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- EMDB-13575: MUC2 Tubules of D1D2D3 domains -

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Basic information

Entry
Database: EMDB / ID: EMD-13575
TitleMUC2 Tubules of D1D2D3 domains
Map data
Sample
  • Complex: MUC2 tubule of domains D1D2D3
    • Protein or peptide: Mucin-2
  • Ligand: CALCIUM IONCalcium
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water
Function / homology
Function and homology information


WxxW domain / Mucin-2 protein WxxW repeating region / 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. ...WxxW domain / Mucin-2 protein WxxW repeating region / 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) / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.8 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 10, 2021-
Header (metadata) releaseFeb 16, 2022-
Map releaseFeb 16, 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: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7pov
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7pov
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13575.png

Downloads & links

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Map

FileDownload / File: emd_13575.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.859 Å
Density
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.03121389 - 0.20503989
Average (Standard dev.)0.00045971407 (±0.012505191)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 515.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8590.8590.859
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z515.400515.400515.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS600600600
D min/max/mean-0.0310.2050.000

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Supplemental data

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Sample components

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Entire : MUC2 tubule of domains D1D2D3

EntireName: MUC2 tubule of domains D1D2D3
Components
  • Complex: MUC2 tubule of domains D1D2D3
    • Protein or peptide: Mucin-2
  • Ligand: CALCIUM IONCalcium
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water

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Supramolecule #1: MUC2 tubule of domains D1D2D3

SupramoleculeName: MUC2 tubule of domains D1D2D3 / 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: Mucin-2

MacromoleculeName: Mucin-2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 137.642609 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SELQTEGRTR NHGHNVCSTW GNFHYKTFDG DVFRFPGLCD YNFASDCRGS YKEFAVHLKR GPGQAEAPAG VESILLTIKD DTIYLTRHL AVLNGAVVST PHYSPGLLIE KSDAYTKVYS RAGLTLMWNR EDALMLELDT KFRNHTCGLC GDYNGLQSYS E FLSDGVLF ...String:
SELQTEGRTR NHGHNVCSTW GNFHYKTFDG DVFRFPGLCD YNFASDCRGS YKEFAVHLKR GPGQAEAPAG VESILLTIKD DTIYLTRHL AVLNGAVVST PHYSPGLLIE KSDAYTKVYS RAGLTLMWNR EDALMLELDT KFRNHTCGLC GDYNGLQSYS E FLSDGVLF SPLEFGNMQK INQPDVVCED PEEEVAPASC SEHRAECERL LTAEAFADCQ DLVPLEPYLR ACQQDRCRCP GG DTCVCST VAEFSRQCSH AGGRPGNWRT ATLCPKTCPG NLVYLESGSP CMDTCSHLEV SSLCEEHRMD GCFCPEGTVY DDI GDSGCV PVSQCHCRLH GHLYTPGQEI TNDCEQCVCN AGRWVCKDLP CPGTCALEGG SHITTFDGKT YTFHGDCYYV LAKG DHNDS YALLGELAPC GSTDKQTCLK TVVLLADKKK NVVVFKSDGS VLLNELQVNL PHVTASFSVF RPSSYHIMVS MAIGV RLQV QLAPVMQLFV TLDQASQGQV QGLCGNFNGL EGDDFKTASG LVEATGAGFA NTWKAQSSCH DKLDWLDDPC SLNIES ANY AEHWCSLLKK TETPFGRCHS AVDPAEYYKR CKYDTCNCQN NEDCLCAALS SYARACTAKG VMLWGWREHV CNKDVGS CP NSQVFLYNLT TCQQTCRSLS EADSHCLEGF APVDGCGCPD HTFLDEKGRC VPLAKCSCYH RGLYLEAGDV VVRQEERC V CRDGRLHCRQ IRLIGQSCTA PKIHMDCSNL TALATSKPRA LSCQTLAAGY YHTECVSGCV CPDGLMDDGR GGCVVEKEC PCVHNNDLYS SGAKIKVDCN TCTCKRGRWV CTQAVCHGTC SIYGSGHYIT FDGKYYDFDG HCSYVAVQDY CGQNSSLGSF SIITENVPC GTTGVTCSKA IKIFMGRTEL KLEDKHRVVI QRDEGHHVAY TTREVGQYLV VESSTGIIVI WDKRTTVFIK L APSYKGTV CGLCGNFDHR SNNDFTTRDH MVVSSELDFG NSWKEAPTCP DVSTNPEPCS LNPHRRSWAE KQCSILKSSV FS ICHSKVD PKPFYEACVH DSCSCDTGGD CECFCSAVAS YAQECTKEGA CVFWRTPDLC PIFCDYYNPP HECEWHYEPC GNR SFETCR TINGIHSNIS VSYLEGCYPR CPKDRPIYEE DLKKCVTADK CGCYVEDTHY PPGASVPTEE TCKSCVCTNS SQVV CRPEE GKILNQTQDG AFCYWEICGP NGTVEKHFNI CSITHHHHHH

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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 6 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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: 4 / 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: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 46 / 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 statehelical array

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Sample preparation

BufferpH: 5.4
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: 69.5 Å
Applied symmetry - Helical parameters - Δ&Phi: 83.2 °
Applied symmetry - Helical parameters - Axial symmetry: D2 (2x2 fold dihedral)
Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 515422
FSC plot (resolution estimation)

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