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- PDB-8fei: CryoEM structure of Conalbumin from chicken egg white (sigma-Cas ... -

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Basic information

Entry
Database: PDB / ID: 8fei
TitleCryoEM structure of Conalbumin from chicken egg white (sigma-Cas 1391-06-6)
ComponentsOvotransferrin
KeywordsMETAL TRANSPORT / conalbumin / egg white / ovotransferrin / iron complex
Function / homology
Function and homology information


organomineral extracellular matrix / iron ion transmembrane transport / antimicrobial humoral response / ferric iron binding / acute-phase response / iron ion transport / recycling endosome / antibacterial humoral response / response to lipopolysaccharide / intracellular iron ion homeostasis ...organomineral extracellular matrix / iron ion transmembrane transport / antimicrobial humoral response / ferric iron binding / acute-phase response / iron ion transport / recycling endosome / antibacterial humoral response / response to lipopolysaccharide / intracellular iron ion homeostasis / early endosome / iron ion binding / response to xenobiotic stimulus / extracellular space / plasma membrane
Similarity search - Function
Transferrin-like domain signature 2. / Transferrin family, iron binding site / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin / Transferrin-like domain / Transferrin / Transferrin-like domain profile. / Transferrin
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsNewton, T.P. / Zimanyi, C. / Kopylov, M.
Funding support United States, 1items
OrganizationGrant numberCountry
Simons FoundationSF349247 United States
CitationJournal: 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
DepositionDec 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ovotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9903
Polymers77,8791
Non-polymers1122
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Ovotransferrin / Allergen Gal d III / Conalbumin / Serum transferrin


Mass: 77878.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P02789
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Conalbumin from chicken egg white / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Gallus gallus (chicken)
Buffer solutionpH: 7.5 / Details: PBS
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 0.001 mm / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 58.53 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: cryoSPARC / Version: 4.0.1 / Category: particle selection
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 495204
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 82144 / Algorithm: FOURIER SPACE / Symmetry type: POINT

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