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- PDB-8qsp: MUC5AC D3 assembly. SNP rs36189285: Arg996Gln. -

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Basic information

Entry
Database: PDB / ID: 8qsp
TitleMUC5AC D3 assembly. SNP rs36189285: Arg996Gln.
ComponentsMucin-5AC
KeywordsSTRUCTURAL PROTEIN / gelforming glycoprotein / Mucin
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.69 Å
AuthorsTrillo-Muyo, S. / Hansson, G.C.
Funding supportEuropean Union, United States, Sweden, 4items
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 11, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mucin-5AC
B: Mucin-5AC
C: Mucin-5AC
D: Mucin-5AC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,3938
Polymers222,2334
Non-polymers1604
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Mucin-5AC / MUC-5AC / Gastric mucin / Major airway glycoprotein / Mucin-5 subtype AC / tracheobronchial / ...MUC-5AC / Gastric mucin / Major airway glycoprotein / Mucin-5 subtype AC / tracheobronchial / Tracheobronchial mucin / TBM


Mass: 55558.141 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MUC5AC, MUC5 / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO lec 3.2.8.1 / References: UniProt: P98088
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: MUC5AC D3 domain / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Cricetulus griseus (Chinese hamster) / Strain: CHO lec 3.2.8.1
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris-HClNH2C(CH2OH)3.HCl1
2150 mMSodium ChlorideNaCl1
310 mMCalcium ChlorideCaCl21
SpecimenConc.: 0.28 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 500 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 1.2 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 5 / Num. of real images: 16392
Image scansMovie frames/image: 40

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Processing

EM software
IDNameVersionCategory
1Topaz0.2.3particle selection
4cryoSPARC4.2.1CTF correction
9cryoSPARC4.2.1initial Euler assignment
10cryoSPARC4.2.1final Euler assignment
11cryoSPARC4.2.1classification
12cryoSPARC4.2.13D reconstruction
13PHENIX1.20.1-4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.69 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 123852 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 165.17 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002710443
ELECTRON MICROSCOPYf_angle_d0.472314215
ELECTRON MICROSCOPYf_chiral_restr0.04151521
ELECTRON MICROSCOPYf_plane_restr0.00311886
ELECTRON MICROSCOPYf_dihedral_angle_d3.72861429

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