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- EMDB-34392: Cryo-EM structure of Abeta2 fibril polymorph1 -

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Basic information

Entry
Database: EMDB / ID: EMD-34392
TitleCryo-EM structure of Abeta2 fibril polymorph1
Map data
Sample
  • Organelle or cellular component: peptide self-assembled antimicrobial fibrils
    • Protein or peptide: peptide self-assembled antimicrobial fibrils
  • Ligand: water
Keywordsantimicrobial fibrils / amyloid / ANTIMICROBIAL PROTEIN
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 2.35 Å
AuthorsXia WC / Zhang MM / Liu C
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chem Sci / Year: 2023
Title: Engineering of antimicrobial peptide fibrils with feedback degradation of bacterial-secreted enzymes.
Authors: Fenghua Wang / Wencheng Xia / Mingming Zhang / Rongrong Wu / Xiaolu Song / Yun Hao / Yonghai Feng / Liwei Zhang / Dan Li / Wenyan Kang / Cong Liu / Lei Liu /
Abstract: Proteins and peptides can assemble into functional amyloid fibrils with distinct architectures. These amyloid fibrils can fulfil various biological functions in living organisms, and then be degraded. ...Proteins and peptides can assemble into functional amyloid fibrils with distinct architectures. These amyloid fibrils can fulfil various biological functions in living organisms, and then be degraded. By incorporating an amyloidogenic segment and enzyme-cleavage segment together, we designed a peptide (enzyme-cleavage amyloid peptides (EAP))-based functional fibril which could be degraded specifically by gelatinase. To gain molecular insights into the assembly and degradation of EAP fibrils, we determined the atomic structure of the EAP fibril using cryo-electron microscopy. The amyloidogenic segment of EAP adopted a β-strand conformation and mediated EAP-fibril formation mainly steric zipper-like interactions. The enzyme-cleavage segment was partially involved in self-assembly, but also exhibited high flexibility in the fibril structure, with accessibility to gelatinase binding and degradation. Moreover, we applied the EAP fibril as a tunable scaffold for developing degradable self-assembled antimicrobial fibrils (SANs) by integrating melittin and EAP together. SANs exhibited superior activity for killing bacteria, and significantly improved the stability and biocompatibility of melittin. SANs were eliminated automatically by the gelatinase secreted from targeted bacteria. Our work provides a new strategy for rational design of functional fibrils with a feedback regulatory loop for optimizing the biocompatibility and biosafety of designed fibrils. Our work may aid further developments of "smart" peptide-based biomaterials for biomedical applications.
History
DepositionSep 26, 2022-
Header (metadata) releaseSep 20, 2023-
Map releaseSep 20, 2023-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34392.png

Downloads & links

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Map

FileDownload / File: emd_34392.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.015
Minimum - Maximum-0.04726665 - 0.07774087
Average (Standard dev.)0.00055587414 (±0.0037580356)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 298.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_34392_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_34392_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : peptide self-assembled antimicrobial fibrils

EntireName: peptide self-assembled antimicrobial fibrils
Components
  • Organelle or cellular component: peptide self-assembled antimicrobial fibrils
    • Protein or peptide: peptide self-assembled antimicrobial fibrils
  • Ligand: water

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Supramolecule #1: peptide self-assembled antimicrobial fibrils

SupramoleculeName: peptide self-assembled antimicrobial fibrils / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: peptide self-assembled antimicrobial fibrils

MacromoleculeName: peptide self-assembled antimicrobial fibrils / type: protein_or_peptide / ID: 1 / Number of copies: 52 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.083346 KDa
SequenceString:
GPLGMLGGVV IA

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 20 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 2.407 Å
Applied symmetry - Helical parameters - Δ&Phi: 179.539 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.35 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 279380
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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