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- EMDB-44603: Encapsulin 2 of a two-component Family 2B encapsulin shell from S... -

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Basic information

Entry
Database: EMDB / ID: EMD-44603
TitleEncapsulin 2 of a two-component Family 2B encapsulin shell from Streptomyces lydicus
Map dataEncapsulin 2 of a two-component Family 2B encapsulin shell from Streptomyces lydicus
Sample
  • Complex: A two-component Family 2B encapsulin shell from Streptomyces lydicus with enriched encapsulin 2
    • Complex: Encapsulin 1 of a two-component Family 2B encapsulin shell from Streptomyces lydicus
    • Protein or peptide: Crp/Fnr family transcriptional regulator
Keywordsencapsulin / nanocompartment / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


DNA-binding transcription factor activity / cytosol
Similarity search - Function
: / Type 2A encapsulin shell protein SrpI-like / Type 2A encapsulin shell protein SrpI-like / : / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold
Similarity search - Domain/homology
Crp/Fnr family transcriptional regulator
Similarity search - Component
Biological speciesStreptomyces lydicus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.59 Å
AuthorsAndreas MP / Dutcher C / Giessen TW
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM133325 United States
CitationJournal: Adv Sci (Weinh) / Year: 2025
Title: A Two-Component Pseudo-Icosahedral Protein Nanocompartment with Variable Shell Composition and Irregular Tiling.
Authors: Cassandra A Dutcher / Michael P Andreas / Tobias W Giessen /
Abstract: Protein shells or capsids are a widespread form of compartmentalization in nature. Viruses use protein capsids to protect and transport their genomes while many cellular organisms use protein shells ...Protein shells or capsids are a widespread form of compartmentalization in nature. Viruses use protein capsids to protect and transport their genomes while many cellular organisms use protein shells for varied metabolic purposes. These protein-based compartments often exhibit icosahedral symmetry and consist of a small number of structural components with defined roles. Encapsulins are a prevalent protein-based compartmentalization strategy in prokaryotes. All encapsulins studied thus far consist of a single shell protein that adopts the viral Hong Kong 97 (HK97)-fold. Here, the characterization of a Family 2B two-component encapsulin from Streptomyces lydicus is reported. The differential assembly behavior of the two shell components and their ability to co-assemble into mixed shells with variable shell composition is demonstrated. The structures of both shell proteins are determined using cryo-electron microscopy. Using 3D-classification and cross-linking studies, the irregular tiling of mixed shells is highlighted. This work expands the known assembly modes of HK97-fold proteins and lays the foundation for future functional and engineering studies on two-component encapsulins.
History
DepositionApr 24, 2024-
Header (metadata) releaseApr 30, 2025-
Map releaseApr 30, 2025-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44603.png

Downloads & links

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Map

FileDownload / File: emd_44603.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEncapsulin 2 of a two-component Family 2B encapsulin shell from Streptomyces lydicus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 480 pix.
= 403.2 Å		0.84 Å/pix.
x 480 pix.
= 403.2 Å		0.84 Å/pix.
x 480 pix.
= 403.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.42
Minimum - Maximum-1.091387 - 2.370538
Average (Standard dev.)0.01885824 (±0.11646068)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 403.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_44603_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_44603_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 : A two-component Family 2B encapsulin shell from Streptomyces lydi...

EntireName: A two-component Family 2B encapsulin shell from Streptomyces lydicus with enriched encapsulin 2
Components
  • Complex: A two-component Family 2B encapsulin shell from Streptomyces lydicus with enriched encapsulin 2
    • Complex: Encapsulin 1 of a two-component Family 2B encapsulin shell from Streptomyces lydicus
    • Protein or peptide: Crp/Fnr family transcriptional regulator

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Supramolecule #1: A two-component Family 2B encapsulin shell from Streptomyces lydi...

SupramoleculeName: A two-component Family 2B encapsulin shell from Streptomyces lydicus with enriched encapsulin 2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Streptomyces lydicus (bacteria)

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Supramolecule #2: Encapsulin 1 of a two-component Family 2B encapsulin shell from S...

SupramoleculeName: Encapsulin 1 of a two-component Family 2B encapsulin shell from Streptomyces lydicus
type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Streptomyces lydicus (bacteria)

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Macromolecule #1: Crp/Fnr family transcriptional regulator

MacromoleculeName: Crp/Fnr family transcriptional regulator / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Streptomyces lydicus (bacteria)
Molecular weightTheoretical: 52.18548 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MHHHHHHTTS VDPTSGPQAS GTEQNRSSLD TAAARKLATT TKTVPQMQGI SSRWLLRVLP WTQVNGGTYR VNRRLTHTLG DGQVEFVNT GAEVRVIPEE LRELAPLRGF TDTPTLEALA GRFAQHEFAP GDVLAQQDQP ADRIILIAHG KLDRLGTGKY G GETVQGQL ...String:
MHHHHHHTTS VDPTSGPQAS GTEQNRSSLD TAAARKLATT TKTVPQMQGI SSRWLLRVLP WTQVNGGTYR VNRRLTHTLG DGQVEFVNT GAEVRVIPEE LRELAPLRGF TDTPTLEALA GRFAQHEFAP GDVLAQQDQP ADRIILIAHG KLDRLGTGKY G GETVQGQL AGGDHLGAAA LLDGGAAWEH TVRAVTRVTA LTLSRGDYEQ VLGGSESLRA HVEAFRAALV PAQNKHGEAA IE VAAGHVG EPSLPGTFAD YDLAPREYEL SVAQTVLKIH SRVADLYNDP MNQMDQQLRL TVEALRERQE HEMINNREFG LLH NADLKQ RIHTRSGPPT PDDLDELISR RRKTQVLLAH PRTIAAIGRE WNARGIYPTG AELHGTDVRA WRGIPLLPCN KIPV TPEQT SSIIAMRLGE ENQGVVGLHQ TGIPDEYQPG LSVRFMGIND QAVIQYLVSA YYSAAVLVPD ALGILEDVEI GH

UniProtKB: Crp/Fnr family transcriptional regulator

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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

Concentration2 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3Tris
150.0 mMNaClsodium chloride

Details: 150 mM NaCl, 20 mM Tris pH 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
Details: The grid was glow discharged for 60 seconds at 5 mA.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV
Details: Blot force: 20 Blot time: 4 seconds Wait time: 0 seconds.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 5607 / Average exposure time: 3.0 sec. / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 288651
CTF correctionSoftware - Name: cryoSPARC (ver. v3.1.0) / Software - details: Patch CTF Estimation / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Ab-initio
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.59 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v3.1.0) / Software - details: Homogeneous Refinement
Details: The map was generated by homogeneous refinement against the initial ab-initio map using I symmetry, per-particle defocus optimization, and per-group CTF parameter optimization.
Number images used: 155190
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v3.1.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v3.1.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

9bhu


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsThe starting encapsulin model was first placed into the map using ChimeraX. It was then refined against the map by alternating rounds of manual refinements in Coot and real-space refinement in PHENIX.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 114.4 / Target criteria: correlation coefficient
Output model

PDB-9bix:
Encapsulin 2 of a two-component Family 2B encapsulin shell from Streptomyces lydicus

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