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- EMDB-32692: Cryo-EM structure of VWF D'D3 dimer -

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Basic information

Entry
Database: EMDB / ID: EMD-32692
TitleCryo-EM structure of VWF D'D3 dimer
Map data
Sample
  • Complex: VWF D'D3 dimer
Keywordsblood / VWF / von Willebrand factor / von Willebrand disease / blood coagulation / blood clotting / multimer assembly / VWF assembly / D'D3 domain / D1D2 domain / D'D3 dimer / D1D2 Dimer / VWF Tube / repeating unit
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.8 Å
AuthorsZeng JW / Shu ZM / Zhou AW
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2016YFA0501103 China
Citation
Journal: Blood / Year: 2022
Title: Structural basis of von Willebrand factor multimerization and tubular storage.
Authors: Jianwei Zeng / Zimei Shu / Qian Liang / Jing Zhang / Wenman Wu / Xuefeng Wang / Aiwu Zhou /
Abstract: The von Willebrand factor (VWF) propeptide (domains D1D2) is essential for the assembly of VWF multimers and its tubular storage in Weibel-Palade bodies. However, detailed molecular mechanism ...The von Willebrand factor (VWF) propeptide (domains D1D2) is essential for the assembly of VWF multimers and its tubular storage in Weibel-Palade bodies. However, detailed molecular mechanism underlying this propeptide dependence is unclear. Here, we prepared Weibel-Palade body-like tubules using the N-terminal fragment of VWF and solved the cryo-electron microscopy structures of the tubule at atomic resolution. Detailed structural and biochemical analysis indicate that the propeptide forms a homodimer at acidic pH through the D2:D2 binding interface and then recruits 2 D'D3 domains, forming an intertwined D1D2D'D3 homodimer in essence. Stacking of these homodimers by the intermolecular D1:D2 interfaces brings 2 D3 domains face-to-face and facilitates their disulfide linkages and multimerization of VWF. Sequential stacking of these homodimers leads to a right-hand helical tubule for VWF storage. The clinically identified VWF mutations in the propeptide disrupted different steps of the assembling process, leading to diminished VWF multimers in von Willebrand diseases (VWD). Overall, these results indicate that the propeptide serves as a pH-sensing template for VWF multimerization and tubular storage. This sheds light on delivering normal propeptide as a template to rectify the defects in multimerization of VWD mutants.
#1: Journal: to be published
Title: Structural mechanism of VWF D'D3 dimer formation
Authors: Shu ZM / Zeng JW / Xia L / Cai HY / Zhou AW
History
DepositionJan 24, 2022-
Header (metadata) releaseMar 9, 2022-
Map releaseMar 9, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_32692.png

Downloads & links

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Map

FileDownload / File: emd_32692.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.7394 Å
Density
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.05456563 - 0.09372197
Average (Standard dev.)0.00012781526 (±0.0024051783)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 278.30402 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.73941.73941.7394
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z278.304278.304278.304
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.0550.0940.000

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Supplemental data

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Sample components

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Entire : VWF D'D3 dimer

EntireName: VWF D'D3 dimer
Components
  • Complex: VWF D'D3 dimer

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Supramolecule #1: VWF D'D3 dimer

SupramoleculeName: VWF D'D3 dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / 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

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 377673
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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