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

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Basic information

Entry
Database: PDB / ID: 9bix
TitleEncapsulin 2 of a two-component Family 2B encapsulin shell from Streptomyces lydicus
ComponentsCrp/Fnr family transcriptional regulator
KeywordsVIRUS LIKE PARTICLE / encapsulin / nanocompartment
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.59 Å
AuthorsAndreas, M.P. / Dutcher, C. / Giessen, T.W.
Funding support United States, 1items
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, M.P. / Giessen, T.W.
History
DepositionApr 24, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Crp/Fnr family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)52,1851
Polymers52,1851
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable, gel filtration, cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Crp/Fnr family transcriptional regulator


Mass: 52185.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lydicus (bacteria) / Gene: ADL29_33310 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0N0GVZ6
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1A two-component Family 2B encapsulin shell from Streptomyces lydicus with enriched encapsulin 2COMPLEXall0RECOMBINANT
2Encapsulin 1 of a two-component Family 2B encapsulin shell from Streptomyces lydicusCOMPLEX1RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Streptomyces lydicus (bacteria)47763
32Streptomyces lydicus (bacteria)47763
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Escherichia coli BL21(DE3) (bacteria)469008
32Escherichia coli BL21(DE3) (bacteria)469008
Buffer solutionpH: 7.5 / Details: 150 mM NaCl, 20 mM Tris pH 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTrisC4H11NO31
2150 mMsodium chlorideNaCl1
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: The grid was glow discharged for 60 seconds at 5 mA.
Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K
Details: Blot force: 20 Blot time: 4 seconds Wait time: 0 seconds

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1000 nm / Nominal defocus min: 500 nm
Image recordingAverage exposure time: 3 sec. / Electron dose: 54 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5607
Image scansWidth: 5760 / Height: 4092 / Movie frames/image: 25

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARCv3.1.0particle selectionTemplate Picker
2Leginonimage acquisition
4cryoSPARCv3.1.0CTF correctionPatch CTF Estimation
7UCSF ChimeraXv 1.2.5model fitting
9cryoSPARCv3.1.0initial Euler assignment
10cryoSPARCv3.1.0final Euler assignment
12cryoSPARCv3.1.03D reconstructionHomogeneous Refinement
13Coot0.8.9.1model refinement
14PHENIX1.20.1-4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 288651
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.59 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 155190
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.
Symmetry type: POINT
Atomic model buildingB value: 114.4 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: correlation coefficient
Details: The 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.
Atomic model buildingPDB-ID: 9BHU

9bhu


Accession code: 9BHU / Source name: PDB / Type: experimental model

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