+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29642 | |||||||||
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Title | YES Complex - E. coli MraY, Protein E ID21, E. coli SlyD | |||||||||
Map data | ||||||||||
Sample |
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Keywords | 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 phage phiX174 (virus) / Escherichia coli K-12 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Orta AK / Clemons WM / Li YE | |||||||||
Funding support | United States, 2 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29642.map.gz | 55.5 MB | EMDB map data format | |
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Header (meta data) | emd-29642-v30.xml emd-29642.xml | 23.4 KB 23.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_29642_fsc.xml | 11.7 KB | Display | FSC data file |
Images | emd_29642.png | 95.5 KB | ||
Filedesc metadata | emd-29642.cif.gz | 6.7 KB | ||
Others | emd_29642_half_map_1.map.gz emd_29642_half_map_2.map.gz | 59.1 MB 59.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29642 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29642 | HTTPS FTP |
-Validation report
Summary document | emd_29642_validation.pdf.gz | 808.2 KB | Display | EMDB validaton report |
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Full document | emd_29642_full_validation.pdf.gz | 807.8 KB | Display | |
Data in XML | emd_29642_validation.xml.gz | 16 KB | Display | |
Data in CIF | emd_29642_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29642 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29642 | HTTPS FTP |
-Related structure data
Related structure data | 8g02MC 8g01C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_29642.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.832 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_29642_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: CryoEM map of the YES complex (phix174)
File | emd_29642_half_map_2.map | ||||||||||||
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Annotation | CryoEM map of the YES complex (phix174) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : YES complex
Entire | Name: YES complex |
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Components |
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-Supramolecule #1: YES complex
Supramolecule | Name: YES complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Hexameric complex of E. coli MraY dimer bound to two molecules of Protein E (phix174), stabilized by E. coli SlyD |
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Molecular weight | Theoretical: 140.32 KDa |
-Supramolecule #2: Lysis Protein E
Supramolecule | Name: Lysis Protein E / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2 / Details: Protein E from PhiX174 phage |
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Source (natural) | Organism: Escherichia phage phiX174 (virus) |
Molecular weight | Theoretical: 11.52476 KDa |
-Supramolecule #3: Dimeric structure of MraY
Supramolecule | Name: Dimeric structure of MraY / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
Molecular weight | Theoretical: 39.88 KDa |
-Supramolecule #4: SlyD
Supramolecule | Name: SlyD / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3 / Details: E. coli SlyD truncated at residue 154 |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
Molecular weight | Theoretical: 20.86 KDa |
-Macromolecule #1: Phospho-N-acetylmuramoyl-pentapeptide-transferase
Macromolecule | Name: Phospho-N-acetylmuramoyl-pentapeptide-transferase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO EC number: phospho-N-acetylmuramoyl-pentapeptide-transferase |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
Molecular weight | Theoretical: 39.909539 KDa |
Recombinant expression | Organism: Escherichia coli K-12 (bacteria) |
Sequence | String: MLVWLAEHLV KYYSGFNVFS YLTFRAIVSL LTALFISLWM GPRMIAHLQK LSFGQVVRND GPESHFSKRG TPTMGGIMIL TAIVISVLL WAYPSNPYVW CVLVVLVGYG VIGFVDDYRK VVRKDTKGLI ARWKYFWMSV IALGVAFALY LAGKDTPATQ L VVPFFKDV ...String: MLVWLAEHLV KYYSGFNVFS YLTFRAIVSL LTALFISLWM GPRMIAHLQK LSFGQVVRND GPESHFSKRG TPTMGGIMIL TAIVISVLL WAYPSNPYVW CVLVVLVGYG VIGFVDDYRK VVRKDTKGLI ARWKYFWMSV IALGVAFALY LAGKDTPATQ L VVPFFKDV MPQLGLFYIL LAYFVIVGTG NAVNLTDGLD GLAIMPTVFV AGGFALVAWA TGNMNFASYL HIPYLRHAGE LV IVCTAIV GAGLGFLWFN TYPAQVFMGD VGSLALGGAL GIIAVLLRQE FLLVIMGGVF VVETLSVILQ VGSFKLRGQR IFR MAPIHH HYELKGWPEP RVIVRFWIIS LMLVLIGLAT LKVR UniProtKB: Phospho-N-acetylmuramoyl-pentapeptide-transferase |
-Macromolecule #2: Lysis protein E
Macromolecule | Name: Lysis protein E / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia phage phiX174 (virus) |
Molecular weight | Theoretical: 11.545908 KDa |
Recombinant expression | Organism: Escherichia coli K-12 (bacteria) |
Sequence | String: MGVRWTLWDT LAFLLLLSLL LPSLLIMFIP STFKRPVSSW KARNLRKTLL MASSVRLKPL NCSRLPCVYA QETLTFLLTQ KKTCVKNYV RKEHHHHHH UniProtKB: Lysis protein E |
-Macromolecule #3: Peptidyl-prolyl cis-trans isomerase
Macromolecule | Name: Peptidyl-prolyl cis-trans isomerase / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: peptidylprolyl isomerase |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
Molecular weight | Theoretical: 16.659486 KDa |
Recombinant expression | Organism: Escherichia coli K-12 (bacteria) |
Sequence | String: MKVAKDLVVS LAYQVRTEDG VLVDESPVSA PLDYLHGHGS LISGLETALE GHEVGDKFDV AVGANDAYGQ YDENLVQRVP KDVFMGVDE LQVGMRFLAE TDQGPVPVEI TAVEDDHVVV DGNHMLAGQN LKFNVEVVAI REATEEELAH GHVHG UniProtKB: Peptidyl-prolyl cis-trans isomerase |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5 mg/mL | ||||||||||||||||||
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Buffer | pH: 7.5 Component:
Details: Supplemented with 2mM E. coli lipid extract | ||||||||||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 10798 / Average exposure time: 2.0 sec. / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |