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- EMDB-36340: Porcine uroplakin complex -

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Basic information

Entry
Database: EMDB / ID: EMD-36340
TitlePorcine uroplakin complex
Map dataUroplakin complex
Sample
  • Organelle or cellular component: Uroplakin complex
    • Protein or peptide: Tetraspanin
    • Protein or peptide: Uroplakin 2
    • Protein or peptide: Uroplakin 3A
    • Protein or peptide: UPK1B
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsUrothelium / 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
Uroplakin-3a / Uroplakin-3 / Tetraspanin, animals / Tetraspanin, EC2 domain superfamily / Tetraspanin/Peripherin / Tetraspanin family
Similarity search - Domain/homology
Uroplakin 3A / UPK1B / Tetraspanin
Similarity search - Component
Biological speciesSus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsOda T / Yanagisawa H / Kikkawa M
Funding support Japan, 5 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP21H02654 Japan
Japan Society for the Promotion of Science (JSPS)JP22H05538 Japan
Japan Society for the Promotion of Science (JSPS)JP21H05248 Japan
Japan Agency for Medical Research and Development (AMED)JP22ama121002 Japan
Japan Agency for Medical Research and Development (AMED)JP23ama121002 Japan
CitationJournal: Commun Biol / Year: 2023
Title: Cryo-EM elucidates the uroplakin complex structure within liquid-crystalline lipids in the porcine urothelial membrane
Authors: Yanagisawa H / Kita Y / Oda T / Kikkawa M
History
DepositionMay 29, 2023-
Header (metadata) releaseJun 14, 2023-
Map releaseJun 14, 2023-
UpdateDec 27, 2023-
Current statusDec 27, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36340.png

Downloads & links

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Map

FileDownload / File: emd_36340.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUroplakin complex
Voxel sizeX=Y=Z: 1.35 Å
Density
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.6115475 - 2.5322022
Average (Standard dev.)-0.005224811 (±0.123521835)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 270.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_36340_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_36340_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_36340_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Uroplakin complex

EntireName: Uroplakin complex
Components
  • Organelle or cellular component: Uroplakin complex
    • Protein or peptide: Tetraspanin
    • Protein or peptide: Uroplakin 2
    • Protein or peptide: Uroplakin 3A
    • Protein or peptide: UPK1B
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Uroplakin complex

SupramoleculeName: Uroplakin complex / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: Asymmetric unit membrane isolated by sarkosyl extraction
Source (natural)Organism: Sus scrofa (pig) / Organ: Urinary bladder / Tissue: Urothelium

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Macromolecule #1: Tetraspanin

MacromoleculeName: Tetraspanin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig) / Organ: Urinary bladder / Tissue: Epithelium
Molecular weightTheoretical: 28.747469 KDa
SequenceString: 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

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Macromolecule #2: Uroplakin 2

MacromoleculeName: Uroplakin 2 / type: protein_or_peptide / ID: 2 / Details: NCBI Reference Sequence: NP_999177.1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig) / Organ: Urinary bladder / Tissue: Epithelium
Molecular weightTheoretical: 19.299869 KDa
SequenceString:
MASPLPVRTL PLILILLAVL APGASDFNIS SLSGPLSPAL TESLLVALPP CHLTGGNATL MVRRANDSKV VKSSFMVPPC RGRRELVSV VDSGSGFTVT RLSAYQVTNL VPGTKYYISY LVTKGASTES SREIPMSTLP RRKAEAIGLG MAPTGGMVVI Q VLLSVAMF LLVVGFITAL ALGARK

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Macromolecule #3: Uroplakin 3A

MacromoleculeName: Uroplakin 3A / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig) / Organ: Urinary bladder / Tissue: Epithelium
Molecular weightTheoretical: 30.339234 KDa
SequenceString: 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

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Macromolecule #4: UPK1B

MacromoleculeName: UPK1B / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig) / Organ: Urinary bladder / Tissue: Epithelium
Molecular weightTheoretical: 29.857492 KDa
SequenceString: 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

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Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state2D array

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Sample preparation

Concentration0.05 mg/mL
BufferpH: 7.4
GridModel: 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
VitrificationCryogen name: ETHANE / Chamber humidity: 99 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 64000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Averaged subtomogram
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 609567
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-8jj5:
Porcine uroplakin complex

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