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Yorodumi- EMDB-10554: Cryo-EM of elastase-treated human uromodulin (UMOD)/Tamm-Horsfall... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10554 | |||||||||||||||
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Title | Cryo-EM of elastase-treated human uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament | |||||||||||||||
Map data | Density-modified cryo-EM map of elastase-treated uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament (estimated resolution 3.96 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 / Asparagine N-linked glycosylation / protein transport into plasma membrane raft / micturition / organ or tissue specific immune response / urate transport ...citric acid secretion / metanephric thick ascending limb development / metanephric distal convoluted tubule development / connective tissue replacement / urea transmembrane transport / Asparagine N-linked glycosylation / protein transport into plasma membrane raft / micturition / organ or tissue specific immune response / urate transport / metanephric ascending thin limb development / collecting duct development / protein localization to vacuole / renal urate salt excretion / regulation of protein transport / antibacterial innate immune response / intracellular phosphate ion homeostasis / intracellular chloride ion homeostasis / renal sodium ion absorption / juxtaglomerular apparatus development / glomerular filtration / neutrophil migration / response to water deprivation / intracellular sodium ion homeostasis / potassium 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 / multicellular organismal response to stress / cellular response to unfolded protein / cellular defense response / side of membrane / chaperone-mediated protein folding / : / tumor necrosis factor-mediated signaling pathway / RNA splicing / apoptotic signaling pathway / cilium / lipid metabolic process / intracellular calcium ion homeostasis / autophagy / regulation of blood pressure / spindle pole / Golgi lumen / basolateral plasma membrane / defense response to Gram-negative bacterium / response to lipopolysaccharide / response to xenobiotic stimulus / inflammatory response / apical plasma membrane / 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: 3.96 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_10554.map.gz | 14.1 MB | EMDB map data format | |
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Header (meta data) | emd-10554-v30.xml emd-10554.xml | 38.7 KB 38.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10554_fsc.xml emd_10554_fsc_2.xml | 16.1 KB 16.1 KB | Display Display | FSC data file |
Images | emd_10554.png | 62.8 KB | ||
Others | emd_10554_additional_1.map.gz emd_10554_additional_2.map.gz emd_10554_half_map_1.map.gz emd_10554_half_map_2.map.gz | 129.3 MB 152.3 MB 129.1 MB 129.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10554 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10554 | HTTPS FTP |
-Related structure data
Related structure data | 6tqlMC 6tqkC 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_10554.map.gz / Format: CCP4 / Size: 15.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Density-modified cryo-EM map of elastase-treated uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament (estimated resolution 3.96 A). | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Unsharpened cryo-EM map of elastase-treated uromodulin (UMOD)/Tamm-Horsfall protein...
File | emd_10554_additional_1.map | ||||||||||||
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Annotation | Unsharpened cryo-EM map of elastase-treated uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Supplemental map: emd 10554 additional 2.map
File | emd_10554_additional_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Unsharpened cryo-EM half map of elastase-treated uromodulin (UMOD)/Tamm-Horsfall...
File | emd_10554_half_map_1.map | ||||||||||||
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Annotation | Unsharpened cryo-EM half map of elastase-treated uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unsharpened cryo-EM half map of elastase-treated uromodulin (UMOD)/Tamm-Horsfall...
File | emd_10554_half_map_2.map | ||||||||||||
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Annotation | Unsharpened cryo-EM half map of elastase-treated 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 / Details: Elastase-resistant fragment |
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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: 33.211594 KDa |
Sequence | String: SVEGTCEECS IDEDCKSNNG RWHCQCKQDF NITDISLLEH RLECGANDMK VSLGKCQLKS LGFDKVFMYL SDSRCSGFND RDNRDWVSV VTPARDGPCG TVLTRNETHA TYSNTLYLAD EIIIRDLNIK INFACSYPLD MKVSLKTALQ PMVSALNIRV G GTGMFTVR ...String: SVEGTCEECS IDEDCKSNNG RWHCQCKQDF NITDISLLEH RLECGANDMK VSLGKCQLKS LGFDKVFMYL SDSRCSGFND RDNRDWVSV VTPARDGPCG TVLTRNETHA TYSNTLYLAD EIIIRDLNIK INFACSYPLD MKVSLKTALQ PMVSALNIRV G GTGMFTVR MALFQTPSYT QPYQGSSVTL STEAFLYVGT MLDGGDLSRF ALLMTNCYAT PSSNATDPLK YFIIQDRCPH TR DSTIQVV ENGESSQGRF SVQMFRFAGN YDLVYLHCEV YLCDTMNEKC KPTCSGTRF |
-Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / 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 | 1.00 mg/mL |
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Buffer | pH: 7 / Component - Concentration: 10.0 mM / Component - Formula: C8H17N2NaO4S / Component - Name: Na-HEPES |
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 |
Details | Obtained by limited proteolysis of purified native human uromodulin filaments with porcine pancreatic elastase. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.0 µm / Calibrated defocus min: 1.4000000000000001 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 165000 |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 5683 / Average exposure time: 6.0 sec. / Average electron dose: 45.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |