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- EMDB-10517: Human MUC2 AAs 21-1397 -

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Basic information

Entry
Database: EMDB / ID: EMD-10517
TitleHuman MUC2 AAs 21-1397
Map data
Sample
  • Complex: Bead complex of MUC2 D1D2D3CysD1
    • Protein or peptide: Mucin-2
    • Protein or peptide: Mucin-2
    • Protein or peptide: Mucin-2
  • Ligand: CALCIUM ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water
KeywordsGlycoprotein / Extracellular / Polymer / STRUCTURAL PROTEIN
Function / homology
Function and homology information


inner mucus layer / outer mucus layer / host-mediated regulation of intestinal microbiota composition / Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-linked glycosylation of mucins / maintenance of gastrointestinal epithelium / mucus secretion ...inner mucus layer / outer mucus layer / host-mediated regulation of intestinal microbiota composition / Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-linked glycosylation of mucins / maintenance of gastrointestinal epithelium / mucus secretion / detoxification of copper ion / cupric ion binding / Dectin-2 family / cuprous ion binding / Golgi lumen / : / plasma membrane
Similarity search - Function
WxxW domain / Mucin-2 protein WxxW repeating region / Von Willebrand factor-like domain / : / C8 domain / Uncharacterised domain, cysteine-rich / C8 / von Willebrand factor, type D domain / von Willebrand factor type D domain / VWFD domain profile. ...WxxW domain / Mucin-2 protein WxxW repeating region / Von Willebrand factor-like domain / : / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsJavitt G / Khmelnitsky L
CitationJournal: Cell / Year: 2020
Title: Assembly Mechanism of Mucin and von Willebrand Factor Polymers.
Authors: Gabriel Javitt / Lev Khmelnitsky / Lis Albert / Lavi Shlomo Bigman / Nadav Elad / David Morgenstern / Tal Ilani / Yaakov Levy / Ron Diskin / Deborah Fass /
Abstract: The respiratory and intestinal tracts are exposed to physical and biological hazards accompanying the intake of air and food. Likewise, the vasculature is threatened by inflammation and trauma. Mucin ...The respiratory and intestinal tracts are exposed to physical and biological hazards accompanying the intake of air and food. Likewise, the vasculature is threatened by inflammation and trauma. Mucin glycoproteins and the related von Willebrand factor guard the vulnerable cell layers in these diverse systems. Colon mucins additionally house and feed the gut microbiome. Here, we present an integrated structural analysis of the intestinal mucin MUC2. Our findings reveal the shared mechanism by which complex macromolecules responsible for blood clotting, mucociliary clearance, and the intestinal mucosal barrier form protective polymers and hydrogels. Specifically, cryo-electron microscopy and crystal structures show how disulfide-rich bridges and pH-tunable interfaces control successive assembly steps in the endoplasmic reticulum and Golgi apparatus. Remarkably, a densely O-glycosylated mucin domain performs an organizational role in MUC2. The mucin assembly mechanism and its adaptation for hemostasis provide the foundation for rational manipulation of barrier function and coagulation.
History
DepositionDec 3, 2019-
Header (metadata) releaseDec 18, 2019-
Map releaseOct 21, 2020-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.17
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.17
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6tm2
  • Surface level: 0.17
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7a5o
  • Surface level: 0.17
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6tm2
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7a5o
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10517.png

Downloads & links

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Map

FileDownload / File: emd_10517.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 400 pix.
= 340. Å		0.85 Å/pix.
x 400 pix.
= 340. Å		0.85 Å/pix.
x 400 pix.
= 340. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.17 / Movie #1: 0.17
Minimum - Maximum-1.867 - 2.7142334
Average (Standard dev.)0.0013420131 (±0.037061818)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 340.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.850.850.85
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z340.000340.000340.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-1.8672.7140.001

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Supplemental data

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Sample components

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Entire : Bead complex of MUC2 D1D2D3CysD1

EntireName: Bead complex of MUC2 D1D2D3CysD1
Components
  • Complex: Bead complex of MUC2 D1D2D3CysD1
    • Protein or peptide: Mucin-2
    • Protein or peptide: Mucin-2
    • Protein or peptide: Mucin-2
  • Ligand: CALCIUM ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water

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Supramolecule #1: Bead complex of MUC2 D1D2D3CysD1

SupramoleculeName: Bead complex of MUC2 D1D2D3CysD1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Mucin-2

MacromoleculeName: Mucin-2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 80.356383 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SELQTEGRTR YHGRNVCSTW GNFHYKTFDG DVFRFPGLCD YNFASDCRGS YKEFAVHLKR GPGQAEAPAG VESILLTIKD DTIYLTRHL AVLNGAVVST PHYSPGLLIE KSDAYTKVYS RAGLTLMWNR EDALMLELDT KFRNHTCGLC GDYNGLQSYS E FLSDGVLF ...String:
SELQTEGRTR YHGRNVCSTW 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 NAVVFKSDGS VLLNQLQVNL PHVTASFSVF RPSSYHIMVS MAIGV RLQV QLAPVMQLFV TLDQASQGQV QGLCGNFNGL EGDDFKTASG LVEATGAGFA NTWKAQSTCH DKLDWLDDPC SLNIES ANY AEHWCSLLKK TETPFGRCHS AVDPAEYYKR CKYDTCNCQN NEDCLCAALS SYARACTAKG VMLWGWREHV CNKDVGS CP NSQVFLYNLT TCQQTCRSLS EADSHCLEGF APVDGCGCPD HTFLDEKGRC VPLAKCSCYH RGLYLEAGDV VVRQEERC V CRDGRLHC

UniProtKB: Mucin-2

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Macromolecule #2: Mucin-2

MacromoleculeName: Mucin-2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.83016 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RQIRLIGQSC TAPKIHMDCS NLTALATSKP RALSCQTLAA GYYHTECVSG CVCPDGLMDD GRGGCVVEKE CPCVHNNDLY SSGAKIKVD CNTCTCKRGR WVCTQAVCHG TCSIYGSGHY ITFDGKYYDF DGHCSYVAVQ DYCGQNSSLG SFSIITENVP C GTTGVTCS ...String:
RQIRLIGQSC TAPKIHMDCS NLTALATSKP RALSCQTLAA GYYHTECVSG CVCPDGLMDD GRGGCVVEKE CPCVHNNDLY SSGAKIKVD CNTCTCKRGR WVCTQAVCHG TCSIYGSGHY ITFDGKYYDF DGHCSYVAVQ DYCGQNSSLG SFSIITENVP C GTTGVTCS KAIKIFMGRT ELKLEDKHRV VIQRDEGHHV AYTTREVGQY LVVESSTGII VIWDKRTTVF IKLAPSYKGT VC GLCGNFD HRSNNDFTTR DHMVVSSELD FGNSWKEAPT CPDVSTNPEP CSLNPHRRSW AEKQCSILKS SVFSICHSKV DPK PFYEAC VHDSCSCDTG GDCECFCSAV ASYAQECTKE GACVFWRTPD LCPIFCDYYN PPHECEWHYE PCGNRSFETC RTIN GIHSN ISVSYLEGCY PRCPKDRPIY EEDLKKCVTA DKCGCYVEDT HYP

UniProtKB: Mucin-2

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Macromolecule #3: Mucin-2

MacromoleculeName: Mucin-2 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.724266 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: PGASVPTEET CKSCVCTNSS QVVCRPEEGK ILNQTQDGAF CYWEICGPNG TVEKHFNICS ITTRPSTLTT FTTITLPTTP TSFTTTTTT TTPTSSTVLS TTPKLCCLWS DWINEDHPSS GSDDGDRETF DGVCGAPEDI ECRSVKDPHL SLEQHGQKVQ C DVSVGFIC ...String:
PGASVPTEET CKSCVCTNSS QVVCRPEEGK ILNQTQDGAF CYWEICGPNG TVEKHFNICS ITTRPSTLTT FTTITLPTTP TSFTTTTTT TTPTSSTVLS TTPKLCCLWS DWINEDHPSS GSDDGDRETF DGVCGAPEDI ECRSVKDPHL SLEQHGQKVQ C DVSVGFIC KNEDQFGNGP FGLCYDYKIR VNCCWPMDKC ITHHHHHH

UniProtKB: Mucin-2

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Macromolecule #5: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 10 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 46 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 5.7
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: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 178136
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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