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- PDB-7k5w: Cryo-EM structure of heterologous protein complex loaded Thermoto... -

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Basic information

Entry
Database: PDB / ID: 7k5w
TitleCryo-EM structure of heterologous protein complex loaded Thermotoga maritima encapsulin capsid
ComponentsMaritimacin
KeywordsHYDROLASE / encapsulin / baculovirus expression system / cargo loading peptide / complex assembly / METAL BINDING PROTEIN
Function / homologyType 1 encapsulin shell protein / Encapsulating protein for peroxidase / encapsulin nanocompartment / Hydrolases; Acting on peptide bonds (peptidases) / peptidase activity / iron ion transport / intracellular iron ion homeostasis / proteolysis / Type 1 encapsulin shell protein
Function and homology information
Biological speciesThermotoga maritima (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsXiong, X. / Sun, C. / Vago, F.S. / Klose, T. / Zhu, J. / Jiang, W.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB27040101 China
CitationJournal: Biomolecules / Year: 2020
Title: Cryo-EM Structure of Heterologous Protein Complex Loaded Encapsulin Capsid.
Authors: Xiansong Xiong / Chen Sun / Frank S Vago / Thomas Klose / Jiankang Zhu / Wen Jiang /
Abstract: Encapsulin is a class of nanocompartments that is unique in bacteria and archaea to confine enzymatic activities and sequester toxic reaction products. Here we present a 2.87 Å resolution cryo-EM ...Encapsulin is a class of nanocompartments that is unique in bacteria and archaea to confine enzymatic activities and sequester toxic reaction products. Here we present a 2.87 Å resolution cryo-EM structure of encapsulin with heterologous protein complex loaded. It is the first successful case of expressing encapsulin and heterologous cargo protein in the insect cell system. Although we failed to reconstruct the cargo protein complex structure due to the signal interference of the capsid shell, we were able to observe some unique features of the cargo-loaded encapsulin shell, for example, an extra density at the fivefold pore that has not been reported before. These results would lead to a more complete understanding of the encapsulin cargo assembly process of .
History
DepositionSep 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
  • EMDB-22617
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Maritimacin


Theoretical massNumber of molelcules
Total (without water)31,4901
Polymers31,4901
Non-polymers00
Water0
1
A: Maritimacin
x 60


Theoretical massNumber of molelcules
Total (without water)1,889,38760
Polymers1,889,38760
Non-polymers00
Water0
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
x 5


  • icosahedral pentamer
  • 157 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)157,4495
Polymers157,4495
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Maritimacin
x 6


  • icosahedral 23 hexamer
  • 189 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)188,9396
Polymers188,9396
Non-polymers00
Water0
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: 31489.787 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_0785
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q9WZP2, Hydrolases; Acting on peptide bonds (peptidases)

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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: Maritimacin / Type: COMPLEX / Source: RECOMBINANT
Molecular weightValue: 0.031 MDa / Experimental value: NO
Source (natural)Organism: Thermotoga maritima (bacteria)
Source (recombinant)Organism: Insect cell expression vector pTIE1 (others)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-2/1
VitrificationCryogen name: ETHANE

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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: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Image recordingElectron dose: 56.4 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter slit width: 20 eV

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Processing

EM software
IDNameCategory
2Leginonimage acquisition
10cryoSPARCinitial Euler assignment
11jsprfinal Euler assignment
13jspr3D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 112241 / Symmetry type: POINT

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