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Yorodumi- EMDB-13897: Structure of the MUCIN-2 Cterminal domains: vWCN to TIL domains w... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13897 | |||||||||
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Title | Structure of the MUCIN-2 Cterminal domains: vWCN to TIL domains with a C2 symmetry | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Mucus / extracellular / net assemble / STRUCTURAL PROTEIN | |||||||||
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 | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Gallego P / Hansson GC | |||||||||
Funding support | Sweden, 1 items
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Citation | Journal: Nat Commun / Year: 2023 Title: The intestinal MUC2 mucin C-terminus is stabilized by an extra disulfide bond in comparison to von Willebrand factor and other gel-forming mucins. Authors: Pablo Gallego / Maria-Jose Garcia-Bonete / Sergio Trillo-Muyo / Christian V Recktenwald / Malin E V Johansson / Gunnar C Hansson / Abstract: The MUC2 mucin polymer is the main building unit of the intestinal mucus layers separating intestinal microbiota from the host epithelium. The MUC2 mucin is a large glycoprotein with a C-terminal ...The MUC2 mucin polymer is the main building unit of the intestinal mucus layers separating intestinal microbiota from the host epithelium. The MUC2 mucin is a large glycoprotein with a C-terminal domain similar to the MUC5AC and MUC5B mucins and the von Willebrand factor (VWF). A structural model of the C-terminal part of MUC2, MUC2-C, was generated by combining Cryo-electron microscopy, AlphaFold prediction, information of its glycosylation, and small angle X-ray scattering information. The globular VWD4 assembly in the N-terminal of MUC2-C is followed by 3.5 linear VWC domains that form an extended flexible structure before the C-terminal cystine-knot. All gel-forming mucins and VWF form tail-tail disulfide-bonded dimers in their C-terminal cystine-knot domain, but interestingly the MUC2 mucin has an extra stabilizing disulfide bond on the N-terminal side of the VWD4 domain, likely essential for a stable intestinal mucus barrier. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_13897.map.gz | 152.5 MB | EMDB map data format | |
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Header (meta data) | emd-13897-v30.xml emd-13897.xml | 11.9 KB 11.9 KB | Display Display | EMDB header |
Images | emd_13897.png | 40.7 KB | ||
Filedesc metadata | emd-13897.cif.gz | 5.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13897 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13897 | HTTPS FTP |
-Validation report
Summary document | emd_13897_validation.pdf.gz | 425.5 KB | Display | EMDB validaton report |
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Full document | emd_13897_full_validation.pdf.gz | 425.1 KB | Display | |
Data in XML | emd_13897_validation.xml.gz | 7.3 KB | Display | |
Data in CIF | emd_13897_validation.cif.gz | 8.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13897 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13897 | HTTPS FTP |
-Related structure data
Related structure data | 7qcnMC 7qclC 7qcuC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_13897.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Muc2 dimer, Mucus assemble
Entire | Name: Muc2 dimer, Mucus assemble |
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Components |
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-Supramolecule #1: Muc2 dimer, Mucus assemble
Supramolecule | Name: Muc2 dimer, Mucus assemble / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Mucin-2
Macromolecule | Name: Mucin-2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 45.157816 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: PPECPDTWWL CDCFMATCKY NNTVEIVKVE CEPPPMPTCS NGLQPVRVED PDGCCWHWEC DCYCTGWGDP HYVTFDGLYY SYQGNCTYV LVEEISPSVD NFGVYIDNYH CDPNDKVSCP RTLIVRHETQ EVLIKTVHMM PMQVQVQAVA LPYKKYGLEV Y QSGINYVV ...String: PPECPDTWWL CDCFMATCKY NNTVEIVKVE CEPPPMPTCS NGLQPVRVED PDGCCWHWEC DCYCTGWGDP HYVTFDGLYY SYQGNCTYV LVEEISPSVD NFGVYIDNYH CDPNDKVSCP RTLIVRHETQ EVLIKTVHMM PMQVQVQAVA LPYKKYGLEV Y QSGINYVV DIPELGVLVS YNGLSFSVRL PYHRFGNNTK GQCGTCTNTT SDDCILPSGE IVSNCEAAAD QWLVNDPSKP HC PDCTPSP LCQLIKDSLF AQCHALVPPQ HYYDACVFDS CFMPGSSLEC ASLQAYAALC AQQNICLDWR NHTHGACLVE CPS HREYQA CGPAEEPTCK SSSSQQNNTV LVEGCFCPEG TMNYAPGFDV CVKTCGCVGP DNVPREFGEH FEFDCKNCVC LEGG SGIIC QP UniProtKB: Mucin-2 |
-Macromolecule #3: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 6 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL | ||||||||||||
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Buffer | pH: 7.4 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 79.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3) / Number images used: 414056 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3) |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-7qcn: |