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- EMDB-41299: Structural basis of peptidoglycan synthesis by E. coli RodA-PBP2 ... -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-41299
TitleStructural basis of peptidoglycan synthesis by E. coli RodA-PBP2 complex
Map data
Sample
  • Complex: RodA-PBP2
    • Protein or peptide: Peptidoglycan glycosyltransferase MrdB
    • Protein or peptide: Peptidoglycan D,D-transpeptidase MrdA
KeywordsPeptidoglycan / glycosyltransferase / enzyme / MEMBRANE PROTEIN
Function / homology
Function and homology information


peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / acyltransferase activity / glycosyltransferase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape ...peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / acyltransferase activity / glycosyltransferase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / proteolysis / plasma membrane
Similarity search - Function
Probable peptidoglycan glycosyltransferase RodA/MrdB / Cell cycle, FtsW / RodA / SpoVE, conserved site / Cell cycle proteins ftsW / rodA / spoVE signature. / Penicillin-binding protein 2 / Probable peptidoglycan glycosyltransferase FtsW/RodA / Cell cycle protein / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily / Penicillin-binding protein, transpeptidase ...Probable peptidoglycan glycosyltransferase RodA/MrdB / Cell cycle, FtsW / RodA / SpoVE, conserved site / Cell cycle proteins ftsW / rodA / spoVE signature. / Penicillin-binding protein 2 / Probable peptidoglycan glycosyltransferase FtsW/RodA / Cell cycle protein / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Peptidoglycan glycosyltransferase MrdB / Peptidoglycan D,D-transpeptidase MrdA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsNygaard R / Mancia F
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM132120 United States
CitationJournal: Nat Commun / Year: 2023
Title: Structural basis of peptidoglycan synthesis by E. coli RodA-PBP2 complex
Authors: Nygaard R / Graham CLB / Belcher Dufrisne M / Colburn JD / Pepe J / Hydorn MA / Corradi S / Brown CM / Ashraf KU / Vickery ON / Briggs NS / Deering JJ / Kloss B / Botta B / Clarke OB / ...Authors: Nygaard R / Graham CLB / Belcher Dufrisne M / Colburn JD / Pepe J / Hydorn MA / Corradi S / Brown CM / Ashraf KU / Vickery ON / Briggs NS / Deering JJ / Kloss B / Botta B / Clarke OB / Columbus L / Dworkin J / Stansfeld PJ / Roper DI / Mancia F
History
DepositionJul 20, 2023-
Header (metadata) releaseAug 30, 2023-
Map releaseAug 30, 2023-
UpdateAug 30, 2023-
Current statusAug 30, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41299.png

Downloads & links

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Map

FileDownload / File: emd_41299.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 0.043
Minimum - Maximum-0.16517833 - 0.8442311
Average (Standard dev.)0.00046289113 (±0.00810673)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 332.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : RodA-PBP2

EntireName: RodA-PBP2
Components
  • Complex: RodA-PBP2
    • Protein or peptide: Peptidoglycan glycosyltransferase MrdB
    • Protein or peptide: Peptidoglycan D,D-transpeptidase MrdA

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Supramolecule #1: RodA-PBP2

SupramoleculeName: RodA-PBP2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Nanodisc were formed using MSP1E3D1 and POPG lipid
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 111.803 KDa

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Macromolecule #1: Peptidoglycan glycosyltransferase MrdB

MacromoleculeName: Peptidoglycan glycosyltransferase MrdB / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 40.508766 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTDNPNKKTF WDKVHLDPTM LLILLALLVY SALVIWSASG QDIGMMERKI GQIAMGLVIM VVMAQIPPRV YEGWAPYLYI ICIILLVAV DAFGAISKGA QRWLDLGIVR FQPSEIAKIA VPLMVARFIN RDVCPPSLKN TGIALVLIFM PTLLVAAQPD L GTSILVAL ...String:
MTDNPNKKTF WDKVHLDPTM LLILLALLVY SALVIWSASG QDIGMMERKI GQIAMGLVIM VVMAQIPPRV YEGWAPYLYI ICIILLVAV DAFGAISKGA QRWLDLGIVR FQPSEIAKIA VPLMVARFIN RDVCPPSLKN TGIALVLIFM PTLLVAAQPD L GTSILVAL SGLFVLFLSG LSWRLIGVAV VLVAAFIPIL WFFLMHDYQR QRVMMLLDPE SDPLGAGYHI IQSKIAIGSG GL RGKGWLH GTQSQLEFLP ERHTDFIFAV LAEELGLVGI LILLALYILL IMRGLWIAAR AQTTFGRVMA GGLMLILFVY VFV NIGMVS GILPVVGVPL PLVSYGGSAL IVLMAGFGIV MSIHTHRKML SKSV

UniProtKB: Peptidoglycan glycosyltransferase MrdB

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Macromolecule #2: Peptidoglycan D,D-transpeptidase MrdA

MacromoleculeName: Peptidoglycan D,D-transpeptidase MrdA / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 70.943414 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKLQNSFRDY TAESALFVRR ALVAFLGILL LTGVLIANLY NLQIVRFTDY QTRSNENRIK LVPIAPSRGI IYDRNGIPLA LNRTIYQIE MMPEKVDNVQ QTLDALRSVV DLTDDDIAAF RKERARSHRF TSIPVKTNLT EVQVARFAVN QYRFPGVEVK G YKRRYYPY ...String:
MKLQNSFRDY TAESALFVRR ALVAFLGILL LTGVLIANLY NLQIVRFTDY QTRSNENRIK LVPIAPSRGI IYDRNGIPLA LNRTIYQIE MMPEKVDNVQ QTLDALRSVV DLTDDDIAAF RKERARSHRF TSIPVKTNLT EVQVARFAVN QYRFPGVEVK G YKRRYYPY GSALTHVIGY VSKINDKDVE RLNNDGKLAN YAATHDIGKL GIERYYEDVL HGQTGYEEVE VNNRGRVIRQ LK EVPPQAG HDIYLTLDLK LQQYIETLLA GSRAAVVVTD PRTGGVLALV STPSYDPNLF VDGISSKDYS ALLNDPNTPL VNR ATQGVY PPASTVKPYV AVSALSAGVI TRNTTLFDPG WWQLPGSEKR YRDWKKWGHG RLNVTRSLEE SADTFFYQVA YDMG IDRLS EWMGKFGYGH YTGIDLAEER SGNMPTREWK QKRFKKPWYQ GDTIPVGIGQ GYWTATPIQM SKALMILIND GIVKV PHLL MSTAEDGKQV PWVQPHEPPV GDIHSGYWEL AKDGMYGVAN RPNGTAHKYF ASAPYKIAAK SGTAQVFGLK ANETYN AHK IAERLRDHKL MTAFAPYNNP QVAVAMILEN GGAGPAVGTL MRQILDHIML GDNNTDLPAE NPAVAAAEDH

UniProtKB: Peptidoglycan D,D-transpeptidase MrdA

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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

Concentration0.66 mg/mL
BufferpH: 7
Component:
ConcentrationNameFormula
20.0 mMHEPES
150.0 mMSodium ChlorideNaClSodium chloride
1.0 mMTCEPtris(2-carboxyethyl)phosphine
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 11120 / Average exposure time: 2.5 sec. / Average electron dose: 58.5 e/Å2

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Image processing

Particle selectionNumber selected: 4415933
Startup modelType of model: OTHER
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.12 and 3.2) / Software - details: Local refinement / Number images used: 399000

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Atomic model buiding 1

Initial modelPDB ID:

4f0a


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-8tj3:
Structural basis of peptidoglycan synthesis by E. coli RodA-PBP2 complex

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