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- PDB-6tm6: MUC2 CysD1 domain -

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Basic information

Entry
Database: PDB / ID: 6tm6
TitleMUC2 CysD1 domain
ComponentsMucin-2
KeywordsSTRUCTURAL PROTEIN / extracellular / polymer / CysD / mucin / calcium / disulfide / WXXW
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 / extracellular matrix / Golgi lumen / collagen-containing extracellular matrix / extracellular space / 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 / 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 signature. / 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
Mucin 2, oligomeric mucus/gel-forming / Mucin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.63 Å
AuthorsKhmelnitsky, L. / Fass, D.
Funding support2items
OrganizationGrant numberCountry
European Research Council310649
Israel Science Foundation1775/12
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, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2020Group: Structure summary / Category: struct_keywords
Item: _struct_keywords.pdbx_keywords / _struct_keywords.text
Revision 1.2Mar 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mucin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9023
Polymers10,8221
Non-polymers802
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.879, 57.854, 27.471
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-1536-

HOH

21A-1610-

HOH

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Components

#1: Protein Mucin-2


Mass: 10822.033 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MUC2 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: A0A0G2JR65, UniProt: Q02817*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM citrate/phosphate buffer, pH 4.4, with 15% ethanol and 1% PEG 1K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.63→15.46 Å / Num. obs: 10882 / % possible obs: 94.93 % / Redundancy: 22.9 % / Biso Wilson estimate: 19.85 Å2 / CC1/2: 1 / Net I/σ(I): 37.79
Reflection shellResolution: 1.63→1.689 Å / Num. unique obs: 737 / CC1/2: 0.938

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Processing

Software
NameVersionClassification
HKL-3000data collection
SHELXDEphasing
PHENIX1.17_3644refinement
RefinementMethod to determine structure: SAD / Resolution: 1.63→15.23 Å / SU ML: 0.1758 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.18
RfactorNum. reflection% reflection
Rfree0.2112 1970 9.94 %
Rwork0.1736 --
obs0.1774 10882 93.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 25.69 Å2
Refinement stepCycle: LAST / Resolution: 1.63→15.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms747 0 2 111 860
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059765
X-RAY DIFFRACTIONf_angle_d0.96071037
X-RAY DIFFRACTIONf_chiral_restr0.0564105
X-RAY DIFFRACTIONf_plane_restr0.0054141
X-RAY DIFFRACTIONf_dihedral_angle_d6.1911101
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.670.2905860.2846708X-RAY DIFFRACTION52.1
1.67-1.720.27171080.22351027X-RAY DIFFRACTION75.12
1.72-1.770.21211140.20621267X-RAY DIFFRACTION91.64
1.77-1.820.20221480.18911323X-RAY DIFFRACTION98.46
1.82-1.890.22221560.17621324X-RAY DIFFRACTION99.33
1.89-1.960.25881530.18131374X-RAY DIFFRACTION99.61
1.96-2.050.21521520.16821347X-RAY DIFFRACTION100
2.05-2.160.19871370.16531358X-RAY DIFFRACTION100
2.16-2.30.20811640.1711366X-RAY DIFFRACTION100
2.3-2.470.24261460.16391347X-RAY DIFFRACTION100
2.47-2.720.22121620.17561346X-RAY DIFFRACTION100
2.72-3.110.23091530.17291351X-RAY DIFFRACTION100
3.11-3.910.1891450.16651351X-RAY DIFFRACTION100
3.91-15.460.18771460.16921364X-RAY DIFFRACTION100

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