+Open data
-Basic information
Entry | Database: PDB / ID: 7s2t | ||||||
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Title | M. xanthus encapsulin EncA bound to EncB targeting peptide | ||||||
Components |
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Keywords | VIRUS LIKE PARTICLE / encapsulin / cargo protein / encapsulated ferritin / nanocage / CYTOSOLIC PROTEIN | ||||||
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 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.45 Å | ||||||
Authors | Eren, E. | ||||||
Funding support | United States, 1items
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Citation | Journal: Structure / Year: 2022 Title: Structural characterization of the Myxococcus xanthus encapsulin and ferritin-like cargo system gives insight into its iron storage mechanism. Authors: Elif Eren / Bing Wang / Dennis C Winkler / Norman R Watts / Alasdair C Steven / Paul T Wingfield / Abstract: Encapsulins are bacterial organelle-like cages involved in various aspects of metabolism, especially protection from oxidative stress. They can serve as vehicles for a wide range of medical ...Encapsulins are bacterial organelle-like cages involved in various aspects of metabolism, especially protection from oxidative stress. They can serve as vehicles for a wide range of medical applications. Encapsulin shell proteins are structurally similar to HK97 bacteriophage capsid protein and their function depends on the encapsulated cargos. The Myxococcus xanthus encapsulin system comprises EncA and three cargos: EncB, EncC, and EncD. EncB and EncC are similar to bacterial ferritins that can oxidize Fe to less toxic Fe. We analyzed EncA, EncB, and EncC by cryo-EM and X-ray crystallography. Cryo-EM shows that EncA cages can have T = 3 and T = 1 symmetry and that EncA T = 1 has a unique protomer arrangement. Also, we define EncB and EncC binding sites on EncA. X-ray crystallography of EncB and EncC reveals conformational changes at the ferroxidase center and additional metal binding sites, suggesting a mechanism for Fe oxidation and storage within the encapsulin shell. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7s2t.cif.gz | 155.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7s2t.ent.gz | 123.2 KB | Display | PDB format |
PDBx/mmJSON format | 7s2t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7s2t_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7s2t_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7s2t_validation.xml.gz | 38.9 KB | Display | |
Data in CIF | 7s2t_validation.cif.gz | 58 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s2/7s2t ftp://data.pdbj.org/pub/pdb/validation_reports/s2/7s2t | HTTPS FTP |
-Related structure data
Related structure data | 24816MC 7s20C 7s21C 7s4qC 7s5cC 7s5kC 7s8tC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 33505.074 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Myxococcus xanthus (bacteria) / Gene: MXAN_3556 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1D6H4 #2: Protein/peptide | Mass: 1354.536 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Myxococcus xanthus (bacteria) / Production host: Escherichia coli (E. coli) |
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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: EncA with T=1 symmetry / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Myxococcus xanthus (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.3 / Details: 20 mM HEPES, pH 7.3, 150 mM NaCl |
Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 46 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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EM software | Name: SerialEM / Category: image acquisition | ||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 7961 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||
Refine LS restraints |
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