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- EMDB-18829: MUC5AC D3 assembly. SNPs rs36189285, rs878913005: Arg996Gln, Arg1... -

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Basic information

Entry
Database: EMDB / ID: EMD-18829
TitleMUC5AC D3 assembly. SNPs rs36189285, rs878913005: Arg996Gln, Arg1201Trp.
Map data
Sample
  • Complex: MUC5AC D3 assembly
    • 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: 3.2 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
DepositionNov 2, 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_18829.png

Downloads & links

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Map

FileDownload / File: emd_18829.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.)
0.85 Å/pix.
x 256 pix.
= 216.678 Å		0.85 Å/pix.
x 256 pix.
= 216.678 Å		0.85 Å/pix.
x 256 pix.
= 216.678 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8464 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.20099755 - 0.4583895
Average (Standard dev.)0.0015402597 (±0.013546997)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 216.6784 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_18829_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_18829_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : MUC5AC D3 assembly

EntireName: MUC5AC D3 assembly
Components
  • Complex: MUC5AC D3 assembly
    • Protein or peptide: Mucin-5AC
  • Ligand: CALCIUM ION

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Supramolecule #1: MUC5AC D3 assembly

SupramoleculeName: MUC5AC D3 assembly / 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: 55.587156 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: DAAQPARRAV RSSRHHHHHH GSATCAVYGD GHYLTFDGQS YSFNGDCEYT LVQNHCGGKD STQDSFRVVT ENVPCGTTGT TCSKAIKIF LGGFELKLSH GKVEVIGTDE SQEVPYTIQQ MGIYLVVDTD IGLVLLWDKK TSIFINLSPE FKGRVCGLCG N FDDIAVND ...String:
DAAQPARRAV RSSRHHHHHH GSATCAVYGD GHYLTFDGQS YSFNGDCEYT LVQNHCGGKD STQDSFRVVT ENVPCGTTGT TCSKAIKIF LGGFELKLSH GKVEVIGTDE SQEVPYTIQQ MGIYLVVDTD IGLVLLWDKK TSIFINLSPE FKGRVCGLCG N FDDIAVND FATRSRSVVG DVLEFGNSWK LSPSCPDALA PKDPCTANPF RKSWAQKQCS ILHGPTFAAC HAHVEPARYY EA CVNDACA CDSGGDCECF CTAVAAYAQA CHEVGLCVSW RTPSICPLFC DYYNPEGQCE WHYQPCGVPC LRTCRNPRGD CLR DVWGLE GCYPKCPPEA PIFDEDKMQC VATCPTPPLP PRCHVHGKSY RPGAVVPSDK NCQSCLCTER GVECTYKAEA CVCT YNGQR FHPGDVIYHT TDGTGGCISA RCGANGTIER RVYPCSPTTP VPPTTFSFST PPLVVSSTHT PSNGPSSAHT GPPSS AWPT TAGTDDDDKT SEQKLISEED LSRKLTR

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

Concentration0.28 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMNH2C(CH2OH)3.HClTris-HCl
150.0 mMNaClSodium Chloride
10.0 mMCaCl2Calcium Chloride
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Support film - Material: GOLD / 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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 7125 / Average electron dose: 1.26 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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 330230
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:

8qtv


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-8r1z:
MUC5AC D3 assembly. SNPs rs36189285, rs878913005: Arg996Gln, Arg1201Trp.

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