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- PDB-9fn9: Icosahedral Encapsulin with a closed pore state -

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Basic information

Entry
Database: PDB / ID: 9fn9
TitleIcosahedral Encapsulin with a closed pore state
Components29 kDa antigen Cfp29
KeywordsBIOSYNTHETIC PROTEIN / Nanocompartment
Function / homologyType 1 encapsulin shell protein / Encapsulating protein for peroxidase / : / encapsulin nanocompartment / Type 1 encapsulin shell protein
Function and homology information
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.81 Å
AuthorsCapper, M.J. / Kohhnke, J.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)101002326European Union
CitationJournal: RSC Chem Biol / Year: 2024
Title: A nanoengineered tandem nitroreductase: designing a robust prodrug-activating nanoreactor.
Authors: Mariia Zmyslia / Michael J Capper / Michael Grimmeisen / Kerstin Sartory / Benedikt Deuringer / Mohamed Abdelsalam / Kaiwei Shen / Manfred Jung / Wolfgang Sippl / Hans-Georg Koch / Laurine ...Authors: Mariia Zmyslia / Michael J Capper / Michael Grimmeisen / Kerstin Sartory / Benedikt Deuringer / Mohamed Abdelsalam / Kaiwei Shen / Manfred Jung / Wolfgang Sippl / Hans-Georg Koch / Laurine Kaul / Regine Süss / Jesko Köhnke / Claudia Jessen-Trefzer /
Abstract: Nitroreductases are important enzymes for a variety of applications, including cancer therapy and bioremediation. They often require encapsulation to improve stability and activity. We focus on ...Nitroreductases are important enzymes for a variety of applications, including cancer therapy and bioremediation. They often require encapsulation to improve stability and activity. We focus on genetically encoded encapsulation of nitroreductases within protein capsids, like encapsulins. Our study showcases the encapsulation of nitroreductase NfsB as functional dimers within encapsulins, which enhances protein activity and stability in diverse conditions. Mutations within the pore region are beneficial for activity of the encapsulated enzyme, potentially by increasing diffusion rates. Cryogenic electron microscopy reveals the overall architecture of the encapsulated dimeric NfsB within the nanoreactor environment and identifies multiple pore states in the shell. These findings highlight the potential of encapsulins as versatile tools for enhancing enzyme performance across various fields.
History
DepositionJun 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 29 kDa antigen Cfp29
AA: 29 kDa antigen Cfp29
AB: 29 kDa antigen Cfp29
B: 29 kDa antigen Cfp29
BA: 29 kDa antigen Cfp29
BB: 29 kDa antigen Cfp29
C: 29 kDa antigen Cfp29
CA: 29 kDa antigen Cfp29
CB: 29 kDa antigen Cfp29
D: 29 kDa antigen Cfp29
DA: 29 kDa antigen Cfp29
DB: 29 kDa antigen Cfp29
E: 29 kDa antigen Cfp29
EA: 29 kDa antigen Cfp29
EB: 29 kDa antigen Cfp29
F: 29 kDa antigen Cfp29
FA: 29 kDa antigen Cfp29
FB: 29 kDa antigen Cfp29
G: 29 kDa antigen Cfp29
GA: 29 kDa antigen Cfp29
GB: 29 kDa antigen Cfp29
H: 29 kDa antigen Cfp29
HA: 29 kDa antigen Cfp29
HB: 29 kDa antigen Cfp29
I: 29 kDa antigen Cfp29
IA: 29 kDa antigen Cfp29
IB: 29 kDa antigen Cfp29
J: 29 kDa antigen Cfp29
JA: 29 kDa antigen Cfp29
K: 29 kDa antigen Cfp29
KA: 29 kDa antigen Cfp29
L: 29 kDa antigen Cfp29
LA: 29 kDa antigen Cfp29
M: 29 kDa antigen Cfp29
MA: 29 kDa antigen Cfp29
N: 29 kDa antigen Cfp29
NA: 29 kDa antigen Cfp29
O: 29 kDa antigen Cfp29
OA: 29 kDa antigen Cfp29
P: 29 kDa antigen Cfp29
PA: 29 kDa antigen Cfp29
Q: 29 kDa antigen Cfp29
QA: 29 kDa antigen Cfp29
R: 29 kDa antigen Cfp29
RA: 29 kDa antigen Cfp29
S: 29 kDa antigen Cfp29
SA: 29 kDa antigen Cfp29
T: 29 kDa antigen Cfp29
TA: 29 kDa antigen Cfp29
UA: 29 kDa antigen Cfp29
V: 29 kDa antigen Cfp29
VA: 29 kDa antigen Cfp29
W: 29 kDa antigen Cfp29
WA: 29 kDa antigen Cfp29
X: 29 kDa antigen Cfp29
XA: 29 kDa antigen Cfp29
Y: 29 kDa antigen Cfp29
YA: 29 kDa antigen Cfp29
Z: 29 kDa antigen Cfp29
ZA: 29 kDa antigen Cfp29


Theoretical massNumber of molelcules
Total (without water)1,802,73560
Polymers1,802,73560
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
29 kDa antigen Cfp29


Mass: 30045.578 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Gene: MSMEG_5830 / Production host: Escherichia coli (E. coli) / References: UniProt: A0R4H0
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

ComponentName: Cryo-EM structure of encapsulin shell containing engineered tandem dimer NfsB
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameBuffer-ID
120 mMHEPES1
2100 mMNaCl1
SpecimenConc.: 20 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 281 K

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 80000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: JEOL CRYOSPECPORTER
Image recordingAverage exposure time: 1.5 sec. / Electron dose: 60.2 e/Å2 / Film or detector model: DIRECT ELECTRON APOLLO (4k x 4k) / Num. of grids imaged: 1
EM imaging opticsEnergyfilter name: In-column Omega Filter

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Processing

EM softwareName: SerialEM / Category: image acquisition
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 308711 / Num. of class averages: 1 / Symmetry type: POINT

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