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- EMDB-62658: Cryo-EM structure of amyloid peptide-silk block protein fibril, Type 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-62658
TitleCryo-EM structure of amyloid peptide-silk block protein fibril, Type 1
Map data
Sample
  • Organelle or cellular component: Cryo-EM structure of amyloid peptide-silk block protein fibril, Type 1
    • Protein or peptide: Major ampullate spidroin 1
KeywordsPROTEIN FIBRIL / amyloid / silk
Biological speciesLatrodectus hesperus (western black widow)
Methodhelical reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsZhang YL / Dai B
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of amyloid peptide-silk block protein fibril, Type 1
Authors: Zhang YL / Dai B
History
DepositionDec 10, 2024-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62658.png

Downloads & links

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Map

FileDownload / File: emd_62658.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 288 pix.
= 239.04 Å		0.83 Å/pix.
x 288 pix.
= 239.04 Å		0.83 Å/pix.
x 288 pix.
= 239.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0114
Minimum - Maximum-0.0437102 - 0.069383204
Average (Standard dev.)0.0002712656 (±0.0025269617)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 239.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_62658_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_62658_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of amyloid peptide-silk block protein fibril, Type 1

EntireName: Cryo-EM structure of amyloid peptide-silk block protein fibril, Type 1
Components
  • Organelle or cellular component: Cryo-EM structure of amyloid peptide-silk block protein fibril, Type 1
    • Protein or peptide: Major ampullate spidroin 1

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Supramolecule #1: Cryo-EM structure of amyloid peptide-silk block protein fibril, Type 1

SupramoleculeName: Cryo-EM structure of amyloid peptide-silk block protein fibril, Type 1
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Latrodectus hesperus (western black widow)

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Macromolecule #1: Major ampullate spidroin 1

MacromoleculeName: Major ampullate spidroin 1 / type: protein_or_peptide / ID: 1
Details: The protein that forms the fibril is a block protein composed of 16 repetitive motifs. Due to the inability to precisely identify which specific repetitive motif contributes to the core ...Details: The protein that forms the fibril is a block protein composed of 16 repetitive motifs. Due to the inability to precisely identify which specific repetitive motif contributes to the core sequence of the fibril, it is not possible to directly correlate the amino acid sequence of each chain with a particular repetitive motif of the protein. Based on the arrangement of these repetitive motifs, we ultimately constructed the atomic model.
Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Latrodectus hesperus (western black widow)
Molecular weightTheoretical: 48.40532 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAKTKGTASG RGGLGGQGAG GDVIEVGGAG QGGYGGLGSQ GTSGRGGLGG QGAGGDVIEV GGAGQGGYGG LGSQGTSGRG GLGGQGAGG DVIEVGGAGQ GGYGGLGSQG TSGRGGLGGQ GAGGDVIEVG GAGQGGYGGL GSQGTSGRGG LGGQGAGGDV I EVGGAGQG ...String:
MAKTKGTASG RGGLGGQGAG GDVIEVGGAG QGGYGGLGSQ GTSGRGGLGG QGAGGDVIEV GGAGQGGYGG LGSQGTSGRG GLGGQGAGG DVIEVGGAGQ GGYGGLGSQG TSGRGGLGGQ GAGGDVIEVG GAGQGGYGGL GSQGTSGRGG LGGQGAGGDV I EVGGAGQG GYGGLGSQGT SGRGGLGGQG AGGDVIEVGG AGQGGYGGLG SQGTSGRGGL GGQGAGGDVI EVGGAGQGGY GG LGSQGTS GRGGLGGQGA GGDVIEVGGA GQGGYGGLGS QGTSGRGGLG GQGAGGDVIE VGGAGQGGYG GLGSQGTSGR GGL GGQGAG GDVIEVGGAG QGGYGGLGSQ GTSGRGGLGG QGAGGDVIEV GGAGQGGYGG LGSQGTSGRG GLGGQGAGGD VIEV GGAGQ GGYGGLGSQG TSGRGGLGGQ GAGGDVIEVG GAGQGGYGGL GSQGTSGRGG LGGQGAGGDV IEVGGAGQGG YGGLG SQGT SGRGGLGGQG AGGDVIEVGG AGQGGYGGLG SQGTSGRGGL GGQGAGGDVI EVGGAGQGGY GGLGSQGTSS GHHHHH HHH HH

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (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: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 2.35 Å
Applied symmetry - Helical parameters - Δ&Phi: -177.57 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 15847
CTF correctionType: NONE
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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