+Open data
-Basic information
Entry | Database: PDB / ID: 8jj5 | ||||||||||||||||||
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Title | Porcine uroplakin complex | ||||||||||||||||||
Components |
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Keywords | MEMBRANE PROTEIN / Urothelium / asymmetric unit membrane / urinary bladder / urinary tract infection / lipid raft | ||||||||||||||||||
Function / homology | Function and homology information apical plasma membrane urothelial plaque / urea transport / urinary bladder development / water transport / sodium ion homeostasis / potassium ion homeostasis / epithelial cell differentiation / kidney development / cell morphogenesis / membrane / plasma membrane Similarity search - Function | ||||||||||||||||||
Biological species | Sus scrofa (pig) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||||||||||||||
Authors | Oda, T. / Yanagisawa, H. / Kikkawa, M. | ||||||||||||||||||
Funding support | Japan, 5items
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Citation | Journal: Commun Biol / Year: 2023 Title: Cryo-EM elucidates the uroplakin complex structure within liquid-crystalline lipids in the porcine urothelial membrane. Authors: Haruaki Yanagisawa / Yoshihiro Kita / Toshiyuki Oda / Masahide Kikkawa / Abstract: The urothelium, a distinct epithelial tissue lining the urinary tract, serves as an essential component in preserving urinary tract integrity and thwarting infections. The asymmetric unit membrane ...The urothelium, a distinct epithelial tissue lining the urinary tract, serves as an essential component in preserving urinary tract integrity and thwarting infections. The asymmetric unit membrane (AUM), primarily composed of the uroplakin complex, constitutes a critical permeability barrier in fulfilling this role. However, the molecular architectures of both the AUM and the uroplakin complex have remained enigmatic due to the paucity of high-resolution structural data. In this study, we utilized cryo-electron microscopy to elucidate the three-dimensional structure of the uroplakin complex within the porcine AUM. While the global resolution achieved was 3.5 Å, we acknowledge that due to orientation bias, the resolution in the vertical direction was determined to be 6.3 Å. Our findings unveiled that the uroplakin complexes are situated within hexagonally arranged crystalline lipid membrane domains, rich in hexosylceramides. Moreover, our research rectifies a misconception in a previous model by confirming the existence of a domain initially believed to be absent, and pinpointing the accurate location of a crucial Escherichia coli binding site implicated in urinary tract infections. These discoveries offer valuable insights into the molecular underpinnings governing the permeability barrier function of the urothelium and the orchestrated lipid phase formation within the plasma membrane. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jj5.cif.gz | 300.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jj5.ent.gz | 245.2 KB | Display | PDB format |
PDBx/mmJSON format | 8jj5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jj5_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 8jj5_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8jj5_validation.xml.gz | 42.4 KB | Display | |
Data in CIF | 8jj5_validation.cif.gz | 62.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jj/8jj5 ftp://data.pdbj.org/pub/pdb/validation_reports/jj/8jj5 | HTTPS FTP |
-Related structure data
Related structure data | 36340MC 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
-Protein , 4 types, 4 molecules ABCD
#1: Protein | Mass: 28747.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Urinary bladder / Tissue: Epithelium / References: UniProt: Q06AT5 |
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#2: Protein | Mass: 19299.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: NCBI Reference Sequence: NP_999177.1 / Source: (natural) Sus scrofa (pig) / Organ: Urinary bladder / Tissue: Epithelium |
#3: Protein | Mass: 30339.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Urinary bladder / Tissue: Epithelium / References: UniProt: A0A287AEW0 |
#4: Protein | Mass: 29857.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Urinary bladder / Tissue: Epithelium / References: UniProt: Q06AT4 |
-Sugars , 4 types, 6 molecules
#5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #7: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #8: Sugar | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: 2D ARRAY / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Uroplakin complex / Type: ORGANELLE OR CELLULAR COMPONENT Details: Asymmetric unit membrane isolated by sarkosyl extraction Entity ID: #1-#4 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Sus scrofa (pig) / Organ: Urinary bladder / Tissue: Urothelium |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 0.05 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER/RHODIUM / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 99 % / Chamber temperature: 277 K |
-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 FIELD / Nominal magnification: 64000 X / Nominal defocus max: 4500 nm / Nominal defocus min: 1100 nm / Cs: 2.7 mm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||
Symmetry | Point symmetry: C6 (6 fold cyclic) | |||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 609567 / Symmetry type: POINT | |||||||||||||||||||||||||||
Atomic model building | Source name: AlphaFold / Type: in silico model | |||||||||||||||||||||||||||
Refine LS restraints |
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