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- EMDB-15004: VWF tubules of D1D2 and D'A1A2A3 -

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Basic information

Entry
Database: EMDB / ID: EMD-15004
TitleVWF tubules of D1D2 and D'A1A2A3
Map data
Sample
  • Complex: VWF tubules of D1D2 and D'D3A1 domains
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 5.74 Å
AuthorsJavitt G / Fass D
Funding support Israel, 1 items
OrganizationGrant numberCountry
Israel Science Foundation2660/20 Israel
CitationJournal: Blood / Year: 2022
Title: Assembly of von Willebrand factor tubules with in vivo helical parameters requires A1 domain insertion.
Authors: Gabriel Javitt / Noa Yeshaya / Lev Khmelnitsky / Deborah Fass /
Abstract: The von Willebrand factor (VWF) glycoprotein is stored in tubular form in Weibel-Palade bodies (WPBs) before secretion from endothelial cells into the bloodstream. The organization of VWF in the ...The von Willebrand factor (VWF) glycoprotein is stored in tubular form in Weibel-Palade bodies (WPBs) before secretion from endothelial cells into the bloodstream. The organization of VWF in the tubules promotes formation of covalently linked VWF polymers and enables orderly secretion without polymer tangling. Recent studies have described the high-resolution structure of helical tubular cores formed in vitro by the D1D2 and D'D3 amino-terminal protein segments of VWF. Here we show that formation of tubules with the helical geometry observed for VWF in intracellular WPBs requires also the VWA1 (A1) domain. We reconstituted VWF tubules from segments containing the A1 domain and discovered it to be inserted between helical turns of the tubule, altering helical parameters and explaining the increased robustness of tubule formation when A1 is present. The conclusion from this observation is that the A1 domain has a direct role in VWF assembly, along with its known activity in hemostasis after secretion.
History
DepositionMay 20, 2022-
Header (metadata) releaseJul 13, 2022-
Map releaseJul 13, 2022-
UpdateJan 11, 2023-
Current statusJan 11, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15004.png

Downloads & links

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Map

FileDownload / File: emd_15004.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.24 Å
Density
Contour LevelBy AUTHOR: 0.055
Minimum - Maximum-0.061616 - 0.36619905
Average (Standard dev.)0.0036679325 (±0.023900345)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 496.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_15004_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_15004_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 : VWF tubules of D1D2 and D'D3A1 domains

EntireName: VWF tubules of D1D2 and D'D3A1 domains
Components
  • Complex: VWF tubules of D1D2 and D'D3A1 domains

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Supramolecule #1: VWF tubules of D1D2 and D'D3A1 domains

SupramoleculeName: VWF tubules of D1D2 and D'D3A1 domains / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 5.9
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 1.5 sec. / Average electron dose: 41.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 27.579 Å
Applied symmetry - Helical parameters - Δ&Phi: 82.600 °
Applied symmetry - Helical parameters - Axial symmetry: D1 (2x1 fold dihedral)
Resolution.type: BY AUTHOR / Resolution: 5.74 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 101153
Startup modelType of model: INSILICO MODEL / In silico model: Helical Ab initio
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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