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- EMDB-18654: MUC5AC D'D3CysD1 domains. -

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Basic information

Entry
Database: EMDB / ID: EMD-18654
TitleMUC5AC D'D3CysD1 domains.
Map data
Sample
  • Complex: MUC5AC D'D3CysD1 domains
    • Protein or peptide: Mucin-5AC
  • Ligand: CALCIUM ION
Keywordsgelforming glycoprotein / Mucin / STRUCTURAL PROTEIN
Function / homology
Function and homology information


mucus layer / Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-linked glycosylation of mucins / extracellular matrix structural constituent / Dectin-2 family / extracellular matrix / Golgi lumen ...mucus layer / Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-linked glycosylation of mucins / extracellular matrix structural constituent / Dectin-2 family / extracellular matrix / Golgi lumen / extracellular space / extracellular exosome / metal ion binding / plasma membrane
Similarity search - Function
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 ...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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsTrillo-Muyo S / Hansson GC
Funding supportEuropean Union, United States, Sweden, 4 items
OrganizationGrant numberCountry
European Research Council (ERC)694181European Union
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U01AI095473 United States
Swedish Research Council2017-00958 Sweden
Knut and Alice Wallenberg Foundation2017-0028 Sweden
CitationJournal: EMBO Rep / Year: 2025
Title: Structure of the MUC5AC VWD3 assembly responsible for the formation of net-like mucin polymers.
Authors: Sergio Trillo-Muyo / Anna Ermund / Gunnar C Hansson /
Abstract: Gel-forming mucins MUC5AC and MUC5B constitute the main structural component of the mucus in the respiratory system. Secreted mucins interact specifically with each other and other molecules giving ...Gel-forming mucins MUC5AC and MUC5B constitute the main structural component of the mucus in the respiratory system. Secreted mucins interact specifically with each other and other molecules giving mucus specific properties. We determined the cryoEM structures of the wild type D3 assembly of the human MUC5AC mucin and the structural single nucleotide polymorphisms (SNP) variants Arg996Gln and Arg1201Trp that affect intermolecular interactions. Our structures explain the MUC5AC N-terminal non-covalent oligomerization after secretion. The D3 assembly forms covalent dimers that can appear in two alternative conformations, open and closed, where the closed conformation dimers interact through an arginine-rich loop in the TIL3 domain to form tetramers. Our study provides a model to explain MUC5AC net-like structures and how the two SNPs will affect mucus organization, something that might affect lung and other diseases.
History
DepositionOct 13, 2023-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateApr 2, 2025-
Current statusApr 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18654.png

Downloads & links

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Map

FileDownload / File: emd_18654.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 256 pix.
= 220.595 Å		0.86 Å/pix.
x 256 pix.
= 220.595 Å		0.86 Å/pix.
x 256 pix.
= 220.595 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8617 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.17566912 - 0.39137483
Average (Standard dev.)0.000215099 (±0.011874465)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 220.5952 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_18654_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_18654_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : MUC5AC D'D3CysD1 domains

EntireName: MUC5AC D'D3CysD1 domains
Components
  • Complex: MUC5AC D'D3CysD1 domains
    • Protein or peptide: Mucin-5AC
  • Ligand: CALCIUM ION

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Supramolecule #1: MUC5AC D'D3CysD1 domains

SupramoleculeName: MUC5AC D'D3CysD1 domains / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Mucin-5AC

MacromoleculeName: Mucin-5AC / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 78.246172 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: DAAQPARRAV RSSRHHHHHH GSPVCAAPMV FFDCRNATPG DTGAGCQKSC HTLDMTCYSP QCVPGCVCPD GLVADGEGGC ITAEDCPCV HNEASYRAGQ TIRVGCNTCT CDSRMWRCTD DPCLATCAVY GDGHYLTFDG QSYSFNGDCE YTLVQNHCGG K DSTQDSFR ...String:
DAAQPARRAV RSSRHHHHHH GSPVCAAPMV FFDCRNATPG DTGAGCQKSC HTLDMTCYSP QCVPGCVCPD GLVADGEGGC ITAEDCPCV HNEASYRAGQ TIRVGCNTCT CDSRMWRCTD DPCLATCAVY GDGHYLTFDG QSYSFNGDCE YTLVQNHCGG K DSTQDSFR VVTENVPCGT TGTTCSKAIK IFLGGFELKL SHGKVEVIGT DESQEVPYTI RQMGIYLVVD TDIGLVLLWD KK TSIFINL SPEFKGRVCG LCGNFDDIAV NDFATRSRSV VGDVLEFGNS WKLSPSCPDA LAPKDPCTAN PFRKSWAQKQ CSI LHGPTF AACHAHVEPA RYYEACVNDA CACDSGGDCE CFCTAVAAYA QACHEVGLCV SWRTPSICPL FCDYYNPEGQ CEWH YQPCG VPCLRTCRNP RGDCLRDVRG LEGCYPKCPP EAPIFDEDKM QCVATCPTPP LPPRCHVHGK SYRPGAVVPS DKNCQ SCLC TERGVECTYK AEACVCTYNG QRFHPGDVIY HTTDGTGGCI SARCGANGTI ERRVYPCSPT TPVPPTTFSF STPPLV VSS THTPSNGPSS AHTGPPSSAW PTTAGTSPRT RLPTASASLP PVCGEKCLWS PWMDVSRPGR GTDSGDFDTL ENLRAHG YR VCESPRSVEC RAEDAPGVPL RALGQRVQCS PDVGLTCRNR EQASGLCYNY QIRVQCCTPL PCTSEQKLIS EEDLSRKL T R

UniProtKB: Mucin-5AC

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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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

Concentration0.16 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMNH2C(CH2OH)3.HClTris-HCl
150.0 mMNaClSodium Chloride
10.0 mMCaCl2Calcium Chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 6754 / Average electron dose: 1.29 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.75 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 216899
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.2.1)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.2.1)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8qtb


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-8qtv:
MUC5AC D'D3CysD1 domains.

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