[English] 日本語
Yorodumi
- EMDB-23482: CryoEM structure of Escherichia coli PBP1b -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-23482
TitleCryoEM structure of Escherichia coli PBP1b
Map dataLocScale sharpened final map.
Sample
  • Complex: Escherichia coli PBP1b in SMA
    • Protein or peptide: Penicillin-binding protein 1B
KeywordsPenicillin binding protein / glycosyltransferase / transpeptidase / TRANSFERASE / HYDROLASE
Function / homology
Function and homology information


peptidoglycan glycosyltransferase / positive regulation of bipolar cell growth / cell wall repair / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / peptidoglycan-based cell wall / regulation of cell shape ...peptidoglycan glycosyltransferase / positive regulation of bipolar cell growth / cell wall repair / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / peptidoglycan-based cell wall / regulation of cell shape / outer membrane-bounded periplasmic space / response to antibiotic / proteolysis / membrane / plasma membrane
Similarity search - Function
Penicillin-binding protein 1B / Bifunctional transglycosylase second domain / Transglycosylase PBP1b, N-terminal transmembrane domain / Transmembrane domain of transglycosylase PBP1 at N-terminal / Bifunctional transglycosylase second domain / Glycosyl transferase, family 51 / Penicillin binding protein transglycosylase domain / Transglycosylase / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain ...Penicillin-binding protein 1B / Bifunctional transglycosylase second domain / Transglycosylase PBP1b, N-terminal transmembrane domain / Transmembrane domain of transglycosylase PBP1 at N-terminal / Bifunctional transglycosylase second domain / Glycosyl transferase, family 51 / Penicillin binding protein transglycosylase domain / Transglycosylase / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Penicillin-binding protein 1B
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Escherichia coli (strain K12) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsCaveney NA / Workman SD
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Nat Commun / Year: 2021
Title: CryoEM structure of the antibacterial target PBP1b at 3.3 Å resolution.
Authors: Nathanael A Caveney / Sean D Workman / Rui Yan / Claire E Atkinson / Zhiheng Yu / Natalie C J Strynadka /
Abstract: The pathway for the biosynthesis of the bacterial cell wall is one of the most prolific antibiotic targets, exemplified by the widespread use of β-lactam antibiotics. Despite this, our structural ...The pathway for the biosynthesis of the bacterial cell wall is one of the most prolific antibiotic targets, exemplified by the widespread use of β-lactam antibiotics. Despite this, our structural understanding of class A penicillin binding proteins, which perform the last two steps in this pathway, is incomplete due to the inherent difficulty in their crystallization and the complexity of their substrates. Here, we determine the near atomic resolution structure of the 83 kDa class A PBP from Escherichia coli, PBP1b, using cryogenic electron microscopy and a styrene maleic acid anhydride membrane mimetic. PBP1b, in its apo form, is seen to exhibit a distinct conformation in comparison to Moenomycin-bound crystal structures. The work herein paves the way for the use of cryoEM in structure-guided antibiotic development for this notoriously difficult to crystalize class of proteins and their complex substrates.
History
DepositionFeb 13, 2021-
Header (metadata) releaseMay 26, 2021-
Map releaseMay 26, 2021-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.12
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.12
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7lq6
  • Surface level: 0.12
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23482.png

Downloads & links

-
Map

FileDownload / File: emd_23482.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocScale sharpened final map.
Voxel sizeX=Y=Z: 0.844 Å
Density
Contour LevelBy AUTHOR: 0.12 / Movie #1: 0.12
Minimum - Maximum-0.16028728 - 0.6042858
Average (Standard dev.)0.00049721263 (±0.009073252)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 324.096 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8440.8440.844
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z324.096324.096324.096
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.1600.6040.000

-
Supplemental data

-
Half map: Half-map 2.

Fileemd_23482_half_map_1.map
AnnotationHalf-map 2.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half-map 1.

Fileemd_23482_half_map_2.map
AnnotationHalf-map 1.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Escherichia coli PBP1b in SMA

EntireName: Escherichia coli PBP1b in SMA
Components
  • Complex: Escherichia coli PBP1b in SMA
    • Protein or peptide: Penicillin-binding protein 1B

-
Supramolecule #1: Escherichia coli PBP1b in SMA

SupramoleculeName: Escherichia coli PBP1b in SMA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 83 KDa

-
Macromolecule #1: Penicillin-binding protein 1B

MacromoleculeName: Penicillin-binding protein 1B / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: peptidoglycan glycosyltransferase
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 83.280352 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: KPRGKRGWLW LLLKLAIVFA VLIAIYGVYL DQKIRSRIDG KVWQLPAAVY GRMVNLEPDM TISKNEMVKL LEATQYRQVS KMTRPGEFT VQANSIEMIR RPFDFPDSKE GQVRARLTFD GDHLATIVNM ENNRQFGFFR LDPRLITMIS SPNGEQRLFV P RSGFPDLL ...String:
KPRGKRGWLW LLLKLAIVFA VLIAIYGVYL DQKIRSRIDG KVWQLPAAVY GRMVNLEPDM TISKNEMVKL LEATQYRQVS KMTRPGEFT VQANSIEMIR RPFDFPDSKE GQVRARLTFD GDHLATIVNM ENNRQFGFFR LDPRLITMIS SPNGEQRLFV P RSGFPDLL VDTLLATEDR HFYEHDGISL YSIGRAVLAN LTAGRTVQGA STLTQQLVKN LFLSSERSYW RKANEAYMAL IM DARYSKD RILELYMNEV YLGQSGDNEI RGFPLASLYY FGRPVEELSL DQQALLVGMV KGASIYNPWR NPKLALERRN LVL RLLQQQ QIIDQELYDM LSARPLGVQP RGGVISPQPA FMQLVRQELQ AKLGDKVKDL SGVKIFTTFD SVAQDAAEKA AVEG IPALK KQRKLSDLET AIVVVDRFSG EVRAMVGGSE PQFAGYNRAM QARRSIGSLA KPATYLTALS QPKIYRLNTW IADAP IALR QPNGQVWSPQ NDDRRYSESG RVMLVDALTR SMNVPTVNLG MALGLPAVTE TWIKLGVPKD QLHPVPAMLL GALNLT PIE VAQAFQTIAS GGNRAPLSAL RSVIAEDGKV LYQSFPQAER AVPAQAAYLT LWTMQQVVQR GTGRQLGAKY PNLHLAG KT GTTNNNVDTW FAGIDGSTVT ITWVGRDNNQ PTKLYGASGA MSIYQRYLAN QTPTPLNLVP PEDIADMGVD YDGNFVCS G GMRILPVWTS DPQSLCQQSE MQQQPS

UniProtKB: Penicillin-binding protein 1B

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.125 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: 3 blot force, 3 second blot.

-
Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 105000 / Illumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: RELION, cryoSPARC) / Number images used: 462997
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more