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- EMDB-11658: MUC2 amino terminal D1D2D3CysD1 2 bead map -

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Basic information

Entry
Database: EMDB / ID: EMD-11658
TitleMUC2 amino terminal D1D2D3CysD1 2 bead map
Map data
Sample
  • Complex: Filament of amino terminal MUC2 comprised of domains D1D2D3CysD1
    • Protein or peptide: MUC2 D1D2D3CysD1
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsJavitt G / Fass D
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
DepositionAug 23, 2020-
Header (metadata) releaseOct 21, 2020-
Map releaseOct 21, 2020-
UpdateNov 11, 2020-
Current statusNov 11, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.099
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.099
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11658.png

Downloads & links

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Map

FileDownload / File: emd_11658.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.859 Å
Density
Contour LevelBy AUTHOR: 0.099 / Movie #1: 0.099
Minimum - Maximum-0.24828374 - 0.5605833
Average (Standard dev.)-0.00013495564 (±0.013079117)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 429.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8590.8590.859
M x/y/z500500500
origin x/y/z0.0000.0000.000
length x/y/z429.500429.500429.500
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS500500500
D min/max/mean-0.2480.561-0.000

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Supplemental data

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Half map: #1

Fileemd_11658_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_11658_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 : Filament of amino terminal MUC2 comprised of domains D1D2D3CysD1

EntireName: Filament of amino terminal MUC2 comprised of domains D1D2D3CysD1
Components
  • Complex: Filament of amino terminal MUC2 comprised of domains D1D2D3CysD1
    • Protein or peptide: MUC2 D1D2D3CysD1

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Supramolecule #1: Filament of amino terminal MUC2 comprised of domains D1D2D3CysD1

SupramoleculeName: Filament of amino terminal MUC2 comprised of domains D1D2D3CysD1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: MUC2 D1D2D3CysD1

MacromoleculeName: MUC2 D1D2D3CysD1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SELQTEGRTR YHGRNVCSTW GNFHYKTFDG DVFRFPGLCD YNFASDCRGS YKEFAVHLKR GPGQAEAPAG VESILLTIKD DTIYLTRHLA VLNGAVVSTP HYSPGLLIE KSDAYTKVYS RAGLTLMWNR EDALMLELDT KFRNHTCGLC GDYNGLQSYS EFLSDGVLFS ...String:
SELQTEGRTR YHGRNVCSTW GNFHYKTFDG DVFRFPGLCD YNFASDCRGS YKEFAVHLKR GPGQAEAPAG VESILLTIKD DTIYLTRHLA VLNGAVVSTP HYSPGLLIE KSDAYTKVYS RAGLTLMWNR EDALMLELDT KFRNHTCGLC GDYNGLQSYS EFLSDGVLFS PLEFGNMQKI NQPDVVCEDP EEEVAPASCS E HRAECERL LTAEAFADCQ DLVPLEPYLR ACQQDRCRCP GGDTCVCSTV AEFSRQCSHA GGRPGNWRTA TLCPKTCPGN LVYLESGSPC MDTCSHLEVS SL CEEHRMD GCFCPEGTVY DDIGDSGCVP VSQCHCRLHG HLYTPGQEIT NDCEQCVCNA GRWVCKDLPC PGTCALEGGS HITTFDGKTY TFHGDCYYVL AKG DHNDSY ALLGELAPCG STDKQTCLKT VVLLADKKKN AVVFKSDGSV LLNQLQVNLP HVTASFSVFR PSSYHIMVSM AIGVRLQVQL APVMQLFVTL DQAS QGQVQ GLCGNFNGLE GDDFKTASGL VEATGAGFAN TWKAQSTCHD KLDWLDDPCS LNIESANYAE HWCSLLKKTE TPFGRCHSAV DPAEYYKRCK YDTCN CQNN EDCLCAALSS YARACTAKGV MLWGWREHVC NKDVGSCPNS QVFLYNLTTC QQTCRSLSEA DSHCLEGFAP VDGCGCPDHT FLDEKGRCVP LAKCSC YHR GLYLEAGDVV VRQEERCVCR DGRLHCRQIR LIGQSCTAPK IHMDCSNLTA LATSKPRALS CQTLAAGYYH TECVSGCVCP DGLMDDGRGG CVVEKEC PC VHNNDLYSSG AKIKVDCNTC TCKRGRWVCT QAVCHGTCSI YGSGHYITFD GKYYDFDGHC SYVAVQDYCG QNSSLGSFSI ITENVPCGTT GVTCSKAI K IFMGRTELKL EDKHRVVIQR DEGHHVAYTT REVGQYLVVE SSTGIIVIWD KRTTVFIKLA PSYKGTVCGL CGNFDHRSNN DFTTRDHMVV SSELDFGNS WKEAPTCPDV STNPEPCSLN PHRRSWAEKQ CSILKSSVFS ICHSKVDPKP FYEACVHDSC SCDTGGDCEC FCSAVASYAQ ECTKEGACVF WRTPDLCPIF CDYYNPPHE CEWHYEPCGN RSFETCRTIN GIHSNISVSY LEGCYPRCPK DRPIYEEDLK KCVTADKCGC YVEDTHYPPG ASVPTEETCK SCVCTNSSQV V CRPEEGKI LNQTQDGAFC YWEICGPNGT VEKHFNICSI TTRPSTLTTF TTITLPTTPT SFTTTTTTTT PTSSTVLSTT PKLCCLWSDW INEDHPSSGS DD GDRETFD GVCGAPEDIE CRSVKDPHLS LEQHGQKVQC DVSVGFICKN EDQFGNGPFG LCYDYKIRVN CCWPMDKCIT HHHHHH

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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 / Instrument: FEI VITROBOT MARK IV

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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: 30.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 160843
FSC plot (resolution estimation)

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