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Yorodumi- EMDB-10553: Cryo-EM of native human uromodulin (UMOD)/Tamm-Horsfall protein (... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10553 | |||||||||||||||
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Title | Cryo-EM of native human uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament. | |||||||||||||||
Map data | Density-modified cryo-em map of native uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament core (estimated resolution 3.35 A). | |||||||||||||||
Sample |
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Function / homology | Function and homology information citric acid secretion / metanephric thick ascending limb development / metanephric distal convoluted tubule development / connective tissue replacement / urea transmembrane transport / protein transport into plasma membrane raft / Asparagine N-linked glycosylation / organ or tissue specific immune response / micturition / metanephric ascending thin limb development ...citric acid secretion / metanephric thick ascending limb development / metanephric distal convoluted tubule development / connective tissue replacement / urea transmembrane transport / protein transport into plasma membrane raft / Asparagine N-linked glycosylation / organ or tissue specific immune response / micturition / metanephric ascending thin limb development / urate transport / collecting duct development / renal urate salt excretion / regulation of protein transport / protein localization to vacuole / antibacterial innate immune response / intracellular chloride ion homeostasis / renal sodium ion absorption / juxtaglomerular apparatus development / glomerular filtration / intracellular phosphate ion homeostasis / neutrophil migration / response to water deprivation / potassium ion homeostasis / intracellular sodium ion homeostasis / regulation of urine volume / endoplasmic reticulum organization / renal water homeostasis / IgG binding / ciliary membrane / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / extrinsic component of membrane / cellular response to unfolded protein / cellular defense response / multicellular organismal response to stress / side of membrane / ERAD pathway / chaperone-mediated protein folding / tumor necrosis factor-mediated signaling pathway / RNA splicing / lipid metabolic process / apoptotic signaling pathway / regulation of blood pressure / cilium / spindle pole / autophagy / intracellular calcium ion homeostasis / Golgi lumen / basolateral plasma membrane / defense response to Gram-negative bacterium / response to lipopolysaccharide / apical plasma membrane / response to xenobiotic stimulus / inflammatory response / negative regulation of cell population proliferation / calcium ion binding / cell surface / endoplasmic reticulum / extracellular space / extracellular exosome / membrane Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) / Human (human) | |||||||||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.35 Å | |||||||||||||||
Authors | Stsiapanava A / Xu C / Carroni M / Wu B / Jovine L | |||||||||||||||
Funding support | Sweden, Singapore, 4 items
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Citation | Journal: Curr Top Dev Biol / Year: 2018 Title: Structure of Zona Pellucida Module Proteins. Authors: Marcel Bokhove / Luca Jovine / Abstract: The egg coat, an extracellular matrix made up of glycoprotein filaments, plays a key role in animal fertilization by acting as a gatekeeper for sperm. Egg coat components polymerize using a common ...The egg coat, an extracellular matrix made up of glycoprotein filaments, plays a key role in animal fertilization by acting as a gatekeeper for sperm. Egg coat components polymerize using a common zona pellucida (ZP) "domain" module that consists of two related immunoglobulin-like domains, called ZP-N and ZP-C. The ZP module has also been recognized in a large number of other secreted proteins with different biological functions, whose mutations are linked to severe human diseases. During the last decade, tremendous progress has been made toward understanding the atomic architecture of the ZP module and the structural basis of its polymerization. Moreover, sperm-binding regions at the N-terminus of mollusk and mammalian egg coat subunits were found to consist of domain repeats that also adopt a ZP-N fold. This discovery revealed an unexpected link between invertebrate and vertebrate fertilization and led to the first structure of an egg coat-sperm protein recognition complex. In this review we summarize these exciting findings, discuss their functional implications, and outline future challenges that must be addressed in order to develop a comprehensive view of this family of biomedically important extracellular molecules. #2: Journal: Biol. Cellulaire / Year: 1980 Title: Etude chimique et ultrastructurale de la glycoproteine de Tamm et Horsfall ou uromucoide. Authors: Delain E / Thiery JP / Coulard D / Joliviene A / Hartman L #14: Journal: bioRxiv / Year: 2020 Title: Cryo-EM structure of native human uromodulin, a zona pellucida module polymer. Authors: Stsiapanava A / Xu C / Brunati M / Zamora-Caballero S / Schaeffer C / Han L / Carroni M / Yasumasu S / Rampoldi L / Wu B / Jovine L | |||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10553.map.gz | 7.3 MB | EMDB map data format | |
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Header (meta data) | emd-10553-v30.xml emd-10553.xml | 40.4 KB 40.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10553_fsc.xml emd_10553_fsc_2.xml | 11.5 KB 12.4 KB | Display Display | FSC data file |
Images | emd_10553.png | 72.6 KB | ||
Others | emd_10553_additional_1.map.gz emd_10553_additional_2.map.gz emd_10553_half_map_1.map.gz emd_10553_half_map_2.map.gz | 12.4 MB 46 MB 46.2 MB 46.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10553 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10553 | HTTPS FTP |
-Validation report
Summary document | emd_10553_validation.pdf.gz | 299.6 KB | Display | EMDB validaton report |
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Full document | emd_10553_full_validation.pdf.gz | 298.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10553 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10553 | HTTPS FTP |
-Related structure data
Related structure data | 6tqkMC 6tqlC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10553.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Density-modified cryo-em map of native uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament core (estimated resolution 3.35 A). | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Density-modified cryo-em map of native uromodulin (UMOD)/Tamm-Horsfall protein...
File | emd_10553_additional_1.map | ||||||||||||
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Annotation | Density-modified cryo-em map of native uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament (estimated resolution 3.76 A). | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened cryo-EM map of native uromodulin (UMOD)/Tamm-Horsfall protein...
File | emd_10553_additional_2.map | ||||||||||||
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Annotation | Unsharpened cryo-EM map of native uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unsharpened cryo-EM half map of native uromodulin (UMOD)/Tamm-Horsfall...
File | emd_10553_half_map_1.map | ||||||||||||
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Annotation | Unsharpened cryo-EM half map of native uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unsharpened cryo-EM half map of native uromodulin (UMOD)/Tamm-Horsfall...
File | emd_10553_half_map_2.map | ||||||||||||
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Annotation | Unsharpened cryo-EM half map of native uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Uromodulin (UMOD)/Tamm-Horsfall protein (THP)
Entire | Name: Uromodulin (UMOD)/Tamm-Horsfall protein (THP) |
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Components |
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-Supramolecule #1: Uromodulin (UMOD)/Tamm-Horsfall protein (THP)
Supramolecule | Name: Uromodulin (UMOD)/Tamm-Horsfall protein (THP) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Uromodulin
Macromolecule | Name: Uromodulin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Human (human) |
Molecular weight | Theoretical: 61.498816 KDa |
Sequence | String: DTSEARWCSE CHSNATCTED EAVTTCTCQE GFTGDGLTCV DLDECAIPGA HNCSANSSCV NTPGSFSCVC PEGFRLSPGL GCTDVDECA EPGLSHCHAL ATCVNVVGSY LCVCPAGYRG DGWHCECSPG SCGPGLDCVP EGDALVCADP CQAHRTLDEY W RSTEYGEG ...String: DTSEARWCSE CHSNATCTED EAVTTCTCQE GFTGDGLTCV DLDECAIPGA HNCSANSSCV NTPGSFSCVC PEGFRLSPGL GCTDVDECA EPGLSHCHAL ATCVNVVGSY LCVCPAGYRG DGWHCECSPG SCGPGLDCVP EGDALVCADP CQAHRTLDEY W RSTEYGEG YACDTDLRGW YRFVGQGGAR MAETCVPVLR CNTAAPMWLN GTHPSSDEGI VSRKACAHWS GHCCLWDASV QV KACAGGY YVYNLTAPPE CHLAYCTDPS SVEGTCEECS IDEDCKSNNG RWHCQCKQDF NITDISLLEH RLECGANDMK VSL GKCQLK SLGFDKVFMY LSDSRCSGFN DRDNRDWVSV VTPARDGPCG TVLTRNETHA TYSNTLYLAD EIIIRDLNIK INFA CSYPL DMKVSLKTAL QPMVSALNIR VGGTGMFTVR MALFQTPSYT QPYQGSSVTL STEAFLYVGT MLDGGDLSRF ALLMT NCYA TPSSNATDPL KYFIIQDRCP HTRDSTIQVV ENGESSQGRF SVQMFRFAGN YDLVYLHCEV YLCDTMNEKC KPTCSG TRF |
-Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / 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 | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 0.85 mg/mL |
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Buffer | pH: 7 |
Grid | Model: Quantifoil R2/2 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber temperature: 294 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 2300 / Average exposure time: 6.0 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.5 µm / Calibrated defocus min: 1.4000000000000001 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |