[English] 日本語
Yorodumi
- EMDB-10799: Pentameric structure of the cellulose synthase regulator protein ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-10799
TitlePentameric structure of the cellulose synthase regulator protein BcsB from Escherichia coli
Map datacomposite map made from two experimental sharpened maps of the same sample data
Sample
  • Complex: Co-expression of Bcs subunits R, Q, A, B, E, F and G lead to the purification of a membrane complex assembly
    • Complex: Homopentameric assembly of the BcsB protein
      • Protein or peptide: Bacterial cellulose secretion regulator BcsB
KeywordsBacterial biofilms / Bacterial cellulose / Bacterial secretion system / regulator protein / SIGNALING 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 / Cyclic di-GMP-binding protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsZouhir S / Krasteva P
Funding support5 items
OrganizationGrant numberCountry
ATIP-Avenir
European Research Council (ERC)BioMatrix, ERC StG #757507
Centre National de la Recherche Scientifique (CNRS)
Institute for Integrative Biology of the Cell (I2BC)
European Institute of Chemistry and Biology (IECB)
CitationJournal: Sci Adv / Year: 2021
Title: Architecture and regulation of an enterobacterial cellulose secretion system.
Authors: Wiem Abidi / Samira Zouhir / Meryem Caleechurn / Stéphane Roche / Petya Violinova Krasteva /
Abstract: Many free-living and pathogenic enterobacteria secrete biofilm-promoting cellulose using a multicomponent, envelope-embedded Bcs secretion system under the control of intracellular second messenger c- ...Many free-living and pathogenic enterobacteria secrete biofilm-promoting cellulose using a multicomponent, envelope-embedded Bcs secretion system under the control of intracellular second messenger c-di-GMP. The molecular understanding of system assembly and cellulose secretion has been largely limited to the crystallographic studies of a distantly homologous BcsAB synthase tandem and a low-resolution reconstruction of an assembled macrocomplex that encompasses most of the inner membrane and cytosolic subunits and features an atypical layered architecture. Here, we present cryo-EM structures of the assembled Bcs macrocomplex, as well as multiple crystallographic snapshots of regulatory Bcs subcomplexes. The structural and functional data uncover the mechanism of asymmetric secretion system assembly and periplasmic crown polymerization and reveal unexpected subunit stoichiometry, multisite c-di-GMP recognition, and ATP-dependent regulation.
History
DepositionMar 27, 2020-
Header (metadata) releaseFeb 24, 2021-
Map releaseFeb 24, 2021-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 10
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 10
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6yg8
  • Surface level: 10
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10799.png

Downloads & links

-
Map

FileDownload / File: emd_10799.map.gz / Format: CCP4 / Size: 262.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcomposite map made from two experimental sharpened maps of the same sample data
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.05 Å/pix.
x 410 pix.
= 431.517 Å		1.05 Å/pix.
x 410 pix.
= 431.517 Å		1.05 Å/pix.
x 410 pix.
= 431.517 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05248 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.5 / Movie #1: 10
Minimum - Maximum-31.928823000000001 - 55.832599999999999
Average (Standard dev.)0.0006355236 (±0.9885274)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions410410410
Spacing410410410
CellA=B=C: 431.51678 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.05248048780491.05248048780491.0524804878049
M x/y/z410410410
origin x/y/z0.0000.0000.000
length x/y/z431.517431.517431.517
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ410410410
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS410410410
D min/max/mean-31.92955.8330.001

-
Supplemental data

-
Additional map: 2.9A locally refined and sharpened map used for...

Fileemd_10799_additional_1.map
Annotation2.9A locally refined and sharpened map used for the main composite map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: 3.1A average resolution sharpened map used for the main composite map

Fileemd_10799_additional_2.map
Annotation3.1A average resolution sharpened map used for the main composite map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Non sharpened map

Fileemd_10799_additional_3.map
AnnotationNon sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Non sharpened map

Fileemd_10799_additional_4.map
AnnotationNon sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Co-expression of Bcs subunits R, Q, A, B, E, F and G lead to the ...

EntireName: Co-expression of Bcs subunits R, Q, A, B, E, F and G lead to the purification of a membrane complex assembly
Components
  • Complex: Co-expression of Bcs subunits R, Q, A, B, E, F and G lead to the purification of a membrane complex assembly
    • Complex: Homopentameric assembly of the BcsB protein
      • Protein or peptide: Bacterial cellulose secretion regulator BcsB

-
Supramolecule #1: Co-expression of Bcs subunits R, Q, A, B, E, F and G lead to the ...

SupramoleculeName: Co-expression of Bcs subunits R, Q, A, B, E, F and G lead to the purification of a membrane complex assembly
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli) / Strain: 1094 / Location in cell: periplasm
Molecular weightTheoretical: 734 KDa

-
Supramolecule #2: Homopentameric assembly of the BcsB protein

SupramoleculeName: Homopentameric assembly of the BcsB protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli) / Strain: 1094 / Location in cell: periplasm

-
Macromolecule #1: Bacterial cellulose secretion regulator BcsB

MacromoleculeName: Bacterial cellulose secretion regulator BcsB / type: protein_or_peptide / ID: 1 / Details: Bacterial cellulose synthesis subunit B / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: 1094
Molecular weightTheoretical: 86.184383 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKRKLFWICA VAMGMSAFPS FMTQATPATQ PLINAEPAVA AQTEQNPQVG QVMPGVQGAD APVVAQNGPS RDVKLTFAQI APPPGSMVL RGINPNGSIE FGMRSDEVVT KAMLNLEYTP SPSLLPVQSQ LKVYLNDELM GVLPVTKEQL GKKTLAQMPI N PLFITDFN ...String:
MKRKLFWICA VAMGMSAFPS FMTQATPATQ PLINAEPAVA AQTEQNPQVG QVMPGVQGAD APVVAQNGPS RDVKLTFAQI APPPGSMVL RGINPNGSIE FGMRSDEVVT KAMLNLEYTP SPSLLPVQSQ LKVYLNDELM GVLPVTKEQL GKKTLAQMPI N PLFITDFN RVRLEFVGHY QDVCENPAST TLWLDVGRSS GLDLTYQTLN VKNDLSHFPV PFFDPRDNRT NTLPMVFAGA PD VGLQQAS AIVASWFGSR SGWRGQNFPV LYNQLPDRNA IVFATNDKRP DFLRDHPAVK APVIEMINHP QNPYVKLLVV FGR DDKDLL QAAKGIAQGN ILFRGESVVV NEVKPLLPRK PYDAPNWVRT DRPVTFGELK TYEEQLQSSG LEPAAINVSL NLPP DLYLM RSTGIDMDIN YRYTMPPVKD SSRMDISLNN QFLQSFNLSS KQEANRLLLR IPVLQGLLDG KTDVSIPALK LGATN QLRF DFEYMNPMPG GSVDNCITFQ PVQNHVVIGD DSTIDFSKYY HFIPMPDLRA FANAGFPFSR MADLSQTITV MPKAPN EAQ METLLNTVGF IGAQTGFPAI NLTVTDDGST IQGKDADIMI IGGIPDKLKD DKQIDLLVQA TESWVKTPMR QTPFPGI VP DESDRAAETR STLTSSGAMA AVIGFQSPYN DQRSVIALLA DSPRGYEMLN DAVNDSGKRA TMFGSVAVIR ESGINSLR V GDVYYVGHLP WFERLWYALA NHPILLAVLA AISVILLAWV LWRLLRIISR RRLNPDNE

UniProtKB: Cyclic di-GMP-binding protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.8 mg/mL
BufferpH: 8
Component:
ConcentrationFormula
0.02 MHEPES
0.12 MNaCl
0.005 MMgCl2
2e-06 MAppCp
2e-06 Mc-di-GMP
0.008 %LM.NPG
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.75 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 130000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

DetailsA total of 9,129 movies recorded on the CM01 Titan Krios transmission electron microscope (Thermo Fisher Scientific) at the ESRF Grenoble operated at 300 kV and equipped with a Gatan K2 Summit direct electron detector and a GIF Quantum LS imaging filter
Startup modelType of model: INSILICO MODEL / In silico model: Ab Initio model generation in cryosparc V2
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v2) / Number images used: 576455
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. V2)
Details: All 2D classification and particle curation was performed in cryoSPARC v2
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. V2)
Final 3D classificationNumber classes: 1 / Software - Name: cryoSPARC (ver. V2)
Details: Final refinement using non-uniform refinement in cryoSPARC v2, followed by density segmation and mask creation in UCSF Chimera, particle subtraction for removal of noisy/unresolved regions ...Details: Final refinement using non-uniform refinement in cryoSPARC v2, followed by density segmation and mask creation in UCSF Chimera, particle subtraction for removal of noisy/unresolved regions and local refinement of a BcsB pentamer in cryoSPARC v2.

-
Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-6yg8:
Cryo-EM structure of a BcsB pentamer in the context of an assembled Bcs 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