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- EMDB-54372: Single particle reconstruction of Rhodospirillum rubrum encapsulin -

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Basic information

Entry
Database: EMDB / ID: EMD-54372
TitleSingle particle reconstruction of Rhodospirillum rubrum encapsulin
Map dataCryosparc map
Sample
  • Complex: Rhodospirillum rubrum encapsulin
    • Protein or peptide: Type 1 encapsulin shell protein
KeywordsEncapsulin / nanocompartment / encapsulated ferritin / STRUCTURAL PROTEIN
Function / homologyType 1 encapsulin shell protein / Encapsulating protein for peroxidase / : / encapsulin nanocompartment / iron ion transport / Type 1 encapsulin shell protein
Function and homology information
Biological speciesRhodospirillum rubrum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.0 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
Authors: McIver Z / McCorvie TJ / Basle A / Marles-Wright J
History
DepositionJul 14, 2025-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54372.png

Downloads & links

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Map

FileDownload / File: emd_54372.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryosparc map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 425.472 Å		0.83 Å/pix.
x 512 pix.
= 425.472 Å		0.83 Å/pix.
x 512 pix.
= 425.472 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.831 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.019355064 - 0.14040527
Average (Standard dev.)0.0010370236 (±0.007586906)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 425.472 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54372_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_54372_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

Fileemd_54372_half_map_1.map
AnnotationHalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map

Fileemd_54372_half_map_2.map
AnnotationHalf map
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 encapsulin

EntireName: Rhodospirillum rubrum encapsulin
Components
  • Complex: Rhodospirillum rubrum encapsulin
    • Protein or peptide: Type 1 encapsulin shell protein

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Supramolecule #1: Rhodospirillum rubrum encapsulin

SupramoleculeName: Rhodospirillum rubrum encapsulin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rhodospirillum rubrum (bacteria)
Molecular weightTheoretical: 1.8 MDa

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Macromolecule #1: Type 1 encapsulin shell protein

MacromoleculeName: Type 1 encapsulin shell protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodospirillum rubrum (bacteria)
Molecular weightTheoretical: 29.765936 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MNDLMRDLAP ISAKAWAEIE TEARGTLTVT LAARKVVDFK GPLGWDASSV SLGRTEALAE EPKAAGSAAV VTVRKRAVQP LIELCVPFT LKRAELEAIA RGASDADLDP VIEAARAIAI AEDRAVFHGF AAGGITGIGE ASAEHALDLP ADLADFPGVL V RALAVLRD ...String:
MNDLMRDLAP ISAKAWAEIE TEARGTLTVT LAARKVVDFK GPLGWDASSV SLGRTEALAE EPKAAGSAAV VTVRKRAVQP LIELCVPFT LKRAELEAIA RGASDADLDP VIEAARAIAI AEDRAVFHGF AAGGITGIGE ASAEHALDLP ADLADFPGVL V RALAVLRD RGVDGPYALV LGRTVYQQLM ETTTPGGYPV LQHVRRLFEG PLIWAPGVDG AMLISQRGGD FELTVGRDFS IG YHDHDAQ SVHLYLQESM TFRCLGPEAA VPLRGLSQAA TKA

UniProtKB: Type 1 encapsulin shell protein

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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: Sample in 50 mM Tris.HCl pH8, 150 mM NaCl
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: blot force 5, wait time 10 s, and blot time 3 seconds.
DetailsSample purified by Size-exclusion on Sephacryl S400

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3438531 / Details: Blob picker
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Ab initio model / Details: C1 startup model
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7) / Number images used: 639134
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7)
Final 3D classificationNumber classes: 9 / Avg.num./class: 71000 / Software - Name: cryoSPARC (ver. 4.7)
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: ModelAngelo model from sequence
DetailsReal space refinement in phenix
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 70 / Target criteria: Cross correlation
Output model

PDB-9ry4:
Single particle reconstruction of Rhodospirillum rubrum encapsulin

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