[English] 日本語
Yorodumi
- EMDB-44383: Myxococcus xanthus EncA encapsulin engineered pore mutant with T=... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-44383
TitleMyxococcus xanthus EncA encapsulin engineered pore mutant with T=1 icosahedral symmetry
Map data
Sample
  • Complex: Myxococcus xanthus EncA encapsulin engineered pore mutant with T=1 icosahedral symmetry
    • Protein or peptide: Type 1 encapsulin shell protein EncA
Keywordsencapsulin / nanocompartment / pore mutant / VIRUS LIKE PARTICLE
Function / homology: / Type 1 encapsulin shell protein / Encapsulating protein for peroxidase / encapsulin nanocompartment / iron ion transport / intracellular iron ion homeostasis / Type 1 encapsulin shell protein EncA
Function and homology information
Biological speciesMyxococcus xanthus DK 1622 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsAndreas MP / Kwon S / Giessen TW
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM133325-05 United States
CitationJournal: ACS Nano / Year: 2024
Title: Pore Engineering as a General Strategy to Improve Protein-Based Enzyme Nanoreactor Performance.
Authors: Seokmu Kwon / Michael P Andreas / Tobias W Giessen /
Abstract: Enzyme nanoreactors are nanoscale compartments consisting of encapsulated enzymes and a selectively permeable barrier. Sequestration and colocalization of enzymes can increase catalytic activity, ...Enzyme nanoreactors are nanoscale compartments consisting of encapsulated enzymes and a selectively permeable barrier. Sequestration and colocalization of enzymes can increase catalytic activity, stability, and longevity, highly desirable features for many biotechnological and biomedical applications of enzyme catalysts. One promising strategy to construct enzyme nanoreactors is to repurpose protein nanocages found in nature. However, protein-based enzyme nanoreactors often exhibit decreased catalytic activity, partially caused by a mismatch of protein shell selectivity and the substrate requirements of encapsulated enzymes. No broadly applicable and modular protein-based nanoreactor platform is currently available. Here, we introduce a pore-engineered universal enzyme nanoreactor platform based on encapsulins-microbial self-assembling protein nanocompartments with programmable and selective enzyme packaging capabilities. We structurally characterize our protein shell designs via cryo-electron microscopy and highlight their polymorphic nature. Through fluorescence polarization assays, we show their improved molecular flux behavior and highlight their expanded substrate range via a number of proof-of-concept enzyme nanoreactor designs. This work lays the foundation for utilizing our encapsulin-based nanoreactor platform for diverse future biotechnological and biomedical applications.
History
DepositionApr 2, 2024-
Header (metadata) releaseSep 18, 2024-
Map releaseSep 18, 2024-
UpdateSep 25, 2024-
Current statusSep 25, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_44383.png

Downloads & links

-
Map

FileDownload / File: emd_44383.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
0.91 Å/pix.
x 360 pix.
= 327.6 Å		0.91 Å/pix.
x 360 pix.
= 327.6 Å		0.91 Å/pix.
x 360 pix.
= 327.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.91 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.17
Minimum - Maximum-0.6840396 - 1.1869308
Average (Standard dev.)0.0021697956 (±0.07088472)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 327.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Myxococcus xanthus EncA encapsulin engineered pore mutant with T=...

EntireName: Myxococcus xanthus EncA encapsulin engineered pore mutant with T=1 icosahedral symmetry
Components
  • Complex: Myxococcus xanthus EncA encapsulin engineered pore mutant with T=1 icosahedral symmetry
    • Protein or peptide: Type 1 encapsulin shell protein EncA

-
Supramolecule #1: Myxococcus xanthus EncA encapsulin engineered pore mutant with T=...

SupramoleculeName: Myxococcus xanthus EncA encapsulin engineered pore mutant with T=1 icosahedral symmetry
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Myxococcus xanthus DK 1622 (bacteria)
Molecular weightTheoretical: 1.9 MDa

-
Macromolecule #1: Type 1 encapsulin shell protein EncA

MacromoleculeName: Type 1 encapsulin shell protein EncA / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Myxococcus xanthus DK 1622 (bacteria)
Molecular weightTheoretical: 30.901014 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MPDFLGHAEN PLREEEWARL NETVIQVARR SLVGRRILDI YGPLGAGVQT VPYDEFQGVS PGAVDIVGEQ ETAMVFTDAR KFKTIPIIY KDFLLHWRDI EAARTHNMPL DVSAAAGAAA LCAQQEDELI FYGDARLGYE GLMTANGRLT VPLGDWTSPG G GFQAIVEA ...String:
MPDFLGHAEN PLREEEWARL NETVIQVARR SLVGRRILDI YGPLGAGVQT VPYDEFQGVS PGAVDIVGEQ ETAMVFTDAR KFKTIPIIY KDFLLHWRDI EAARTHNMPL DVSAAAGAAA LCAQQEDELI FYGDARLGYE GLMTANGRLT VPLGDWTSPG G GFQAIVEA TRKLNEQGHF GPYAVVLSPR LYSQLHRGGE IETIRQLASD GVYQSNRLRG ESGVVVSTGR ENMDLAVSMD MV AAYLGAS RMNHPFRVLE ALLLRIKHPD AICTLEGAGA TERR

UniProtKB: Type 1 encapsulin shell protein EncA

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3.0 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
20.0 mMC4H11NO3tris(hydroxymethyl)aminomethane

Details: 150 mM NaCl, 20 mM Tris pH 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
Details: The grid was glow discharged at 5 mA for 60 seconds under vacuum.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV
Details: Blot force: 20 Blot time: 4 seconds Wait time: 0 seconds.

-
Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Number grids imaged: 1 / Number real images: 711 / Average exposure time: 4.0 sec. / Average electron dose: 39.18 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 45000
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 66813
Startup modelType of model: INSILICO MODEL / Details: Ab-initio model
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.10.0) / Software - details: Homogeneous refinement
Details: CryoSPARC homogeneous refinement was performed with I symmetry, per-particle defocus optimization, per-group CTF-parameterization, and Ewald sphere correction enabled.
Number images used: 61808
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.10.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.10.0)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

7s21


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsChimeraX v1.2.5 was first used to place the starting model (PDB: 7S21) in the cryo-EM map by using the fit in map command. The model was then manually refined using Coot v 0.9.8.1, followed by iterative real-space refinements in Phenix v1.20.1-4487-000. BioMT operators were identified from the cryo-EM map using map_symmetry command in Phenix then applied to the model using the apply_ncs command to assemble the complete shell. Real-space refinement was repeated in Phenix with NCS constraints applied. The BioMT operators were then identified using find_ncs command in Phenix and applied to the header of a protomer of the NCS-refined model.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 126.4 / Target criteria: cross-correlation coefficient
Output model

PDB-9b9i:
Myxococcus xanthus EncA encapsulin engineered pore mutant with T=1 icosahedral symmetry

+
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://pdbjlvh1.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