[English] 日本語
Yorodumi
- EMDB-51636: MUC5AC mucin amino acids 28 to 1483 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-51636
TitleMUC5AC mucin amino acids 28 to 1483
Map datamap resulting from local refinement around one bead of the MUC5AC two-start helix
Sample
  • Complex: filament of the MUC5AC amino-terminal segment
    • Protein or peptide: Mucin-5AC
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
  • Ligand: COPPER (II) ION
  • Ligand: water
Keywordsmucin / lung / filament / polymer / disulfide / PROTEIN FIBRIL
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 / 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
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.91 Å
AuthorsHaberman M / Kamyshinsky R / Fass D
Funding supportEuropean Union, Israel, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)101097867European Union
Israel Science Foundation2660/20 Israel
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: MUC5AC filaments illuminate the structural diversification of respiratory and intestinal mucins.
Authors: Meital Haberman / Roman Kamyshinsky / Nava Reznik / Noa Yeshaya / Lev Khmelnitsky / Elizabeth G Plender / Evan E Eichler / Deborah Fass /
Abstract: Secreted mucins are multimegadalton glycoprotein polymers that share the function of protecting mucosal tissues but diversified for activities in different organs of the body. Structural studies of ...Secreted mucins are multimegadalton glycoprotein polymers that share the function of protecting mucosal tissues but diversified for activities in different organs of the body. Structural studies of secreted mucins are complicated by the enormous sizes, flexibility, and complex supramolecular assembly modes of these glycoproteins. The two major respiratory mucins are MUC5AC and MUC5B. Here, we present structures of a large amino-terminal segment of MUC5AC in the form of helical filaments. These filaments differ from filamentous and tubular structures observed previously for the intestinal mucin MUC2 and the partial mucin homolog VWF. Nevertheless, the MUC5AC helical filaments support the proposed mechanism, based on MUC2 and VWF, for how noncovalent interactions between mucin monomers guide disulfide crosslinking to form polymers. The high-resolution MUC5AC structures show how local and limited changes in amino acid sequence can profoundly affect higher-order assembly while preserving the overall folds and polymerization activity of mucin glycoproteins. Differences in supramolecular assembly are likely to be functionally significant considering the divergence of mechanical properties and physiological requirements between respiratory and intestinal mucins. Determining the high-resolution structures of respiratory mucins provides a foundation for understanding the mechanisms by which they clean and protect the lungs. Moreover, the MUC5AC structure enables visualization of the sites of human amino acid sequence variation and disease-associated mutations.
History
DepositionSep 24, 2024-
Header (metadata) releaseDec 4, 2024-
Map releaseDec 4, 2024-
UpdateMar 19, 2025-
Current statusMar 19, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_51636.png

Downloads & links

-
Map

FileDownload / File: emd_51636.map.gz / Format: CCP4 / Size: 634.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap resulting from local refinement around one bead of the MUC5AC two-start helix
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 550 pix.
= 453.31 Å		0.82 Å/pix.
x 550 pix.
= 453.31 Å		0.82 Å/pix.
x 550 pix.
= 453.31 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8242 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.256
Minimum - Maximum-0.92513466 - 1.3125702
Average (Standard dev.)0.001104921 (±0.031936783)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions550550550
Spacing550550550
CellA=B=C: 453.31 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_51636_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_51636_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : filament of the MUC5AC amino-terminal segment

EntireName: filament of the MUC5AC amino-terminal segment
Components
  • Complex: filament of the MUC5AC amino-terminal segment
    • Protein or peptide: Mucin-5AC
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
  • Ligand: COPPER (II) ION
  • Ligand: water

-
Supramolecule #1: filament of the MUC5AC amino-terminal segment

SupramoleculeName: filament of the MUC5AC amino-terminal segment / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human) / Tissue: lung / Location in cell: secreted

-
Macromolecule #1: Mucin-5AC

MacromoleculeName: Mucin-5AC / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 157.080688 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QDGSSESSYK HHPALSPIAR GPSGVPLRGA TVFPSLRTIP VVRASNPAHN GRVCSTWGSF HYKTFDGDVF RFPGLCNYVF SEHCGAAYE DFNIQLRRSQ ESAAPTLSRV LMKVDGVVIQ LTKGSVLVNG HPVLLPFSQS GVLIQQSSSY TKVEARLGLV L MWNHDDSL ...String:
QDGSSESSYK HHPALSPIAR GPSGVPLRGA TVFPSLRTIP VVRASNPAHN GRVCSTWGSF HYKTFDGDVF RFPGLCNYVF SEHCGAAYE DFNIQLRRSQ ESAAPTLSRV LMKVDGVVIQ LTKGSVLVNG HPVLLPFSQS GVLIQQSSSY TKVEARLGLV L MWNHDDSL LLELDTKYAN KTCGLCGDFN GMPVVSELLS HNTKLTPMEF GNLQKMDDPT DQCQDPVPEP PRNCSTGFGI CE ELLHGQL FSGCVALVDV GSYLEACRQD LCFCEDTDLL SCVCHTLAEY SRQCTHAGGL PQDWRGPDFC PQKCPNNMQY HEC RSPCAD TCSNQEHSRA CEDHCVAGCF CPEGTVLDDI GQTGCVPVSK CACVYNGAAY APGATYSTDC TNCTCSGGRW SCQE VPCPG TCSVLGGAHF STFDGKQYTV HGDCSYVLTK PCDSSAFTVL AELRRCGLTD SETCLKSVTL SLDGAQTVVV IKASG EVFL NQIYTQLPIS AANVTIFRPS TFFIIAQTSL GLQLNLQLVP TMQLFMQLAP KLRGQTCGLC GNFNSIQADD FRTLSG VVE ATAAAFFNTF KTQAACPNIR NSFEDPCSLS VENEKYAQHW CSQLTDADGP FGRCHAAVKP GTYYSNCMFD TCNCERS ED CLCAALSSYV HACAAKGVQL GGWRDGVCTK PMTTCPKSMT YHYHVSTCQP TCRSLSEGDI TCSVGFIPVD GCICPKGT F LDDTGKCVQA SNCPCYHRGS MIPNGESVHD SGAICTCTHG KLSCIGGQAP APVCAAPMVF FDCRNATPGD TGAGCQKSC HTLDMTCYSP QCVPGCVCPD GLVADGEGGC ITAEDCPCVH NEASYRAGQT IRVGCNTCTC DSRMWRCTDD PCLATCAVYG DGHYLTFDG QSYSFNGDCE YTLVQNHCGG KDSTQDSFRV VTENVPCGTT GTTCSKAIKI FLGGFELKLS HGKVEVIGTD E SQEVPYTI RQMGIYLVVD TDIGLVLLWD KKTSIFINLS PEFKGRVCGL CGNFDDIAVN DFATRSRSVV GDVLEFGNSW KL SPSCPDA LAPKDPCTAN PFRKSWAQKQ CSILHGPTFA ACHAHVEPAR YYEACVNDAC ACDSGGDCEC FCTAVAAYAQ ACH EVGLCV SWRTPSICPL FCDYYNPEGQ CEWHYQPCGV PCLRTCRNPR GDCLRDVRGL EGCYPKCPPE APIFDEDKMQ CVAT CPTPP LPPRCHVHGK SYRPGAVVPS DKNCQSCLCT ERGVECTYKA EACVCTYNGQ RFHPGDVIYH TTDGTGGCIS ARCGA NGTI ERRVYPCSPT TPVPPTTFSF STPPLVVSST HTPSNGPSSA HTGPPSSAWP TTAGTSPRTR LPTASASLPP VCGEKC LWS PWMDVSRPGR GTDSGDFDTL ENLRAHGYRV CESPRSVECR AEDAPGVPLR ALGQRVQCSP DVGLTCRNRE QASGLCY NY QIRVQCCTPL PCST

UniProtKB: Mucin-5AC

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 6 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 6 / Formula: CA
Molecular weightTheoretical: 40.078 Da

-
Macromolecule #4: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION

-
Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 177 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

-
Sample preparation

Concentration0.45 mg/mL
BufferpH: 5.2
Component:
ConcentrationNameFormula
100.0 mM2-(N-morpholino)ethanesulfonic acid
1.0 Msodium chlorideNaCl
10.0 mMcalcium chlorideCaCl2
45.0 micromolarzinc chloride
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 198256
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

+
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