03 Å | |||||||||
Authors | Lopez-Redondo, M.L. / Hussein, A.K. / Stokes, D.L. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published Title: Characterization of individual Zn2+ binding sites of YiiP Authors: Lopez-Redondo, M.L. / Hussein, A.K. / Stokes, D.L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8f6i.cif.gz | 234.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8f6i.ent.gz | 190.9 KB | Display | PDB format |
PDBx/mmJSON format | 8f6i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8f6i_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8f6i_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8f6i_validation.xml.gz | 53 KB | Display | |
Data in CIF | 8f6i_validation.cif.gz | 78.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/8f6i ftp://data.pdbj.org/pub/pdb/validation_reports/f6/8f6i | HTTPS FTP |
-Related structure data
Related structure data | 28884MC 8f6eC 8f6fC 8f6hC 8f6jC 8f6kC 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: 32441.203 Da / Num. of mol.: 2 / Mutation: D70A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella oneidensis MR-1 (bacteria) / Gene: fieF, SO_4475 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8E919 #2: Antibody | Mass: 23580.242 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #3: Antibody | Mass: 25406.352 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #4: Chemical | ChemComp-ZN / Has ligand of interest | Y | |
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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: D70A symmetrical Zinc-loaded YiiP-Fab complex / Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES | |||||||||||||||||||||||||
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Molecular weight | Value: 0.163024 MDa / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: Escherichia coli (E. coli) | |||||||||||||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Details: PELCO easiGLOW / Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3 | |||||||||||||||||||||||||
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 |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 700 nm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 2.5 sec. / Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3420 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
Image scans | Sampling size: 5 µm / Width: 5760 / Height: 4092 |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1702119 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.03 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 182413 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 126 / Protocol: BACKBONE TRACE / Space: REAL / Target criteria: cross-correlation | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 7KZZ | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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