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- EMDB-82367: Cryo-EM map of the vitreous body collagen fibril at 4.7 angstrom -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-82367
TitleCryo-EM map of the vitreous body collagen fibril at 4.7 angstrom
Map data
Sample
  • Complex: vitreous body collagen fibrils
KeywordsCollagen / PROTEIN FIBRIL
Biological speciesSus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsLou X / Cong Y / Xu 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 mammalian vitreous body collagen fibrils
Authors: Lou X / Cong Y / Xu Y / Yan C
History
DepositionJul 20, 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_82367.png

Downloads & links

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Map

FileDownload / File: emd_82367.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.72 Å/pix.
x 512 pix.
= 878.387 Å		1.72 Å/pix.
x 512 pix.
= 878.387 Å		1.72 Å/pix.
x 512 pix.
= 878.387 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.7156 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-0.56971765 - 1.349213
Average (Standard dev.)-0.00047755943 (±0.037016746)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 878.3872 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_82367_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_82367_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_82367_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 fibrils

EntireName: vitreous body collagen fibrils
Components
  • Complex: vitreous body collagen fibrils

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Supramolecule #1: vitreous body collagen fibrils

SupramoleculeName: vitreous body collagen fibrils / 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: 2.0 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: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 140403
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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