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- EMDB-16431: Pontibacter korlensis curli subunit CsgA -

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Basic information

Entry
Database: EMDB / ID: EMD-16431
TitlePontibacter korlensis curli subunit CsgA
Map data
Sample
  • Complex: curli fiber of Pontibacteri korlensis CsgA
    • Protein or peptide: Curlin associated repeat-containing protein
Keywordsbacterial functional amyloid / PROTEIN FIBRIL
Function / homologyCurlin associated / Curlin associated repeat / pilus / cell adhesion / Curlin associated repeat-containing protein
Function and homology information
Biological speciesPontibacter korlensis (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 7.6 Å
AuthorsRemaut H / Sleutel M / Pradhan B
Funding support Belgium, European Union, 3 items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G0G0818N Belgium
Research Foundation - Flanders (FWO)G043021N Belgium
European Research Council (ERC)649082European Union
CitationJournal: Nat Commun / Year: 2023
Title: Structural analysis and architectural principles of the bacterial amyloid curli.
Authors: Mike Sleutel / Brajabandhu Pradhan / Alexander N Volkov / Han Remaut /
Abstract: Two decades have passed since the initial proposition that amyloids are not only (toxic) byproducts of an unintended aggregation cascade, but that they can also be produced by an organism to serve a ...Two decades have passed since the initial proposition that amyloids are not only (toxic) byproducts of an unintended aggregation cascade, but that they can also be produced by an organism to serve a defined biological function. That revolutionary idea was borne out of the realization that a large fraction of the extracellular matrix that holds Gram-negative cells into a persistent biofilm is composed of protein fibers (curli; tafi) with cross-β architecture, nucleation-dependent polymerization kinetics and classic amyloid tinctorial properties. The list of proteins shown to form so-called functional amyloid fibers in vivo has greatly expanded over the years, but detailed structural insights have not followed at a similar pace in part due to the associated experimental barriers. Here we combine extensive AlphaFold2 modelling and cryo-electron transmission microscopy to propose an atomic model of curli protofibrils, and their higher modes of organization. We uncover an unexpected structural diversity of curli building blocks and fibril architectures. Our results allow for a rationalization of the extreme physico-chemical robustness of curli, as well as earlier observations of inter-species curli promiscuity, and should facilitate further engineering efforts to expand the repertoire of curli-based functional materials.
History
DepositionJan 5, 2023-
Header (metadata) releaseJun 28, 2023-
Map releaseJun 28, 2023-
UpdateJun 28, 2023-
Current statusJun 28, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16431.png

Downloads & links

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Map

FileDownload / File: emd_16431.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.49 Å/pix.
x 150 pix.
= 222.75 Å		1.49 Å/pix.
x 150 pix.
= 222.75 Å		1.49 Å/pix.
x 150 pix.
= 222.75 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.485 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0175
Minimum - Maximum-0.047862876 - 0.07084798
Average (Standard dev.)0.000025754442 (±0.0031930818)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions150150150
Spacing150150150
CellA=B=C: 222.75 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_16431_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_16431_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : curli fiber of Pontibacteri korlensis CsgA

EntireName: curli fiber of Pontibacteri korlensis CsgA
Components
  • Complex: curli fiber of Pontibacteri korlensis CsgA
    • Protein or peptide: Curlin associated repeat-containing protein

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Supramolecule #1: curli fiber of Pontibacteri korlensis CsgA

SupramoleculeName: curli fiber of Pontibacteri korlensis CsgA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Sample is generated by in vitro polymerisation of Pontibacter korlensis Csga subunits
Source (natural)Organism: Pontibacter korlensis (bacteria)

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Macromolecule #1: Curlin associated repeat-containing protein

MacromoleculeName: Curlin associated repeat-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pontibacter korlensis (bacteria)
Molecular weightTheoretical: 38.033785 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: QGTTSSATTS QTGNTNTAVI DQVGGLNNSA EASQAGDGNV ATVTQAEGMD NAVYIDQVGL TNTATVLQEG GLDNDADVDQ DGDLNVAYI WQNLGEDNDA DIDQDGTLND AAIEQDGGED NDADIDQDGS ENAAYVGQTG GEDNDADIDQ DGTFNNAYIG Q FGGEDNEA ...String:
QGTTSSATTS QTGNTNTAVI DQVGGLNNSA EASQAGDGNV ATVTQAEGMD NAVYIDQVGL TNTATVLQEG GLDNDADVDQ DGDLNVAYI WQNLGEDNDA DIDQDGTLND AAIEQDGGED NDADIDQDGS ENAAYVGQTG GEDNDADIDQ DGTFNNAYIG Q FGGEDNEA DLDQDGDANY AAILQDGGED NDADIDQDGT NNWAETNQIQ GNDNDVEVDQ DGSDNIAEVW QMHGEDNEAN VD QDGDLNN AYILQEGGMN NLADVHQNGV SNTAEIYQYG GMDNEAYLIQ DGDMHTGVIT QSGDGANYAE LNQMGLMNTG SIT QDGMGN SAITSQGGSM NMSTVTQSGT GNISLVNQHG GHHHHHH

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 6 / Details: 15 mM MES pH 6.0
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: GATAN CRYOPLUNGE 3

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 60000
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 4455 / Average electron dose: 64.66 e/Å2

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Image processing

Segment selectionNumber selected: 1817890 / Software - Name: crYOLO
Details: 1000 filaments were manually boxed using e2helixboxer.py of the EMAN2 package and used as a training dataset for SPHIRE-crYOLO.
Startup modelType of model: OTHER / Details: cylinder of 4nm
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.1)
Final reconstructionApplied symmetry - Helical parameters - Δz: 72.0 Å
Applied symmetry - Helical parameters - Δ&Phi: 180 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 7.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 64138
FSC plot (resolution estimation)

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