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- PDB-7kq5: Cryo-EM structure of a thermostable encapsulin from T. maritima -

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Basic information

Entry
Database: PDB / ID: 7kq5
TitleCryo-EM structure of a thermostable encapsulin from T. maritima
ComponentsMaritimacin
KeywordsVIRUS LIKE PARTICLE / Encapsulin / HK97 fold / flavin-binding / icosahedral
Function / homology
Function and homology information


encapsulin nanocompartment / Hydrolases; Acting on peptide bonds (peptidases) / peptidase activity / iron ion transport / intracellular iron ion homeostasis / proteolysis
Similarity search - Function
Type 1 encapsulin shell protein / Encapsulating protein for peroxidase
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Type 1 encapsulin shell protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2 Å
AuthorsWiryaman, T.I. / Toor, N.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM123275 United States
National Institutes of Health/Office of the Director2T32GM007240 United States
National Institutes of Health/Office of the DirectorU24GM129547 United States
CitationJournal: IUCrJ / Year: 2021
Title: Cryo-EM structure of a thermostable bacterial nanocompartment.
Authors: Timothy Wiryaman / Navtej Toor /
Abstract: Protein nanocompartments are widespread in bacteria and archaea, but their functions are not yet well understood. Here, the cryo-EM structure of a nanocompartment from the thermophilic bacterium is ...Protein nanocompartments are widespread in bacteria and archaea, but their functions are not yet well understood. Here, the cryo-EM structure of a nanocompartment from the thermophilic bacterium is reported at 2.0 Å resolution. The high resolution of this structure shows that interactions in the E-loop domain may be important for the thermostability of the nanocompartment assembly. Also, the channels at the fivefold axis, threefold axis and dimer interface are assessed for their ability to transport iron. Finally, an unexpected flavin ligand was identified on the exterior of the shell, indicating that this nanocompartment may also play a direct role in iron metabolism.
History
DepositionNov 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1May 12, 2021Group: Data collection / Database references / Category: citation / em_imaging
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year / _em_imaging.nominal_defocus_max / _em_imaging.nominal_defocus_min
Revision 1.2May 19, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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Assembly

Deposited unit
A: Maritimacin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9732
Polymers30,5171
Non-polymers4561
Water2,666148
1
A: Maritimacin
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)1,858,388120
Polymers1,831,00760
Non-polymers27,38160
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Maritimacin
hetero molecules
x 5


  • icosahedral pentamer
  • 155 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)154,86610
Polymers152,5845
Non-polymers2,2825
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Maritimacin
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 186 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)185,83912
Polymers183,1016
Non-polymers2,7386
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Maritimacin / Thermotoga bacteriocin


Mass: 30516.787 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_0785 / Plasmid: pET-11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2
References: UniProt: Q9WZP2, Hydrolases; Acting on peptide bonds (peptidases)
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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

ComponentName: Encapsulin / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 1.82868 MDa / Experimental value: NO
Source (natural)Organism: Thermotoga maritima MSB8 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: Rosetta2(DE3) / Plasmid: pET-11a
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMtrisC4H11NO31
2150 mMsodium chlorideNaClSodium chloride1
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Plasma cleaned in Gatan Solarus system / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: PROPANE / Humidity: 90 % / Chamber temperature: 277 K
Details: 3 ul sample applied to the carbon side of the grid and blotted for 4s before plunging.

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 81000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.5 sec. / Electron dose: 33.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 2772
Image scansWidth: 11520 / Height: 8184

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM software
IDNameVersionCategoryDetails
1crYOLO1.5.4particle selectioncrYOLO was trained on 10 micrographs and the model was used to pick the rest of the micrographs
2SerialEMimage acquisition
4CTFFIND4.1.9CTF correctionCTFFIND was used in RELION
7PHENIX1.18.2model fittingPHENIX Dock in map was used to dock 3DKT chain A into density
9RELION3.1initial Euler assignmentRELION 3.1 Class3D was used to assign the initial angles
10RELION3.1final Euler assignmentRelion 3.1 Refine3D was used to for final refinement
12RELION3.13D reconstruction
13PHENIX1.18.2model refinementPHENIX Real-space refinement was used to refine model
CTF correctionType: NONE
Particle selectionNum. of particles selected: 204251 / Details: Picked with trained cryolo model
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 185459 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER
Details: Map was cropped to a 342 box size and density modified with PHENIX ResolveCryoEM
Atomic model buildingPDB-ID: 3DKT

3dkt


Pdb chain-ID: A / Accession code: 3DKT / Pdb chain residue range: 4-269 / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00513362
ELECTRON MICROSCOPYf_angle_d0.83318066
ELECTRON MICROSCOPYf_dihedral_angle_d6.5241740
ELECTRON MICROSCOPYf_chiral_restr0.0551980
ELECTRON MICROSCOPYf_plane_restr0.0032298

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