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Yorodumi- PDB-7dyr: CryoEM Structure of Mannose Transporter ManYZ and Microcin E492 (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dyr | |||||||||
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Title | CryoEM Structure of Mannose Transporter ManYZ and Microcin E492 (MceA) complex | |||||||||
Components |
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Keywords | PROTEIN TRANSPORT / MceA / Microcin E492 / Bacteriocin / PTS / ManYZ / transporter / Mannose | |||||||||
Function / homology | Function and homology information mannose transmembrane transport / protein-N(PI)-phosphohistidine-mannose phosphotransferase system transporter activity / glucose import across plasma membrane / cytolysis / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / monoatomic ion transport / defense response to bacterium / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) Klebsiella pneumoniae (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.28 Å | |||||||||
Authors | Wang, J.W. / Zeng, J.W. | |||||||||
Funding support | China, 2items
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Citation | Journal: Cell Discov / Year: 2021 Title: Structure of the mannose phosphotransferase system (man-PTS) complexed with microcin E492, a pore-forming bacteriocin. Authors: Kai Huang / Jianwei Zeng / Xueli Liu / Tianyu Jiang / Jiawei Wang / | |||||||||
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 | 7dyr.cif.gz | 292.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dyr.ent.gz | 239.3 KB | Display | PDB format |
PDBx/mmJSON format | 7dyr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dyr_validation.pdf.gz | 882.8 KB | Display | wwPDB validaton report |
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Full document | 7dyr_full_validation.pdf.gz | 898.3 KB | Display | |
Data in XML | 7dyr_validation.xml.gz | 54.7 KB | Display | |
Data in CIF | 7dyr_validation.cif.gz | 85.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/7dyr ftp://data.pdbj.org/pub/pdb/validation_reports/dy/7dyr | HTTPS FTP |
-Related structure data
Related structure data | 30923MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 27647.621 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: manY, pel, ptsP, b1818, JW1807 / Variant: K-12 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Variant (production host): BL21 / References: UniProt: P69801 #2: Protein | Mass: 30983.373 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: manZ, gptB, ptsM, b1819, JW1808 / Variant: K-12 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Variant (production host): BL21 / References: UniProt: P69805 #3: Protein | Mass: 7887.492 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: mceA Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q9Z4N4 #4: Sugar | Has ligand of interest | Y | |
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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: ManYZ trimer complex with Microcin E492 (MceA) / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
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Molecular weight | Value: 0.53 kDa/nm / Experimental value: YES |
Source (natural) | Organism: Escherichia coli (E. coli) / Strain: K12 |
Source (recombinant) | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain: BL21 |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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 FIELD |
Image recording | Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18.1_3865: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 92076 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||
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