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- EMDB-13541: VWF Tubules of D1D2D'D3 domains -

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Basic information

Entry
Database: EMDB / ID: EMD-13541
TitleVWF Tubules of D1D2D'D3 domains
Map data
Sample
  • Complex: 2 beads from a VWF tubule of domains D1D2D'D3
    • Protein or peptide: von Willebrand factor
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM IONCalcium
  • Ligand: water
Function / homology
Function and homology information


Weibel-Palade body / Defective F8 binding to von Willebrand factor / hemostasis / Platelet Adhesion to exposed collagen / platelet alpha granule / positive regulation of intracellular signal transduction / GP1b-IX-V activation signalling / p130Cas linkage to MAPK signaling for integrins / cell-substrate adhesion / Defective F8 cleavage by thrombin ...Weibel-Palade body / Defective F8 binding to von Willebrand factor / hemostasis / Platelet Adhesion to exposed collagen / platelet alpha granule / positive regulation of intracellular signal transduction / GP1b-IX-V activation signalling / p130Cas linkage to MAPK signaling for integrins / cell-substrate adhesion / Defective F8 cleavage by thrombin / immunoglobulin binding / Platelet Aggregation (Plug Formation) / GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin cell surface interactions / collagen binding / Intrinsic Pathway of Fibrin Clot Formation / Integrin signaling / extracellular matrix / platelet alpha granule lumen / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / platelet activation / response to wounding / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / blood coagulation / integrin binding / Platelet degranulation / protein-folding chaperone binding / collagen-containing extracellular matrix / protease binding / cell adhesion / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
von Willebrand factor, VWA N-terminal domain / Von Willebrand factor / VWA N-terminal / C8 domain / Uncharacterised domain, cysteine-rich / C8 / von Willebrand factor, type D domain / von Willebrand factor type D domain / VWFD domain profile. / von Willebrand factor (vWF) type D domain ...von Willebrand factor, VWA N-terminal domain / Von Willebrand factor / VWA N-terminal / C8 domain / Uncharacterised domain, cysteine-rich / C8 / von Willebrand factor, type D domain / von Willebrand factor type D domain / VWFD domain profile. / von Willebrand factor (vWF) type D domain / C-terminal cystine knot signature. / von Willebrand factor (vWF) type C domain / Trypsin Inhibitor-like, cysteine rich domain / Serine protease inhibitor-like superfamily / Trypsin Inhibitor like cysteine rich domain / C-terminal cystine knot domain profile. / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
von Willebrand factor
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsJavitt G / Fass D
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: Helical self-assembly of a mucin segment suggests an evolutionary origin for von Willebrand factor tubules.
Authors: Gabriel Javitt / Deborah Fass /
Abstract: The glycoprotein von Willebrand factor (VWF) contributes to hemostasis by stanching injuries in blood vessel walls. A distinctive feature of VWF is its assembly into long, helical tubules in ...The glycoprotein von Willebrand factor (VWF) contributes to hemostasis by stanching injuries in blood vessel walls. A distinctive feature of VWF is its assembly into long, helical tubules in endothelial cells prior to secretion. When VWF is released into the bloodstream, these tubules unfurl to release linear polymers that bind subendothelial collagen at wound sites, recruit platelets, and initiate the clotting cascade. VWF evolved from gel-forming mucins, the polymeric glycoproteins that coat and protect exposed epithelia. Despite the divergent function of VWF in blood vessel repair, sequence conservation and shared domain organization imply that VWF retained key aspects of the mucin bioassembly mechanism. Here, we show using cryo-electron microscopy that the ability to form tubules, a property hitherto thought to have arisen as a VWF adaptation to the vasculature, is a feature of the amino-terminal region of mucin. This segment of the human intestinal gel-forming mucin (MUC2) was found to self-assemble into tubules with a striking resemblance to those of VWF itself. To facilitate a comparison, we determined the residue-resolution structure of tubules formed by the homologous segment of VWF. The structures of the MUC2 and VWF tubules revealed the flexible joints and the intermolecular interactions required for tubule formation. Steric constraints in full-length MUC2 suggest that linear filaments, a previously observed supramolecular assembly form, are more likely than tubules to be the physiological mucin storage intermediate. Nevertheless, MUC2 tubules indicate a possible evolutionary origin for VWF tubules and elucidate design principles present in mucins and VWF.
History
DepositionSep 2, 2021-
Header (metadata) releaseFeb 23, 2022-
Map releaseFeb 23, 2022-
UpdateMay 25, 2022-
Current statusMay 25, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7pmv
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7pmv
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13541.png

Downloads & links

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Map

FileDownload / File: emd_13541.map.gz / Format: CCP4 / Size: 55.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.12174 Å
Density
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.1
Minimum - Maximum-2.5118122 - 3.195886
Average (Standard dev.)-4.1410825e-05 (±0.05812693)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin9079143
Dimensions238246249
Spacing246238249
CellA: 275.94785 Å / B: 266.97394 Å / C: 279.31308 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.12173983739841.12173949579831.1217389558233
M x/y/z246238249
origin x/y/z0.0000.0000.000
length x/y/z275.948266.974279.313
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS7990143
NC/NR/NS246238249
D min/max/mean-2.5123.196-0.000

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Supplemental data

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Additional map: #1

Fileemd_13541_additional_1.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 : 2 beads from a VWF tubule of domains D1D2D'D3

EntireName: 2 beads from a VWF tubule of domains D1D2D'D3
Components
  • Complex: 2 beads from a VWF tubule of domains D1D2D'D3
    • Protein or peptide: von Willebrand factor
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM IONCalcium
  • Ligand: water

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Supramolecule #1: 2 beads from a VWF tubule of domains D1D2D'D3

SupramoleculeName: 2 beads from a VWF tubule of domains D1D2D'D3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant strain: HEK 293F / Recombinant plasmid: pCDNA3.1

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Macromolecule #1: von Willebrand factor

MacromoleculeName: von Willebrand factor / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 136.516797 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MIPARFAGVL LALALILPGT LCAEGTRGRS STARCSLFGS DFVNTFDGSM YSFAGYCSYL LAGGCQKRSF SIIGDFQNGK RVSLSVYLG EFFDIHLFVN GTVTQGDQRV SMPYASKGLY LETEAGYYKL SGEAYGFVAR IDGSGNFQVL LSDRYFNKTC G LCGNFNIF ...String:
MIPARFAGVL LALALILPGT LCAEGTRGRS STARCSLFGS DFVNTFDGSM YSFAGYCSYL LAGGCQKRSF SIIGDFQNGK RVSLSVYLG EFFDIHLFVN GTVTQGDQRV SMPYASKGLY LETEAGYYKL SGEAYGFVAR IDGSGNFQVL LSDRYFNKTC G LCGNFNIF AEDDFMTQEG TLTSDPYDFA NSWALSSGEQ WCERASPPSS SCNISSGEMQ KGLWEQCQLL KSTSVFARCH PL VDPEPFV ALCEKTLCEC AGGLECACPA LLEYARTCAQ EGMVLYGWTD HSACSPVCPA GMEYRQCVSP CARTCQSLHI NEM CQERCV DGCSCPEGQL LDEGLCVEST ECPCVHSGKR YPPGTSLSRD CNTCICRNSQ WICSNEECPG ECLVTGQSHF KSFD NRYFT FSGICQYLLA RDCQDHSFSI VIETVQCADD RDAVCTRSVT VRLPGLHNSL VKLKHGAGVA MDGQDVQLPL LKGDL RIQH TVTASVRLSY GEDLQMDWDG RGRLLVKLSP VYAGKTCGLC GNYNGNQGDD FLTPSGLAEP RVEDFGNAWK LHGDCQ DLQ KQHSDPCALN PRMTRFSEEA CAVLTSPTFE ACHRAVSPLP YLRNCRYDVC SCSDGRECLC GALASYAAAC AGRGVRV AW REPGRCELNC PKGQVYLQCG TPCNLTCRSL SYPDEECNEA CLEGCFCPPG LYMDERGDCV PKAQCPCYYD GEIFQPED I FSDHHTMCYC EDGFMHCTMS GVPGSLLPDA VLSSPLSHRS KRSLSCRPPM VKLVCPADNL RAEGLECTKT CQNYDLECM SMGCVSGCLC PPGMVRHENR CVALERCPCF HQGKEYAPGE TVKIGCNTCV CRDRKWNCTD HVCDATCSTI GMAHYLTFDG LKYLFPGEC QYVLVQDYCG SNPGTFRILV GNKGCSHPSV KCKKRVTILV EGGEIELFDG EVNVKRPMKD ETHFEVVESG R YIILLLGK ALSVVWDRHL SISVVLKQTY QEKVCGLCGN FDGIQNNDLT SSNLQVEEDP VDFGNSWKVS SQCADTRKVP LD SSPATCH NNIMKQTMVD SSCRILTSDV FQDCNKLVDP EPYLDVCIYD TCSCESIGDC ACFCDTIAAY AHVCAQHGKV VTW RTATLC PQSCEERNLR ENGYECEWRY NSCAPACQVT CQHPEPLACP VQCVEGCHAH CPPGKILDEL LQTCVDPEDC PVCE VAGRR FASGKKVTLN PSDPEHCQIC HCDVVNLTCE ACQEPG

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 16 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Macromolecule #5: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 12 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 4 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 48.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 28.5 Å
Applied symmetry - Helical parameters - Δ&Phi: 86.0 °
Applied symmetry - Helical parameters - Axial symmetry: D1 (2x1 fold dihedral)
Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 88715
FSC plot (resolution estimation)

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