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- EMDB-26996: Cryo-EM structure of Ferritin 2 from Caenorhabditis elegans, FTN-2 -

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Basic information

Entry
Database: EMDB / ID: EMD-26996
TitleCryo-EM structure of Ferritin 2 from Caenorhabditis elegans, FTN-2
Map dataFerritin 2 from Caenorhabditis elegans, FTN-2
Sample
  • Complex: Homo 24-mer of Ferritin 2
    • Protein or peptide: Ferritin
  • Ligand: FE (III) ION
  • Ligand: water
KeywordsOxidoreductase / ferroxidase
Function / homology
Function and homology information


Iron uptake and transport / Neutrophil degranulation / ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / ferrous iron binding / intracellular iron ion homeostasis / defense response to Gram-positive bacterium / identical protein binding / cytoplasm
Similarity search - Function
Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
Biological speciesCaenorhabditis elegans (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.91 Å
AuthorsMalcolm TR / Brown HG / Hanssen E
Funding support Australia, 1 items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: To Be Published
Title: Biochemical Characterization of Caenorhabditis elegans Ferritins
Authors: Mubarak SMM / Malcolm TR / Brown HG / Hanssen E / Maher MJ / McColl G / Jameson GNL
History
DepositionMay 16, 2022-
Header (metadata) releaseMay 24, 2023-
Map releaseMay 24, 2023-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26996.png

Downloads & links

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Map

FileDownload / File: emd_26996.map.gz / Format: CCP4 / Size: 134.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFerritin 2 from Caenorhabditis elegans, FTN-2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 328 pix.
= 268.96 Å		0.82 Å/pix.
x 328 pix.
= 268.96 Å		0.82 Å/pix.
x 328 pix.
= 268.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.16086045 - 0.56562036
Average (Standard dev.)-0.00029617202 (±0.026290549)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions328328328
Spacing328328328
CellA=B=C: 268.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Ferritin 2 from Caenorhabditis elegans, FTN-2

Fileemd_26996_half_map_1.map
AnnotationFerritin 2 from Caenorhabditis elegans, FTN-2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Ferritin 2 from Caenorhabditis elegans, FTN-2

Fileemd_26996_half_map_2.map
AnnotationFerritin 2 from Caenorhabditis elegans, FTN-2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Homo 24-mer of Ferritin 2

EntireName: Homo 24-mer of Ferritin 2
Components
  • Complex: Homo 24-mer of Ferritin 2
    • Protein or peptide: Ferritin
  • Ligand: FE (III) ION
  • Ligand: water

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Supramolecule #1: Homo 24-mer of Ferritin 2

SupramoleculeName: Homo 24-mer of Ferritin 2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Caenorhabditis elegans (invertebrata)

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Macromolecule #1: Ferritin

MacromoleculeName: Ferritin / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO / EC number: ferroxidase
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 19.371547 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SLARQNYHSE VEAAVNKQIN IELYASYVYL SMSFYFDRDD VALPNIAKFF KEQSDEEREH ATELMRVQNL RGGRVVLQDI QKPENDEWG TALKAFEAAL ALEKFNNESL LKLHSTAGNH NDAHLTDFIE EKYLDEQVKS INEFARMVAN LKRVGPGVGE Y VFDKEHFS

UniProtKB: Ferritin

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Macromolecule #2: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 2 / Number of copies: 24 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 2271 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 8
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 47.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7urh

Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.91 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 398769
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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