[English] 日本語
Yorodumi
- EMDB-50567: Cryo-EM structure of the BcsB hexameric crown from the E. coli ce... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-50567
TitleCryo-EM structure of the BcsB hexameric crown from the E. coli cellulose secretion macrocomplex
Map dataDeep EMhancer sharpened map of the locally refined hexameric BcsB periplasmic crown of the E. coli Bcs cellulose secretion macrocomplex
Sample
  • Complex: Locally refined hexameric BcsB periplasmic crown from the E. coli cellulose secretion system
    • Protein or peptide: Cyclic di-GMP-binding protein
KeywordsBacterial cellulose secretion / MEMBRANE PROTEIN
Function / homologyCellulose synthase, subunit B / Cellulose synthase BcsB, bacterial / Bacterial cellulose synthase subunit / cellulose biosynthetic process / UDP-alpha-D-glucose metabolic process / plasma membrane / Cyclic di-GMP-binding protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.35 Å
AuthorsAnso I / Krasteva PV
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)757507European Union
CitationJournal: Nat Commun / Year: 2024
Title: Structural basis for synthase activation and cellulose modification in the E. coli Type II Bcs secretion system.
Authors: Itxaso Anso / Samira Zouhir / Thibault Géry Sana / Petya Violinova Krasteva /
Abstract: Bacterial cellulosic polymers constitute a prevalent class of biofilm matrix exopolysaccharides that are synthesized by several types of bacterial cellulose secretion (Bcs) systems, which include ...Bacterial cellulosic polymers constitute a prevalent class of biofilm matrix exopolysaccharides that are synthesized by several types of bacterial cellulose secretion (Bcs) systems, which include conserved cyclic diguanylate (c-di-GMP)-dependent cellulose synthase modules together with diverse accessory subunits. In E. coli, the biogenesis of phosphoethanolamine (pEtN)-modified cellulose relies on the BcsRQABEFG macrocomplex, encompassing inner-membrane and cytosolic subunits, and an outer membrane porin, BcsC. Here, we use cryogenic electron microscopy to shed light on the molecular mechanisms of BcsA-dependent recruitment and stabilization of a trimeric BcsG pEtN-transferase for polymer modification, and a dimeric BcsF-dependent recruitment of an otherwise cytosolic BcsERQ regulatory complex. We further demonstrate that BcsE, a secondary c-di-GMP sensor, can remain dinucleotide-bound and retain the essential-for-secretion BcsRQ partners onto the synthase even in the absence of direct c-di-GMP-synthase complexation, likely lowering the threshold for c-di-GMP-dependent synthase activation. Such activation-by-proxy mechanism could allow Bcs secretion system activity even in the absence of substantial intracellular c-di-GMP increase, and is reminiscent of other widespread synthase-dependent polysaccharide secretion systems where dinucleotide sensing and/or synthase stabilization are carried out by key co-polymerase subunits.
History
DepositionJun 7, 2024-
Header (metadata) releaseOct 16, 2024-
Map releaseOct 16, 2024-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_50567.png

Downloads & links

-
Map

FileDownload / File: emd_50567.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeep EMhancer sharpened map of the locally refined hexameric BcsB periplasmic crown of the E. coli Bcs cellulose secretion macrocomplex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 500 pix.
= 419.5 Å		0.84 Å/pix.
x 500 pix.
= 419.5 Å		0.84 Å/pix.
x 500 pix.
= 419.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.839 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.0018597553 - 1.456673
Average (Standard dev.)0.00082765333 (±0.020536587)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 419.5 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_50567_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: CryoSPARC sharpened map of the locally refined hexameric...

Fileemd_50567_additional_1.map
AnnotationCryoSPARC sharpened map of the locally refined hexameric BcsB periplasmic crown of the E. coli Bcs cellulose secretion macrocomplex (B-factor 80)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Unsharpened map of the locally refined hexameric BcsB...

Fileemd_50567_additional_2.map
AnnotationUnsharpened map of the locally refined hexameric BcsB periplasmic crown of the E. coli Bcs cellulose secretion macrocomplex (B-factor 80)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half-map of the locally refined hexameric BcsB periplasmic...

Fileemd_50567_half_map_1.map
AnnotationHalf-map of the locally refined hexameric BcsB periplasmic crown of the E. coli Bcs cellulose secretion macrocomplex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half-map of the locally refined hexameric BcsB periplasmic...

Fileemd_50567_half_map_2.map
AnnotationHalf-map of the locally refined hexameric BcsB periplasmic crown of the E. coli Bcs cellulose secretion macrocomplex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Locally refined hexameric BcsB periplasmic crown from the E. coli...

EntireName: Locally refined hexameric BcsB periplasmic crown from the E. coli cellulose secretion system
Components
  • Complex: Locally refined hexameric BcsB periplasmic crown from the E. coli cellulose secretion system
    • Protein or peptide: Cyclic di-GMP-binding protein

-
Supramolecule #1: Locally refined hexameric BcsB periplasmic crown from the E. coli...

SupramoleculeName: Locally refined hexameric BcsB periplasmic crown from the E. coli cellulose secretion system
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Local refinement in the context of an assembled macrocomplex
Source (natural)Organism: Escherichia coli (E. coli) / Strain: 1094
Molecular weightTheoretical: 990 KDa

-
Macromolecule #1: Cyclic di-GMP-binding protein

MacromoleculeName: Cyclic di-GMP-binding protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: 1094
Molecular weightTheoretical: 83.345844 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: TPATQPLINA EPAVAAQTEQ NPQVGQVMPG VQGADAPVVA QNGPSRDVKL TFAQIAPPPG SMVLRGINPN GSIEFGMRSD EVVTKAMLN LEYTPSPSLL PVQSQLKVYL NDELMGVLPV TKEQLGKKTL AQMPINPLFI TDFNRVRLEF VGHYQDVCEN P ASTTLWLD ...String:
TPATQPLINA EPAVAAQTEQ NPQVGQVMPG VQGADAPVVA QNGPSRDVKL TFAQIAPPPG SMVLRGINPN GSIEFGMRSD EVVTKAMLN LEYTPSPSLL PVQSQLKVYL NDELMGVLPV TKEQLGKKTL AQMPINPLFI TDFNRVRLEF VGHYQDVCEN P ASTTLWLD VGRSSGLDLT YQTLNVKNDL SHFPVPFFDP RDNRTNTLPM VFAGAPDVGL QQASAIVASW FGSRSGWRGQ NF PVLYNQL PDRNAIVFAT NDKRPDFLRD HPAVKAPVIE MINHPQNPYV KLLVVFGRDD KDLLQAAKGI AQGNILFRGE SVV VNEVKP LLPRKPYDAP NWVRTDRPVT FGELKTYEEQ LQSSGLEPAA INVSLNLPPD LYLMRSTGID MDINYRYTMP PVKD SSRMD ISLNNQFLQS FNLSSKQEAN RLLLRIPVLQ GLLDGKTDVS IPALKLGATN QLRFDFEYMN PMPGGSVDNC ITFQP VQNH VVIGDDSTID FSKYYHFIPM PDLRAFANAG FPFSRMADLS QTITVMPKAP NEAQMETLLN TVGFIGAQTG FPAINL TVT DDGSTIQGKD ADIMIIGGIP DKLKDDKQID LLVQATESWV KTPMRQTPFP GIVPDESDRA AETRSTLTSS GAMAAVI GF QSPYNDQRSV IALLADSPRG YEMLNDAVND SGKRATMFGS VAVIRESGIN SLRVGDVYYV GHLPWFERLW YALANHPI L LAVLAAISVI LLAWVLWRLL RIISRRRLNP DNE

UniProtKB: Cyclic di-GMP-binding protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2 mg/mL
BufferpH: 8
Details: 120 mM NaCL 20 mM HEPES pH8 5 mM MgCl2 10 uM ApppCp 4 uM c-di-GMP 0.01% LM-NPG
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K
DetailsPurified Bcs macrocomplex with stoichiometry BcsA-BcsB6-BcsR2-BcsQ2-BcsE2-BcsF2-BcsG3

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 2 / Number real images: 20022 / Average electron dose: 49.35 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

DetailsGIF Quantum LS
Particle selectionNumber selected: 1359795
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6yg8

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.35 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4) / Number images used: 834077
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. V4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. v4)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

6yg8


Chain - Chain ID: C / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9fmt:
Cryo-EM structure of the BcsB hexameric crown from the E. coli cellulose secretion macrocomplex

+
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