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- EMDB-42975: Myxococcus xanthus EncA 3xHis pore mutant with tetrahedral symmetry -

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Basic information

Entry
Database: EMDB / ID: EMD-42975
TitleMyxococcus xanthus EncA 3xHis pore mutant with tetrahedral symmetry
Map data
Sample
  • Complex: Myxococcus xanthus EncA 3xHis pore mutant with tetrahedral symmetry
    • Protein or peptide: Type 1 encapsulin shell protein EncA
KeywordsEncapsulin / VIRUS LIKE PARTICLE
Function / homologyType 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: 2.71 Å
AuthorsSzyszka TN / Andreas MP / Lie F / Miller LM / Adamson LSR / Fatehi F / Twarock R / Draper BE / Jarrold MF / Giessen TW / Lau YH
Funding support Australia, United States, 4 items
OrganizationGrant numberCountry
Australian Research Council (ARC)DE19010062 Australia
Australian Research Council (ARC)DP230101045 Australia
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM133325 United States
Other privateWestpac Scholars Trust WRF2020 Australia
CitationJournal: Proc Natl Acad Sci U S A / Year: 2024
Title: Point mutation in a virus-like capsid drives symmetry reduction to form tetrahedral cages.
Authors: Taylor N Szyszka / Michael P Andreas / Felicia Lie / Lohra M Miller / Lachlan S R Adamson / Farzad Fatehi / Reidun Twarock / Benjamin E Draper / Martin F Jarrold / Tobias W Giessen / Yu Heng Lau /
Abstract: Protein capsids are a widespread form of compartmentalization in nature. Icosahedral symmetry is ubiquitous in capsids derived from spherical viruses, as this geometry maximizes the internal volume ...Protein capsids are a widespread form of compartmentalization in nature. Icosahedral symmetry is ubiquitous in capsids derived from spherical viruses, as this geometry maximizes the internal volume that can be enclosed within. Despite the strong preference for icosahedral symmetry, we show that simple point mutations in a virus-like capsid can drive the assembly of unique symmetry-reduced structures. Starting with the encapsulin from , a 180-mer bacterial capsid that adopts the well-studied viral HK97 fold, we use mass photometry and native charge detection mass spectrometry to identify a triple histidine point mutant that forms smaller dimorphic assemblies. Using cryoelectron microscopy, we determine the structures of a precedented 60-mer icosahedral assembly and an unexpected 36-mer tetrahedron that features significant geometric rearrangements around a new interaction surface between capsid protomers. We subsequently find that the tetrahedral assembly can be generated by triple-point mutation to various amino acids and that even a single histidine point mutation is sufficient to form tetrahedra. These findings represent a unique example of tetrahedral geometry when surveying all characterized encapsulins, HK97-like capsids, or indeed any virus-derived capsids reported in the Protein Data Bank, revealing the surprising plasticity of capsid self-assembly that can be accessed through minimal changes in the protein sequence.
History
DepositionNov 29, 2023-
Header (metadata) releaseMay 22, 2024-
Map releaseMay 22, 2024-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42975.png

Downloads & links

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Map

FileDownload / File: emd_42975.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 384 pix.
= 332.934 Å		0.87 Å/pix.
x 384 pix.
= 332.934 Å		0.87 Å/pix.
x 384 pix.
= 332.934 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86702 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.21
Minimum - Maximum-2.0384965 - 2.7298357
Average (Standard dev.)0.0022918272 (±0.047148008)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 332.93414 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_42975_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_42975_half_map_2.map
Projections & Slices
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Sample components

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Entire : Myxococcus xanthus EncA 3xHis pore mutant with tetrahedral symmetry

EntireName: Myxococcus xanthus EncA 3xHis pore mutant with tetrahedral symmetry
Components
  • Complex: Myxococcus xanthus EncA 3xHis pore mutant with tetrahedral symmetry
    • Protein or peptide: Type 1 encapsulin shell protein EncA

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Supramolecule #1: Myxococcus xanthus EncA 3xHis pore mutant with tetrahedral symmetry

SupramoleculeName: Myxococcus xanthus EncA 3xHis pore mutant with tetrahedral symmetry
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Myxococcus xanthus DK 1622 (bacteria)
Molecular weightTheoretical: 1.14 MDa

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Macromolecule #1: Type 1 encapsulin shell protein EncA

MacromoleculeName: Type 1 encapsulin shell protein EncA / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Myxococcus xanthus DK 1622 (bacteria) / Strain: DK1622
Molecular weightTheoretical: 31.819082 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 LYSQLHRIYE HHHVLEIETI RQLASDGVYQ SNRLRGESGV VVSTGRENMD LA VSMDMVA AYLGASRMNH PFRVLEALLL RIKHPDAICT LEGAGATERR

UniProtKB: Type 1 encapsulin shell protein EncA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3.0 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMC4H11NO3tris
200.0 mMNaClsodium chloride

Details: 50 mM Tris pH 8.0, 200 mM NaCl
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Details: 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: 5 Blot time: 2 seconds.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 4092 pixel / Digitization - Dimensions - Height: 5760 pixel / Number grids imaged: 1 / Number real images: 3765 / Average exposure time: 2.0972 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 495482
Startup modelType of model: INSILICO MODEL / In silico model: Ab-Initio model with tetrahedral symmetry
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.71 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Software - details: Homogenous refinement
Details: Local refinement of the asymmetric unit containing three copies of the protomer from a starting map with tetrahedral symmetry. The particles used for refinement were generated by symmetry ...Details: Local refinement of the asymmetric unit containing three copies of the protomer from a starting map with tetrahedral symmetry. The particles used for refinement were generated by symmetry expansion using tetrahedral symmetry from 233,299 particles.
Number images used: 2799588
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: ESMfold was used to make starting model
DetailsThe starting model was generated using ESMfold then fit into the map using ChimeraX. The placed coordinates were then manually refined using Coot, followed by real space refinement in Phenix.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 118.3 / Target criteria: Cross-correlation coefficient
Output model

PDB-8v4q:
Myxococcus xanthus EncA 3xHis pore mutant with tetrahedral symmetry

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