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Yorodumi- PDB-8fei: CryoEM structure of Conalbumin from chicken egg white (sigma-Cas ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8fei | ||||||
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Title | CryoEM structure of Conalbumin from chicken egg white (sigma-Cas 1391-06-6) | ||||||
Components | Ovotransferrin | ||||||
Keywords | METAL TRANSPORT / conalbumin / egg white / ovotransferrin / iron complex | ||||||
Function / homology | Function and homology information extracellular sequestering of iron ion / organomineral extracellular matrix / antimicrobial humoral response / intracellular sequestering of iron ion / ferric iron binding / acute-phase response / recycling endosome / iron ion transport / antibacterial humoral response / response to lipopolysaccharide ...extracellular sequestering of iron ion / organomineral extracellular matrix / antimicrobial humoral response / intracellular sequestering of iron ion / ferric iron binding / acute-phase response / recycling endosome / iron ion transport / antibacterial humoral response / response to lipopolysaccharide / early endosome / response to xenobiotic stimulus / iron ion binding / extracellular space / plasma membrane Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||
Authors | Newton, T.P. / Zimanyi, C. / Kopylov, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: CryoEM structure of Conalbumin from chicken egg white (sigma-Cas 1391-06-6) Authors: Newton, T.P. / Zimanyi, C. / Kopylov, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fei.cif.gz | 124.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fei.ent.gz | 97.4 KB | Display | PDB format |
PDBx/mmJSON format | 8fei.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fei_validation.pdf.gz | 995.8 KB | Display | wwPDB validaton report |
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Full document | 8fei_full_validation.pdf.gz | 999.9 KB | Display | |
Data in XML | 8fei_validation.xml.gz | 37.5 KB | Display | |
Data in CIF | 8fei_validation.cif.gz | 53.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fe/8fei ftp://data.pdbj.org/pub/pdb/validation_reports/fe/8fei | HTTPS FTP |
-Related structure data
Related structure data | 29028MC 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: 77878.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P02789 | ||
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#2: Chemical | 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: Conalbumin from chicken egg white / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Gallus gallus (chicken) |
Buffer solution | pH: 7.5 / Details: PBS |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil |
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: 2000 nm / Nominal defocus min: 1000 nm / Cs: 0.001 mm / C2 aperture diameter: 100 µm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 58.53 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software | Name: cryoSPARC / Version: 4.0.1 / Category: particle selection |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
Particle selection | Num. of particles selected: 495204 |
Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 82144 / Algorithm: FOURIER SPACE / Symmetry type: POINT |