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Yorodumi- PDB-8v4q: Myxococcus xanthus EncA 3xHis pore mutant with tetrahedral symmetry -
+Open data
-Basic information
Entry | Database: PDB / ID: 8v4q | |||||||||||||||
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Title | Myxococcus xanthus EncA 3xHis pore mutant with tetrahedral symmetry | |||||||||||||||
Components | Type 1 encapsulin shell protein EncA | |||||||||||||||
Keywords | VIRUS LIKE PARTICLE / Encapsulin | |||||||||||||||
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 species | Myxococcus xanthus DK 1622 (bacteria) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.71 Å | |||||||||||||||
Authors | Szyszka, T.N. / Andreas, M.P. / Lie, F. / Miller, L.M. / Adamson, L.S.R. / Fatehi, F. / Twarock, R. / Draper, B.E. / Jarrold, M.F. / Giessen, T.W. / Lau, Y.H. | |||||||||||||||
Funding support | Australia, United States, 4items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8v4q.cif.gz | 140.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8v4q.ent.gz | 111.3 KB | Display | PDB format |
PDBx/mmJSON format | 8v4q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/8v4q ftp://data.pdbj.org/pub/pdb/validation_reports/v4/8v4q | HTTPS FTP |
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-Related structure data
Related structure data | 42975MC 8v4nC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 31819.082 Da / Num. of mol.: 3 / Mutation: K199H, T200H, G201H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Myxococcus xanthus DK 1622 (bacteria) / Strain: DK1622 / Gene: encA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q1D6H4 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Myxococcus xanthus EncA 3xHis pore mutant with tetrahedral symmetry Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | |||||||||||||||
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Molecular weight | Value: 1.14 MDa / Experimental value: YES | |||||||||||||||
Source (natural) | Organism: Myxococcus xanthus DK 1622 (bacteria) | |||||||||||||||
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) | |||||||||||||||
Buffer solution | pH: 8 / Details: 50 mM Tris pH 8.0, 200 mM NaCl | |||||||||||||||
Buffer component |
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Specimen | Conc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Specimen support | Details: 5 mA for 60 seconds under vacuum / Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1 | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K / Details: Blot force: 5 Blot time: 2 seconds |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 2.0972 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3765 |
Image scans | Width: 4092 / Height: 5760 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 495482 | ||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.71 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2799588 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. Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 118.3 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient Details: The 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. | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Details: ESMfold was used to make starting model / Source name: Other / Type: in silico model | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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