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- EMDB-29028: CryoEM structure of Conalbumin from chicken egg white (sigma-Cas ... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-29028
TitleCryoEM structure of Conalbumin from chicken egg white (sigma-Cas 1391-06-6)
Map dataFinal map
Sample
  • Organelle or cellular component: Conalbumin from chicken egg white
    • Protein or peptide: Ovotransferrin
  • Ligand: FE (III) ION
Keywordsconalbumin / egg white / ovotransferrin / iron complex / METAL TRANSPORT
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsNewton TP / Zimanyi C / Kopylov M
Funding support United States, 1 items
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 TP / Zimanyi C / Kopylov M
History
DepositionDec 6, 2022-
Header (metadata) releaseFeb 8, 2023-
Map releaseFeb 8, 2023-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29028.png

Downloads & links

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Map

FileDownload / File: emd_29028.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.67 Å/pix.
x 320 pix.
= 215.68 Å		0.67 Å/pix.
x 320 pix.
= 215.68 Å		0.67 Å/pix.
x 320 pix.
= 215.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.674 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.278
Minimum - Maximum-0.3551497 - 0.85305256
Average (Standard dev.)-0.00058632094 (±0.026010169)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 215.68001 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_29028_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Final half map A

Fileemd_29028_half_map_1.map
AnnotationFinal half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Final half map B

Fileemd_29028_half_map_2.map
AnnotationFinal half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Conalbumin from chicken egg white

EntireName: Conalbumin from chicken egg white
Components
  • Organelle or cellular component: Conalbumin from chicken egg white
    • Protein or peptide: Ovotransferrin
  • Ligand: FE (III) ION

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Supramolecule #1: Conalbumin from chicken egg white

SupramoleculeName: Conalbumin from chicken egg white / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Gallus gallus (chicken)

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Macromolecule #1: Ovotransferrin

MacromoleculeName: Ovotransferrin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Gallus gallus (chicken)
Molecular weightTheoretical: 77.878531 KDa
SequenceString: MKLILCTVLS LGIAAVCFAA PPKSVIRWCT ISSPEEKKCN NLRDLTQQER ISLTCVQKAT YLDCIKAIAN NEADAISLDG GQAFEAGLA PYKLKPIAAE VYEHTEGSTT SYYAVAVVKK GTEFTVNDLQ GKTSCHTGLG RSAGWNIPIG TLLHRGAIEW E GIESGSVE ...String:
MKLILCTVLS LGIAAVCFAA PPKSVIRWCT ISSPEEKKCN NLRDLTQQER ISLTCVQKAT YLDCIKAIAN NEADAISLDG GQAFEAGLA PYKLKPIAAE VYEHTEGSTT SYYAVAVVKK GTEFTVNDLQ GKTSCHTGLG RSAGWNIPIG TLLHRGAIEW E GIESGSVE QAVAKFFSAS CVPGATIEQK LCRQCKGDPK TKCARNAPYS GYSGAFHCLK DGKGDVAFVK HTTVNENAPD QK DEYELLC LDGSRQPVDN YKTCNWARVA AHAVVARDDN KVEDIWSFLS KAQSDFGVDT KSDFHLFGPP GKKDPVLKDL LFK DSAIML KRVPSLMDSQ LYLGFEYYSA IQSMRKDQLT PSPRENRIQW CAVGKDEKSK CDRWSVVSNG DVECTVVDET KDCI IKIMK GEADAVALDG GLVYTAGVCG LVPVMAERYD DESQCSKTDE RPASYFAVAV ARKDSNVNWN NLKGKKSCHT AVGRT AGWV IPMGLIHNRT GTCNFDEYFS EGCAPGSPPN SRLCQLCQGS GGIPPEKCVA SSHEKYFGYT GALRCLVEKG DVAFIQ HST VEENTGGKNK ADWAKNLQMD DFELLCTDGR RANVMDYREC NLAEVPTHAV VVRPEKANKI RDLLERQEKR FGVNGSE KS KFMMFESQNK DLLFKDLTKC LFKVREGTTY KEFLGDKFYT VISSLKTCNP SDILQMCSFL EGK

UniProtKB: Ovotransferrin

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Macromolecule #2: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5 / Details: PBS
GridModel: UltrAuFoil / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 58.53 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.001 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 495204
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 82144
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 50
FSC plot (resolution estimation)

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