+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11388 | |||||||||||||||
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Title | 3.5 A cryo-EM structure of human uromodulin filament core | |||||||||||||||
Map data | half map 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 | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||||||||
Authors | Stanisich JJ / Zyla D / Afanasyev P / Xu J / Pilhofer M / Boeringer D / Glockshuber R | |||||||||||||||
Funding support | Switzerland, 4 items
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Citation | Journal: Elife / Year: 2020 Title: The cryo-EM structure of the human uromodulin filament core reveals a unique assembly mechanism. Authors: Jessica J Stanisich / Dawid S Zyla / Pavel Afanasyev / Jingwei Xu / Anne Kipp / Eric Olinger / Olivier Devuyst / Martin Pilhofer / Daniel Boehringer / Rudi Glockshuber / Abstract: The glycoprotein uromodulin (UMOD) is the most abundant protein in human urine and forms filamentous homopolymers that encapsulate and aggregate uropathogens, promoting pathogen clearance by urine ...The glycoprotein uromodulin (UMOD) is the most abundant protein in human urine and forms filamentous homopolymers that encapsulate and aggregate uropathogens, promoting pathogen clearance by urine excretion. Despite its critical role in the innate immune response against urinary tract infections, the structural basis and mechanism of UMOD polymerization remained unknown. Here, we present the cryo-EM structure of the UMOD filament core at 3.5 Å resolution, comprised of the bipartite zona pellucida (ZP) module in a helical arrangement with a rise of ~65 Å and a twist of ~180°. The immunoglobulin-like ZPN and ZPC subdomains of each monomer are separated by a long linker that interacts with the preceding ZPC and following ZPN subdomains by β-sheet complementation. The unique filament architecture suggests an assembly mechanism in which subunit incorporation could be synchronized with proteolytic cleavage of the C-terminal pro-peptide that anchors assembly-incompetent UMOD precursors to the membrane. | |||||||||||||||
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_11388.map.gz | 118 MB | EMDB map data format | |
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Header (meta data) | emd-11388-v30.xml emd-11388.xml | 21.8 KB 21.8 KB | Display Display | EMDB header |
Images | emd_11388.png | 91.2 KB | ||
Masks | emd_11388_msk_1.map | 125 MB | Mask map | |
Others | emd_11388_additional.map.gz emd_11388_half_map_1.map.gz emd_11388_half_map_2.map.gz | 4.9 MB 116.2 MB 116.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11388 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11388 | HTTPS FTP |
-Related structure data
Related structure data | 6zs5MC 6zyaMC M: atomic model generated by this map C: citing same article (ref.) |
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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_11388.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | half map A | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.084 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_11388_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: density modified main map
File | emd_11388_additional.map | ||||||||||||
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Annotation | density modified main map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map B
File | emd_11388_half_map_1.map | ||||||||||||
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Annotation | half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map B
File | emd_11388_half_map_2.map | ||||||||||||
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Annotation | half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Native human uromodulin filament core
Entire | Name: Native human uromodulin filament core |
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Components |
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-Supramolecule #1: Native human uromodulin filament core
Supramolecule | Name: Native human uromodulin filament core / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Native uromodulin was purified from healthy human urine. |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Experimental: 1.28 kDa/nm |
-Macromolecule #1: Uromodulin
Macromolecule | Name: Uromodulin / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Human (human) |
Molecular weight | Theoretical: 69.82168 KDa |
Sequence | String: MGQPSLTWML MVVVASWFIT TAATDTSEAR WCSECHSNAT CTEDEAVTTC TCQEGFTGDG LTCVDLDECA IPGAHNCSAN SSCVNTPGS FSCVCPEGFR LSPGLGCTDV DECAEPGLSH CHALATCVNV VGSYLCVCPA GYRGDGWHCE CSPGSCGPGL D CVPEGDAL ...String: MGQPSLTWML MVVVASWFIT TAATDTSEAR WCSECHSNAT CTEDEAVTTC TCQEGFTGDG LTCVDLDECA IPGAHNCSAN SSCVNTPGS FSCVCPEGFR LSPGLGCTDV DECAEPGLSH CHALATCVNV VGSYLCVCPA GYRGDGWHCE CSPGSCGPGL D CVPEGDAL VCADPCQAHR TLDEYWRSTE YGEGYACDTD LRGWYRFVGQ GGARMAETCV PVLRCNTAAP MWLNGTHPSS DE GIVSRKA CAHWSGHCCL WDASVQVKAC AGGYYVYNLT APPECHLAYC TDPSSVEGTC EECSIDEDCK SNNGRWHCQC KQD FNITDI SLLEHRLECG ANDMKVSLGK CQLKSLGFDK VFMYLSDSRC SGFNDRDNRD WVSVVTPARD GPCGTVLTRN ETHA TYSNT LYLADEIIIR DLNIKINFAC SYPLDMKVSL KTALQPMVSA LNIRVGGTGM FTVRMALFQT PSYTQPYQGS SVTLS TEAF LYVGTMLDGG DLSRFALLMT NCYATPSSNA TDPLKYFIIQ DRCPHTRDST IQVVENGESS QGRFSVQMFR FAGNYD LVY LHCEVYLCDT MNEKCKPTCS GTRFRSGSVI DQSRVLNLGP ITRKGVQATV SRAFSSLGLL KVWLPLLLSA TLTLTFQ |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 1.58 mg/mL |
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Buffer | pH: 8.2 / Component - Concentration: 0.5 mM / Component - Formula: EDTAEthylenediaminetetraacetic acid / Component - Name: Ethylenediaminetetraacetic acid |
Grid | Model: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: LACEY / Support film - Film thickness: 3.0 nm |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 282 K / Instrument: FEI VITROBOT MARK IV Details: 3.5 ul sample, 30 s wait time, 0.5 s drain time, 13.5 s blotting from the back. |
Details | individual, isolated fibers |
-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: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.3 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Number grids imaged: 2 / Number real images: 9543 / Average exposure time: 6.0 sec. / Average electron dose: 45.0 e/Å2 / Details: Data was joined from two sessions |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 1310000 Details: Autopicking based on the 2D classes from manually chosen filaments |
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CTF correction | Software - Name: Gctf (ver. 1.06) |
Startup model | Type of model: OTHER / Details: Ab initio map generated in cryoSPARC 2 |
Initial angle assignment | Type: NOT APPLICABLE / Software - Name: cryoSPARC (ver. 2.15) |
Final 3D classification | Number classes: 10 / Software - Name: cryoSPARC (ver. 2.15) / Details: only the best resolved 3D class was selected |
Final angle assignment | Type: NOT APPLICABLE / Software - Name: cryoSPARC (ver. 2.15) |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15) / Number images used: 145000 |
Details | Motion correction with dose-weighting |
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A / Chain - Residue range: 400-710 |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 49.9714 / Target criteria: Correlation coefficient |
Output model | PDB-6zs5: PDB-6zya: |