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- EMDB-54434: Focused refinement of Rhodospirillum rubrum encapsulated ferritin... -

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Basic information

Entry
Database: EMDB / ID: EMD-54434
TitleFocused refinement of Rhodospirillum rubrum encapsulated ferritin within the encapsulin nanocompartment
Map dataExperimental map
Sample
  • Complex: Rhodospirillum rubrum encapsulated ferritin
    • Complex: Rhodospirillum rubrum encapsulated ferritin
      • Protein or peptide: Encapsulated ferritin-like protein
  • Ligand: FE (III) ION
KeywordsEncapsulin / nanocompartment / encapsulated ferritin / STRUCTURAL PROTEIN / OXIDOREDUCTASE
Function / homology
Function and homology information


encapsulin nanocompartment / ferroxidase / ferroxidase activity / iron ion transport / metal ion binding
Similarity search - Function
Ferritin-like protein / : / EncFtn-like / Ferritin-like superfamily
Similarity search - Domain/homology
Encapsulated ferritin-like protein
Similarity search - Component
Biological speciesRhodospirillum rubrum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsMcIver Z / McCorvie TJ / Basle A / Marles-Wright J
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)2306768 United Kingdom
CitationJournal: To Be Published
Title: Single particle reconstruction of Rhodospirillum rubrum encapsulin:encapsulated ferritin complex
Authors: McIver Z / McCorvie TJ / Basle A / Marles-Wright J
History
DepositionJul 17, 2025-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54434.png

Downloads & links

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Map

FileDownload / File: emd_54434.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationExperimental map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.13 Å/pix.
x 384 pix.
= 432.576 Å		1.13 Å/pix.
x 384 pix.
= 432.576 Å		1.13 Å/pix.
x 384 pix.
= 432.576 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1265 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.1127357 - 2.11997
Average (Standard dev.)-0.0005701054 (±0.03465276)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 432.576 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54434_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: B-factor sharpened map

Fileemd_54434_additional_1.map
AnnotationB-factor sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_54434_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_54434_half_map_2.map
AnnotationHalf 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 : Rhodospirillum rubrum encapsulated ferritin

EntireName: Rhodospirillum rubrum encapsulated ferritin
Components
  • Complex: Rhodospirillum rubrum encapsulated ferritin
    • Complex: Rhodospirillum rubrum encapsulated ferritin
      • Protein or peptide: Encapsulated ferritin-like protein
  • Ligand: FE (III) ION

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Supramolecule #1: Rhodospirillum rubrum encapsulated ferritin

SupramoleculeName: Rhodospirillum rubrum encapsulated ferritin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Rhodospirillum rubrum (bacteria)
Molecular weightTheoretical: 150 KDa

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Supramolecule #2: Rhodospirillum rubrum encapsulated ferritin

SupramoleculeName: Rhodospirillum rubrum encapsulated ferritin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Rhodospirillum rubrum (bacteria)

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Macromolecule #1: Encapsulated ferritin-like protein

MacromoleculeName: Encapsulated ferritin-like protein / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO / EC number: ferroxidase
Source (natural)Organism: Rhodospirillum rubrum (bacteria)
Molecular weightTheoretical: 15.21172 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MAQSSNSTHE PLEVLKEETV NRHRAIVSVM EELEAVDWYD QRVDASTDPE LTAILAHNRD EEKEHAAMTL EWLRRNDAKW AEHLRTYLF TEGPITAIEA ADTAGEGSGG DAAKGATAQG DGSLGIGSLK GEAALARPPR L

UniProtKB: Encapsulated ferritin-like protein

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Macromolecule #2: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 2 / Number of copies: 10 / 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

Concentration3 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chloride
50.0 mMC4H11NO3Tris

Details: 150 mM NaCl, 50 mM Tris-HCl, pH 8.0
GridModel: Quantifoil / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV
Details: 4 uL of sample was applied to the grids, which were then blotted 100% humidity blot force 5 wait time 10 s blot time 3 seconds.
DetailsComplex of Rhodospirillum rubrum encapsulin and encapsulated ferritin

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Electron microscopy

MicroscopeTFS GLACIOS
TemperatureMin: 80.0 K
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 2 / Number real images: 7994 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 346315
Details: Particles from icosahedral reconstruction of Encapsulin:Encapsulated Ferritin complex
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
In silico model: C1 ab initio model from cryoSPARC with focus mask on Encapsulated ferritin cargo proteins
Details: 10 classes for ab initio with circular mask to remove encapsulin density.
Final reconstructionNumber classes used: 14 / Applied symmetry - Point group: D5 (2x5 fold dihedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7)
Details: Final reconstruction performed by local refinement of aligned encapsulated ferritin decamers from custom symmetry expansion.
Number images used: 272846
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 6 / Avg.num./class: 35000 / Software - Name: cryoSPARC
Details: 3D classes showing clear encapsulated ferritin complexes chosen for further analysis
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: model produced in ModelAngelo
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 146.6 / Target criteria: Cross-correlation coefficient
Output model

PDB-9s13:
Focused refinement of Rhodospirillum rubrum encapsulated ferritin within the encapsulin nanocompartment

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