+Open data
-Basic information
Entry | Database: PDB / ID: 8g02 | |||||||||
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Title | YES Complex - E. coli MraY, Protein E PhiX174, E. coli SlyD | |||||||||
Components |
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Keywords | TRANSFERASE/ISOMERASE / inhibitor / antibiotic / chaperone / membrane / bacteriophage / TRANSFERASE-ISOMERASE complex | |||||||||
Function / homology | Function and homology information suppression by virus of host peptidoglycan biosynthetic process / viral release via suppression of host peptidoglycan biosynthetic process / phospho-N-acetylmuramoyl-pentapeptide-transferase / UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelyl-D-alanyl-D-alanine:undecaprenyl-phosphate transferase activity / phospho-N-acetylmuramoyl-pentapeptide-transferase activity / cell wall macromolecule biosynthetic process / enzyme inhibitor activity / peptidoglycan biosynthetic process / viral release from host cell by cytolysis / peptidylprolyl isomerase ...suppression by virus of host peptidoglycan biosynthetic process / viral release via suppression of host peptidoglycan biosynthetic process / phospho-N-acetylmuramoyl-pentapeptide-transferase / UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelyl-D-alanyl-D-alanine:undecaprenyl-phosphate transferase activity / phospho-N-acetylmuramoyl-pentapeptide-transferase activity / cell wall macromolecule biosynthetic process / enzyme inhibitor activity / peptidoglycan biosynthetic process / viral release from host cell by cytolysis / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / cell wall organization / protein folding / regulation of cell shape / killing of cells of another organism / cell division / host cell plasma membrane / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli K-12 (bacteria) Escherichia phage phiX174 (virus) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Orta, A.K. / Clemons, W.M. / Li, Y.E. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Science / Year: 2023 Title: The mechanism of the phage-encoded protein antibiotic from ΦX174. Authors: Anna K Orta / Nadia Riera / Yancheng E Li / Shiho Tanaka / Hyun Gi Yun / Lada Klaic / William M Clemons / Abstract: The historically important phage ΦX174 kills its host bacteria by encoding a 91-residue protein antibiotic called protein E. Using single-particle electron cryo-microscopy, we demonstrate that ...The historically important phage ΦX174 kills its host bacteria by encoding a 91-residue protein antibiotic called protein E. Using single-particle electron cryo-microscopy, we demonstrate that protein E bridges two bacterial proteins to form the transmembrane YES complex [MraY, protein E, sensitivity to lysis D (SlyD)]. Protein E inhibits peptidoglycan biosynthesis by obstructing the MraY active site leading to loss of lipid I production. We experimentally validate this result for two different viral species, providing a clear model for bacterial lysis and unifying previous experimental data. Additionally, we characterize the MraY structure-revealing features of this essential enzyme-and the structure of the chaperone SlyD bound to a protein. Our structures provide insights into the mechanism of phage-mediated lysis and for structure-based design of phage therapeutics. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8g02.cif.gz | 380.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8g02.ent.gz | 313.5 KB | Display | PDB format |
PDBx/mmJSON format | 8g02.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8g02_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8g02_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8g02_validation.xml.gz | 45.2 KB | Display | |
Data in CIF | 8g02_validation.cif.gz | 67.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g0/8g02 ftp://data.pdbj.org/pub/pdb/validation_reports/g0/8g02 | HTTPS FTP |
-Related structure data
Related structure data | 29642MC 8g01C 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: 39909.539 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: mraY, murX, b0087, JW0085 / Production host: Escherichia coli K-12 (bacteria) References: UniProt: P0A6W3, phospho-N-acetylmuramoyl-pentapeptide-transferase #2: Protein | Mass: 11545.908 Da / Num. of mol.: 2 / Mutation: Gly insertion position 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia phage phiX174 (virus) / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P03639 #3: Protein | Mass: 16659.486 Da / Num. of mol.: 2 / Fragment: UNP residues 1-154 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: ECDG_03916 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: D6IEN4, peptidylprolyl isomerase |
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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 |
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Molecular weight |
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 / Details: Supplemented with 2mM E. coli lipid extract | |||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 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: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-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: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 5000 nm / Nominal defocus min: 500 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 2 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 10798 |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1516368 | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 155270 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 2K8I Pdb chain-ID: A / Accession code: 2K8I / Chain residue range: 1-154 / Pdb chain residue range: 1-154 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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