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- EMDB-65682: Averaged map of fibroin in silkworm silk -

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Basic information

Entry
Database: EMDB / ID: EMD-65682
TitleAveraged map of fibroin in silkworm silk
Map data
Sample
  • Organelle or cellular component: fibroin extracted from silk glands of silkworm
Keywordssilk fibroin nanofibril / PROTEIN FIBRIL
Biological speciesBombyx mori (domestic silkworm)
Methodsubtomogram averaging / cryo EM / Resolution: 20.4 Å
AuthorsHaonan Z / Kai S / Yan L / Ping Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32302816 China
CitationJournal: Nat Commun / Year: 2026
Title: Cryo-ET comparison of the hierarchical ultrastructure of silkworm, spider, and artificial silk fibers.
Authors: Kai Song / Haonan Zhang / Xueli Zhang / Yan Li / Ping Zhu /
Abstract: Spider and silkworm silks are renowned for their exceptional mechanical properties, which arises from their ultrastructural organization. However, this architecture remains incompletely understood. ...Spider and silkworm silks are renowned for their exceptional mechanical properties, which arises from their ultrastructural organization. However, this architecture remains incompletely understood. Here, we apply cryo-electron tomography to examine the hierarchical organization of silkworm, spider, and artificial silks. In silkworm silk, we observe nanofibrils of ~3.6 nm in diameter, interconnected by abundant bridges and representing the smallest fibrillar features currently accessible by cryo-ET. These nanofibrils align with the fiber axis and are organized into a herringbone pattern, with stacked layers building the micron-scale filament. Spider silk displays densely packed nanofibrils with near-perfect axial alignment and minimal voids. In contrast, silkworm silk shows regionally heterogeneous gaps, whereas artificial silk lacks the ordered packing characteristic of natural materials. These observations provide a structural basis for understanding silk formation and may guide future biomimetic fiber design.
History
DepositionAug 4, 2025-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65682.png

Downloads & links

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Map

FileDownload / File: emd_65682.map.gz / Format: CCP4 / Size: 2.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
2.73 Å/pix.
x 90 pix.
= 245.7 Å		2.73 Å/pix.
x 90 pix.
= 245.7 Å		2.73 Å/pix.
x 90 pix.
= 245.7 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.579
Minimum - Maximum-1.0797292 - 1.3017906
Average (Standard dev.)0.0013195036 (±0.17289488)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions909090
Spacing909090
CellA=B=C: 245.7 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65682_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65682_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_65682_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 : fibroin extracted from silk glands of silkworm

EntireName: fibroin extracted from silk glands of silkworm
Components
  • Organelle or cellular component: fibroin extracted from silk glands of silkworm

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Supramolecule #1: fibroin extracted from silk glands of silkworm

SupramoleculeName: fibroin extracted from silk glands of silkworm / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Bombyx mori (domestic silkworm)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
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 K2 SUMMIT (4k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 5.5 µm / Calibrated defocus min: 3.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.5 µm / Nominal defocus min: 3.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 20.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number subtomograms used: 404
ExtractionNumber tomograms: 7 / Number images used: 16191 / Software - Name: crYOLO
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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