[English] 日本語
Yorodumi
- EMDB-13896: Structure of the MUCIN-2 Cterminal domains -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-13896
TitleStructure of the MUCIN-2 Cterminal domains
Map data
Sample
  • Complex: Muc2 dimer, Mucus assemble
    • Protein or peptide: Mucin-2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM IONCalcium
KeywordsMucus / 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
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. ...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: 3.36 Å
AuthorsGallego P / Hansson GC
Funding support Sweden, 1 items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: 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
DepositionNov 24, 2021-
Header (metadata) releaseMar 8, 2023-
Map releaseMar 8, 2023-
UpdateSep 27, 2023-
Current statusSep 27, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_13896.png

Downloads & links

-
Map

FileDownload / File: emd_13896.map.gz / Format: CCP4 / Size: 729 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 576 pix.
= 495.36 Å		0.86 Å/pix.
x 576 pix.
= 495.36 Å		0.86 Å/pix.
x 576 pix.
= 495.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.27324465 - 0.64305216
Average (Standard dev.)-0.00026476596 (±0.007040511)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions576576576
Spacing576576576
CellA=B=C: 495.36002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Muc2 dimer, Mucus assemble

EntireName: Muc2 dimer, Mucus assemble
Components
  • Complex: Muc2 dimer, Mucus assemble
    • Protein or peptide: Mucin-2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM IONCalcium

-
Supramolecule #1: Muc2 dimer, Mucus assemble

SupramoleculeName: Muc2 dimer, Mucus assemble / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Mucin-2

MacromoleculeName: Mucin-2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 64.296707 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: KPPECPDFDP PRQENETWWL CDCFMATCKY NNTVEIVKVE CEPPPMPTCS NGLQPVRVED PDGCCWHWEC DCYCTGWGDP HYVTFDGLY YSYQGNCTYV LVEEISPSVD NFGVYIDNYH CDPNDKVSCP RTLIVRHETQ EVLIKTVHMM PMQVQVQVNR Q AVALPYKK ...String:
KPPECPDFDP PRQENETWWL CDCFMATCKY NNTVEIVKVE CEPPPMPTCS NGLQPVRVED PDGCCWHWEC DCYCTGWGDP HYVTFDGLY YSYQGNCTYV LVEEISPSVD NFGVYIDNYH CDPNDKVSCP RTLIVRHETQ EVLIKTVHMM PMQVQVQVNR Q AVALPYKK YGLEVYQSGI NYVVDIPELG VLVSYNGLSF SVRLPYHRFG NNTKGQCGTC TNTTSDDCIL PSGEIVSNCE AA ADQWLVN DPSKPHCPHS SSTTKRPAVT VPGGGKTTPH KDCTPSPLCQ LIKDSLFAQC HALVPPQHYY DACVFDSCFM PGS SLECAS LQAYAALCAQ QNICLDWRNH THGACLVECP SHREYQACGP AEEPTCKSSS SQQNNTVLVE GCFCPEGTMN YAPG FDVCV KTCGCVGPDN VPREFGEHFE FDCKNCVCLE GGSGIICQPK RCSQKPVTHC VEDGTYLATE VNPADTCCNI TVCKC NTSL CKEKPSVCPL GFEVKSKMVP GRCCPFYWCE SKGVCVHGNA EYQPGSPVYS SKCQDCVCTD KVDNNTLLNV IACTHV PCN TSCSPGFELM EAPGECCKKC

UniProtKB: Mucin-2

-
Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

-
Macromolecule #9: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 9 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chlorideSodiumchloride
25.0 mMHepes
5.0 mMCaCl2Calcium chloride
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Details: 15mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK III

-
Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 79.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6rbf

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 369150

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7qcl:
Structure of the MUCIN-2 Cterminal domains

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more