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- EMDB-50567: Cryo-EM structure of the BcsB hexameric crown from the E. coli ce... -

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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: Anso I / Zouhir S / Sana TG / Krasteva PV
History
DepositionJun 7, 2024-
Header (metadata) releaseOct 16, 2024-
Map releaseOct 16, 2024-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50567.png

Downloads & links

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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 °

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Supplemental data

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Mask #1

Fileemd_50567_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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)

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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)

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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)

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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)

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Sample components

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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

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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

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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

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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

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

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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

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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)

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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

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