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- EMDB-80346: Cryo-EM map of the S2 inner region for the vitreous body collagen... -

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Basic information

Entry
Database: EMDB / ID: EMD-80346
TitleCryo-EM map of the S2 inner region for the vitreous body collagen fibril at 3.18 angstrom
Map data
Sample
  • Complex: Vitreous body collagen fibril
KeywordsType II collagen / Type V/XI collagen / Type IX collagen / Opticin / Glycosylation / PROTEIN FIBRIL
Biological speciesSus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsLou X / Cong Y / Xu Y / Liu Y / Yan C
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32341016 China
CitationJournal: To Be Published
Title: The molecular architecture of a mammalian collagen fibril
Authors: Lou X / Cong Y / Xu Y / Liu Y / Yan C
History
DepositionApr 16, 2026-
Header (metadata) releaseAug 5, 2026-
Map releaseAug 5, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_80346.png

Downloads & links

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Map

FileDownload / File: emd_80346.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 360 pix.
= 395.28 Å		1.1 Å/pix.
x 360 pix.
= 395.28 Å		1.1 Å/pix.
x 360 pix.
= 395.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.098 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.045
Minimum - Maximum-0.28211167 - 0.5400849
Average (Standard dev.)0.0010940843 (±0.012351222)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 395.28003 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_80346_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_80346_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_80346_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 : Vitreous body collagen fibril

EntireName: Vitreous body collagen fibril
Components
  • Complex: Vitreous body collagen fibril

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Supramolecule #1: Vitreous body collagen fibril

SupramoleculeName: Vitreous body collagen fibril / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Sus scrofa (pig)

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 596646
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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