[English] 日本語
Yorodumi
- PDB-9fna: CryoEM structure of Encapsulin::tdNfsB with an open pore state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9fna
TitleCryoEM structure of Encapsulin::tdNfsB with an open 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 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.22 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 19, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
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 (bacteria) / Gene: MSMEG_5830 / Production host: Escherichia coli (E. coli) / References: UniProt: A0R4H0
Has protein modificationN

-
Experimental details

-
Experiment

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

-
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

-
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
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

-
Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2SerialEMimage acquisition
4cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 546841 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more