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- PDB-8oer: MUC5B amino acids 26-1435 -

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Basic information

Entry
Database: PDB / ID: 8oer
TitleMUC5B amino acids 26-1435
Components(Mucin-5B) x 3
KeywordsSTRUCTURAL PROTEIN / Mucin / fibrils / disulfide bonds
Function / homology
Function and homology information


Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-linked glycosylation of mucins / Dectin-2 family / extracellular matrix / Golgi lumen / intracellular membrane-bounded organelle / extracellular space ...Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-linked glycosylation of mucins / Dectin-2 family / extracellular matrix / Golgi lumen / intracellular membrane-bounded organelle / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsKhmelnitsky, L. / Fass, D.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation2660/20 Israel
CitationJournal: To Be Published
Title: Pulmonary Fibrosis Linked to Impaired Mucin 5B Supramolecular Assembly
Authors: Khmelnitsky, L. / Javitt, G. / Reznik, N. / Yeshaya, N. / Elad, N. / Anikster, Y. / Shalva, N. / Barel, O. / Pode-Shakked, B. / Greenberg, L.J. / Segel, M.J. / Fass, D.
History
DepositionMar 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Jul 9, 2025Group: Data collection / Category: em_software / Item: _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)288,49523
Polymers286,1846
Non-polymers2,31117
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Mucin-5B / MUC-5B / Cervical mucin / High molecular weight salivary mucin MG1 / Mucin-5 subtype B / ...MUC-5B / Cervical mucin / High molecular weight salivary mucin MG1 / Mucin-5 subtype B / tracheobronchial / Sublingual gland mucin


Mass: 81780.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MUC5B, MUC5 / Cell line (production host): HEK-293F / Production host: Homo sapiens (human) / References: UniProt: Q9HC84
#2: Protein Mucin-5B / MUC-5B / Cervical mucin / High molecular weight salivary mucin MG1 / Mucin-5 subtype B / ...MUC-5B / Cervical mucin / High molecular weight salivary mucin MG1 / Mucin-5 subtype B / tracheobronchial / Sublingual gland mucin


Mass: 49860.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MUC5B, MUC5 / Cell line (production host): HEK-293F / Production host: Homo sapiens (human) / References: UniProt: Q9HC84
#3: Protein Mucin-5B / MUC-5B / Cervical mucin / High molecular weight salivary mucin MG1 / Mucin-5 subtype B / ...MUC-5B / Cervical mucin / High molecular weight salivary mucin MG1 / Mucin-5 subtype B / tracheobronchial / Sublingual gland mucin


Mass: 11450.999 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MUC5B, MUC5 / Cell line (production host): HEK-293F / Production host: Homo sapiens (human) / References: UniProt: Q9HC84
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: MUC5B N-terminal filaments / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 5.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 48 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 88708 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00759238
ELECTRON MICROSCOPYf_angle_d0.72980637
ELECTRON MICROSCOPYf_dihedral_angle_d5.1868382
ELECTRON MICROSCOPYf_chiral_restr0.0468792
ELECTRON MICROSCOPYf_plane_restr0.00610779

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