+Open data
-Basic information
Entry | Database: PDB / ID: 8oer | ||||||
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Title | MUC5B amino acids 26-1435 | ||||||
Components | (Mucin-5B) x 3 | ||||||
Keywords | STRUCTURAL 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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||
Authors | Khmelnitsky, L. / Fass, D. | ||||||
Funding support | Israel, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8oer.cif.gz | 486.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8oer.ent.gz | 394.1 KB | Display | PDB format |
PDBx/mmJSON format | 8oer.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oe/8oer ftp://data.pdbj.org/pub/pdb/validation_reports/oe/8oer | HTTPS FTP |
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-Related structure data
Related structure data | 8oesC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | 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 | 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 | 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 / #5: Chemical | ChemComp-CA / Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: MUC5B N-terminal filaments / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 5.2 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 48 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 88708 / Symmetry type: POINT | ||||||||||||||||||||||||
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