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- EMDB-29641: YES Complex - E. coli MraY, Protein E ID21, E. coli SlyD -

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Basic information

Entry
Database: EMDB / ID: EMD-29641
TitleYES Complex - E. coli MraY, Protein E ID21, E. coli SlyD
Map dataCryoEM map of the YES complex (E. coli MraY, Protein E ID21, E. coli SlyD). DeepEMhancer post-processed.
Sample
  • Complex: YES complex
    • Complex: Lysis Protein E
      • Protein or peptide: GPE
    • Complex: Dimeric structure of MraY
      • Protein or peptide: Phospho-N-acetylmuramoyl-pentapeptide-transferase
    • Complex: SlyD
      • Protein or peptide: FKBP-type peptidyl-prolyl cis-trans isomerase SlyD
Keywordsinhibitor / antibiotic / chaperone / membrane / bacteriophage / TRANSFERASE-ISOMERASE complex
Function / homology
Function and homology information


phospho-N-acetylmuramoyl-pentapeptide-transferase / phospho-N-acetylmuramoyl-pentapeptide-transferase activity / UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelyl-D-alanyl-D-alanine:undecaprenyl-phosphate transferase activity / cell wall macromolecule biosynthetic process / cobalt ion binding / nickel cation binding / enzyme inhibitor activity / peptidoglycan biosynthetic process / protein maturation / peptidylprolyl isomerase ...phospho-N-acetylmuramoyl-pentapeptide-transferase / phospho-N-acetylmuramoyl-pentapeptide-transferase activity / UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelyl-D-alanyl-D-alanine:undecaprenyl-phosphate transferase activity / cell wall macromolecule biosynthetic process / cobalt ion binding / nickel cation binding / enzyme inhibitor activity / peptidoglycan biosynthetic process / protein maturation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / cell wall organization / unfolded protein binding / regulation of cell shape / response to heat / protein refolding / killing of cells of another organism / protein stabilization / copper ion binding / cell division / zinc ion binding / metal ion binding / membrane / plasma membrane / cytosol
Similarity search - Function
Microvirus lysis protein (E) / Microvirus lysis protein (E), C terminus / : / Phospho-N-acetylmuramoyl-pentapeptide transferase / Phospho-N-acetylmuramoyl-pentapeptide transferase, conserved site / Phospho-N-acetylmuramoyl-pentapeptide-transferase signature 1 / MraY family signature 1. / MraY family signature 2. / Glycosyl transferase, family 4 / Glycosyl transferase family 4 ...Microvirus lysis protein (E) / Microvirus lysis protein (E), C terminus / : / Phospho-N-acetylmuramoyl-pentapeptide transferase / Phospho-N-acetylmuramoyl-pentapeptide transferase, conserved site / Phospho-N-acetylmuramoyl-pentapeptide-transferase signature 1 / MraY family signature 1. / MraY family signature 2. / Glycosyl transferase, family 4 / Glycosyl transferase family 4 / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / Peptidyl-prolyl cis-trans isomerase domain superfamily
Similarity search - Domain/homology
Phospho-N-acetylmuramoyl-pentapeptide-transferase / FKBP-type peptidyl-prolyl cis-trans isomerase SlyD / GPE
Similarity search - Component
Biological speciesEscherichia phage ID21 (virus) / Escherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsOrta AK / Clemons WM / Riera N
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM114611 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM105385 United States
CitationJournal: 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
DepositionJan 31, 2023-
Header (metadata) releaseJul 26, 2023-
Map releaseJul 26, 2023-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29641.png

Downloads & links

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Map

FileDownload / File: emd_29641.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM map of the YES complex (E. coli MraY, Protein E ID21, E. coli SlyD). DeepEMhancer post-processed.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 212.992 Å		0.83 Å/pix.
x 256 pix.
= 212.992 Å		0.83 Å/pix.
x 256 pix.
= 212.992 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.016213909 - 1.7765907
Average (Standard dev.)0.0023169403 (±0.031370346)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.992 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: CryoEM map of the YES complex (E. coli...

Fileemd_29641_additional_1.map
AnnotationCryoEM map of the YES complex (E. coli MraY, Protein E ID21, E. coli SlyD).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_29641_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_29641_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : YES complex

EntireName: YES complex
Components
  • Complex: YES complex
    • Complex: Lysis Protein E
      • Protein or peptide: GPE
    • Complex: Dimeric structure of MraY
      • Protein or peptide: Phospho-N-acetylmuramoyl-pentapeptide-transferase
    • Complex: SlyD
      • Protein or peptide: FKBP-type peptidyl-prolyl cis-trans isomerase SlyD

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Supramolecule #1: YES complex

SupramoleculeName: 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 (ID21), stabilized by E. coli SlyD
Molecular weightTheoretical: 140.32 KDa

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Supramolecule #2: Lysis Protein E

SupramoleculeName: Lysis Protein E / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2 / Details: Protein E from ID21 phage
Source (natural)Organism: Escherichia phage ID21 (virus)
Molecular weightTheoretical: 8.65 KDa

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Supramolecule #3: Dimeric structure of MraY

SupramoleculeName: Dimeric structure of MraY / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 39.88 KDa

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Supramolecule #4: SlyD

SupramoleculeName: SlyD / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3 / Details: E. coli SlyD truncated at residue 154
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 20.86 KDa

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Macromolecule #1: Phospho-N-acetylmuramoyl-pentapeptide-transferase

MacromoleculeName: Phospho-N-acetylmuramoyl-pentapeptide-transferase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
EC number: phospho-N-acetylmuramoyl-pentapeptide-transferase
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 39.909539 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: 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

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Macromolecule #2: GPE

MacromoleculeName: GPE / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage ID21 (virus)
Molecular weightTheoretical: 9.489507 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
MGHWTLSGIL AFLLLLSLLL PSLLIMFIPL TFRRPASSWK ARSLQKILLM ASSVRLKPLS SSRIPCVLRP DSKRRFHHHH HH

UniProtKB: GPE

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Macromolecule #3: FKBP-type peptidyl-prolyl cis-trans isomerase SlyD

MacromoleculeName: FKBP-type peptidyl-prolyl cis-trans isomerase SlyD / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: peptidylprolyl isomerase
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 16.659486 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
MKVAKDLVVS LAYQVRTEDG VLVDESPVSA PLDYLHGHGS LISGLETALE GHEVGDKFDV AVGANDAYGQ YDENLVQRVP KDVFMGVDE LQVGMRFLAE TDQGPVPVEI TAVEDDHVVV DGNHMLAGQN LKFNVEVVAI REATEEELAH GHVHG

UniProtKB: FKBP-type peptidyl-prolyl cis-trans isomerase SlyD

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
10.0 mMC8H18N2O4SHEPES
75.0 mMNaClSodium Chloride
5.0 %C3H8O3Glycerol
0.03 %C24H46O11n-Dodecyl-beta-maltoside
5.0 mMC2H6OS2-Mercaptoethanol

Details: Supplemented with 2mM E. coli lipid extract
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 12070 / Average exposure time: 2.0 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 11700795
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v3.2.0+210817) / Number images used: 122452
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v3.2.0+210817)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v3.2.0+210817)
Final 3D classificationNumber classes: 4 / Avg.num./class: 69806 / Software - Name: cryoSPARC (ver. v3.2.0+210817)
Details: Two classes had about 100,000+ particles, one had about 37,000 and the final class about 5,000
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

4j72

chain_id: A, residue_range: 1-365, source_name: PDB, initial_model_type: experimental model

2k8i

chain_id: A, residue_range: 1-154, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8g01:
YES Complex - E. coli MraY, Protein E ID21, E. coli SlyD

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