+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36340 | ||||||||||||||||||
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Title | Porcine uroplakin complex | ||||||||||||||||||
Map data | Uroplakin complex | ||||||||||||||||||
Sample |
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Keywords | Urothelium / asymmetric unit membrane / urinary bladder / urinary tract infection / lipid raft / MEMBRANE PROTEIN | ||||||||||||||||||
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 | single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||||||||||||||
Authors | Oda T / Yanagisawa H / Kikkawa M | ||||||||||||||||||
Funding support | Japan, 5 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36340.map.gz | 28.2 MB | EMDB map data format | |
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Header (meta data) | emd-36340-v30.xml emd-36340.xml | 20.6 KB 20.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_36340_fsc.xml | 16.8 KB | Display | FSC data file |
Images | emd_36340.png | 93.2 KB | ||
Masks | emd_36340_msk_1.map | 30.5 MB | Mask map | |
Filedesc metadata | emd-36340.cif.gz | 6.6 KB | ||
Others | emd_36340_half_map_1.map.gz emd_36340_half_map_2.map.gz | 28.2 MB 28.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36340 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36340 | HTTPS FTP |
-Validation report
Summary document | emd_36340_validation.pdf.gz | 1021.6 KB | Display | EMDB validaton report |
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Full document | emd_36340_full_validation.pdf.gz | 1021.2 KB | Display | |
Data in XML | emd_36340_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | emd_36340_validation.cif.gz | 24.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36340 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36340 | HTTPS FTP |
-Related structure data
Related structure data | 8jj5MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_36340.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Uroplakin complex | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_36340_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: half map A
File | emd_36340_half_map_1.map | ||||||||||||
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Annotation | half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map B
File | emd_36340_half_map_2.map | ||||||||||||
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Annotation | half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Uroplakin complex
Entire | Name: Uroplakin complex |
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Components |
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-Supramolecule #1: Uroplakin complex
Supramolecule | Name: Uroplakin complex / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 Details: Asymmetric unit membrane isolated by sarkosyl extraction |
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Source (natural) | Organism: Sus scrofa (pig) / Organ: Urinary bladder / Tissue: Urothelium |
-Macromolecule #1: Tetraspanin
Macromolecule | Name: Tetraspanin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Sus scrofa (pig) / Organ: Urinary bladder / Tissue: Epithelium |
Molecular weight | Theoretical: 28.747469 KDa |
Sequence | String: MASAAAEGEK GSPVVVGLLV VGNIIILLSG LALFAETIWV TADQYRVYPL MGVSGKDDVF AGAWIAIFCG FSFFVVASFG VGAALCRRR SMILTYLVLM LIVYIFECAS CITSYTHRDY MVSNPSLITK QMLTFYSADS DQGRELTRLW DRVMIEQECC G TSGPMDWV ...String: MASAAAEGEK GSPVVVGLLV VGNIIILLSG LALFAETIWV TADQYRVYPL MGVSGKDDVF AGAWIAIFCG FSFFVVASFG VGAALCRRR SMILTYLVLM LIVYIFECAS CITSYTHRDY MVSNPSLITK QMLTFYSADS DQGRELTRLW DRVMIEQECC G TSGPMDWV NFTSAFRAST PEVVFPWPPL CCRRTGNFIP VNEEGCRLGH LDYLFTKGCF EHIGHAIDSY TWGISWFGFA IL MWTLPVM LIAMYFYTTL UniProtKB: Tetraspanin |
-Macromolecule #2: Uroplakin 2
Macromolecule | Name: Uroplakin 2 / type: protein_or_peptide / ID: 2 / Details: NCBI Reference Sequence: NP_999177.1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Sus scrofa (pig) / Organ: Urinary bladder / Tissue: Epithelium |
Molecular weight | Theoretical: 19.299869 KDa |
Sequence | String: MASPLPVRTL PLILILLAVL APGASDFNIS SLSGPLSPAL TESLLVALPP CHLTGGNATL MVRRANDSKV VKSSFMVPPC RGRRELVSV VDSGSGFTVT RLSAYQVTNL VPGTKYYISY LVTKGASTES SREIPMSTLP RRKAEAIGLG MAPTGGMVVI Q VLLSVAMF LLVVGFITAL ALGARK |
-Macromolecule #3: Uroplakin 3A
Macromolecule | Name: Uroplakin 3A / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Sus scrofa (pig) / Organ: Urinary bladder / Tissue: Epithelium |
Molecular weight | Theoretical: 30.339234 KDa |
Sequence | String: MPLLWALLAL GCLQLGSGVN LQPQLASVTF ATNNPTLTTV ALEKPLCMFD SSAALHGTYE VYLYVLVDSA SSRNASVQDS TKTPLSSTP QETEGGRTGP YKAAAFDLAP CSDLPSLDAV RDVSQASEIL NAYLVRVGIN GTCLSDPNFR GLCNPPLSAA T EYRFKYVL ...String: MPLLWALLAL GCLQLGSGVN LQPQLASVTF ATNNPTLTTV ALEKPLCMFD SSAALHGTYE VYLYVLVDSA SSRNASVQDS TKTPLSSTP QETEGGRTGP YKAAAFDLAP CSDLPSLDAV RDVSQASEIL NAYLVRVGIN GTCLSDPNFR GLCNPPLSAA T EYRFKYVL VNISTGLVQD QTLWSDPVCT NQLTPYSAID TWPGRRSGGM IVITSILGSL PFFLLVGFAG AIVLSLMDMG GA DGEMTHD SQITQEAVPK GTSEPSYTSV NRGPPLDRAE VYASKLQD UniProtKB: Uroplakin 3A |
-Macromolecule #4: UPK1B
Macromolecule | Name: UPK1B / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Sus scrofa (pig) / Organ: Urinary bladder / Tissue: Epithelium |
Molecular weight | Theoretical: 29.857492 KDa |
Sequence | String: MAKDDSTVRC FQSLLVFGNV IIGMCGIALT AECIFFVSDQ YSLYPLLEAT DNDDIYGAAW IGIFVGICLF CLSVLGIVGI MKSNRKILL VYFILMFIVY GFEVASCITA ATQRDFFTPN LFLKQMLERY QNNSPPSNDD KWKNNGVTKT WDRLMLQDYC C GVNGPSDW ...String: MAKDDSTVRC FQSLLVFGNV IIGMCGIALT AECIFFVSDQ YSLYPLLEAT DNDDIYGAAW IGIFVGICLF CLSVLGIVGI MKSNRKILL VYFILMFIVY GFEVASCITA ATQRDFFTPN LFLKQMLERY QNNSPPSNDD KWKNNGVTKT WDRLMLQDYC C GVNGPSDW QKYTSAFRTE NNDADYPWPR QCCVMNKLKE PLNLEACKLG VPGYYHNQGC YELISGPMNR HAWGVAWFGF AI LCWTFWV LLGTMFYWSR IEY UniProtKB: UPK1B |
-Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 2 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | 2D array |
-Sample preparation
Concentration | 0.05 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER/RHODIUM / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 99 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 64000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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Output model | PDB-8jj5: |