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- EMDB-44632: Encapsulin 1 of a two-component Family 2B encapsulin shell from S... -

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Basic information

Entry
Database: EMDB / ID: EMD-44632
TitleEncapsulin 1 of a two-component Family 2B encapsulin shell from Streptomyces lydicus
Map dataEncapsulin 1 of a two-component Family 2B encapsulin shell from Streptomyces lydicus
Sample
  • Complex: A two-component Family 2B encapsulin shell from Streptomyces lydicus with Encapsulin 1 enriched
    • Complex: Encapsulin 2 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: 2.58 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: To Be Published
Title: A two-component quasi-icosahedral protein nanocompartment with variable shell composition and irregular tiling
Authors: Dutcher C / Andreas MP / Giessen TW
History
DepositionApr 25, 2024-
Header (metadata) releaseApr 30, 2025-
Map releaseApr 30, 2025-
UpdateApr 30, 2025-
Current statusApr 30, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44632.png

Downloads & links

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Map

FileDownload / File: emd_44632.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEncapsulin 1 of a two-component Family 2B encapsulin shell from Streptomyces lydicus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
0.91 Å/pix.
x 440 pix.
= 400.4 Å		0.91 Å/pix.
x 440 pix.
= 400.4 Å		0.91 Å/pix.
x 440 pix.
= 400.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.91 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.90908194 - 1.5705898
Average (Standard dev.)0.0016787363 (±0.07034674)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 400.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_44632_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_44632_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 Encapsulin 1 enriched
Components
  • Complex: A two-component Family 2B encapsulin shell from Streptomyces lydicus with Encapsulin 1 enriched
    • Complex: Encapsulin 2 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 Encapsulin 1 enriched
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Streptomyces lydicus (bacteria)

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

SupramoleculeName: Encapsulin 2 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: 52.256594 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MHHHHHHTIV DETLNGNPED TAHSSLSTAA ARNLATTTKT VPQMQGITSR WLLRLLPWVQ VSGGTYRVNR RLSHTVGDGR IDFDISGSD VAIIPEELRE LPALRDFTDT EVLAALGERF TQREYAPGEL IAEAGRPGDR LVLIAHGRVD RIGTGKYGDT T VLAALAGG ...String:
MHHHHHHTIV DETLNGNPED TAHSSLSTAA ARNLATTTKT VPQMQGITSR WLLRLLPWVQ VSGGTYRVNR RLSHTVGDGR IDFDISGSD VAIIPEELRE LPALRDFTDT EVLAALGERF TQREYAPGEL IAEAGRPGDR LVLIAHGRVD RIGTGKYGDT T VLAALAGG DHLGDAPLTS DEVTWEFSYR AVTRVTVVEL PRRAALEIIE RSPGLREHLA GVRQGPVHPT NSSGESAVAV AS GHRGEPS LPGAFADYDL APREYELSVA QTVLRTHTRV GDLYNDPMNQ VEEQLKLTVQ ALRERQEHEM INNREFGLLH NAD LKQRIP TRSGPPTPDD LDDLLATVWK DPGFLLAHPR AIAAMAREWS ARGLYPTAVD FHGHSLPSWR GVPIFPCNKI PVTK ERTSS ILLLRTGEEK QGVVGLHQTG IPDEYEPSLS VRFMGIDDRA VINYLVSAYY SAAVLVPDAL GVLEDVEVGL

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: Grids were glow discharged for 60 seconds at 5 mA under vacuum.
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 TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Number grids imaged: 1 / Number real images: 1658 / Average exposure time: 5.0 sec. / Average electron dose: 45.5 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 45000
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 77425
Startup modelType of model: INSILICO MODEL / In silico model: Ab-initio
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.58 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v3.2.0+210511)
Details: Homogeneous refinement was performed against the ab-initio map with I symmetry, per-particle defocus optimization, per-group CTF parameterization, and Ewald sphere correction with negative curvature.
Number images used: 69590
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v3.2.0+210511)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v3.2.0+210511)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

9bix


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsThe starting encapsulin model was first placed into the map using Chimera. It was then refined against the map by alternating rounds of manual refinement in Coot and real-space refinement in PHENIX.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 99.9 / Target criteria: correlation coefficient
Output model

PDB-9bje:
Encapsulin 1 of a two-component Family 2B encapsulin shell from Streptomyces lydicus

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