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- EMDB-54408: Focused refinement of closed encapsulin pentamer from symmetry ex... -

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Basic information

Entry
Database: EMDB / ID: EMD-54408
TitleFocused refinement of closed encapsulin pentamer from symmetry expansion of icosahedral single particle reconstruction of the Rhodospirillum rubrum encapsulin:encapsulated ferritin complex
Map dataExperimental map
Sample
  • Complex: Complex of Rhodospirillum rubrum encapsulin and encapsulated ferritin
    • Complex: Rhodospirillum rubrum encapsulin
    • Complex: Rhodospirillum rubrum encapsulated ferritin
    • Protein or peptide: Type 1 encapsulin shell protein
    • Protein or peptide: Encapsulated ferritin-like protein
KeywordsEncapsulin / nanocompartment / encapsulated ferritin / STRUCTURAL PROTEIN
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 / Type 1 encapsulin shell protein / Encapsulating protein for peroxidase / : / Ferritin-like superfamily
Similarity search - Domain/homology
Type 1 encapsulin shell protein / Encapsulated ferritin-like protein
Similarity search - Component
Biological speciesRhodospirillum rubrum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.63 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: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionJul 16, 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_54408.png

Downloads & links

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Map

FileDownload / File: emd_54408.map.gz / Format: CCP4 / Size: 729 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.)
0.75 Å/pix.
x 576 pix.
= 432.576 Å		0.75 Å/pix.
x 576 pix.
= 432.576 Å		0.75 Å/pix.
x 576 pix.
= 432.576 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.751 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.041942067 - 0.13693437
Average (Standard dev.)0.000040713443 (±0.00408027)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions576576576
Spacing576576576
CellA=B=C: 432.576 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54408_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_54408_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_54408_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_54408_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 : Complex of Rhodospirillum rubrum encapsulin and encapsulated ferritin

EntireName: Complex of Rhodospirillum rubrum encapsulin and encapsulated ferritin
Components
  • Complex: Complex of Rhodospirillum rubrum encapsulin and encapsulated ferritin
    • Complex: Rhodospirillum rubrum encapsulin
    • Complex: Rhodospirillum rubrum encapsulated ferritin
    • Protein or peptide: Type 1 encapsulin shell protein
    • Protein or peptide: Encapsulated ferritin-like protein

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Supramolecule #1: Complex of Rhodospirillum rubrum encapsulin and encapsulated ferritin

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

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Supramolecule #2: Rhodospirillum rubrum encapsulin

SupramoleculeName: Rhodospirillum rubrum encapsulin / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Rhodospirillum rubrum (bacteria)

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Supramolecule #3: Rhodospirillum rubrum encapsulated ferritin

SupramoleculeName: Rhodospirillum rubrum encapsulated ferritin / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Rhodospirillum rubrum (bacteria)

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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: 5 / 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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Macromolecule #2: Encapsulated ferritin-like protein

MacromoleculeName: Encapsulated ferritin-like protein / type: protein_or_peptide / ID: 2 / Number of copies: 5 / 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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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: 7200000
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
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.63 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7) / Number images used: 1701084
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 10 / Avg.num./class: 720000 / Software - Name: cryoSPARC / Details: 3D classes selected with well resolved density
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: 99.4 / Target criteria: Cross-correlation coefficient
Output model

PDB-9rzu:
Focused refinement of closed encapsulin pentamer from symmetry expansion of icosahedral single particle reconstruction of the Rhodospirillum rubrum encapsulin:encapsulated ferritin complex

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