2024-10-09 REL PDBe PDBe PDBe 2019-12-16 2020-11-04 2020-11-04 2024-10-09 Swedish Research Council 2016-03999 Sweden Knut and Alice Wallenberg Foundation 2018.0042 Sweden Ministry of Education (MoE, Singapore) 2017-T1-001-168 Singapore Ministry of Education (MoE, Singapore) 2016-T2-1-010 Singapore Cryo-EM of native human uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament Stsiapanava A Xu C ZP MODULE, ZP DOMAIN, ZP-N DOMAIN, ZP-C DOMAIN, INTERDOMAIN LINKER, EGF DOMAIN, EXTRACELLULAR MATRIX, GLYCOPROTEIN, N-GLYCAN, STRUCTURAL PROTEIN, PROTEIN FILAMENT, PROTEIN POLYMERIZATION Stsiapanava A Xu C Brunati M Zamora-Caballero S Schaeffer C Bokhove M Han L Hebert H Carroni M Yasumasu S Rampoldi L Wu B Jovine L Cryo-EM structure of native human uromodulin, a zona pellucida module polymer. Embo J. UK 39 e106807 e106807 2020 33196145 doi:10.15252/embj.2020106807 1460-2075 0897 EMJODG Tamm I Horsfall FL Characterization and separation of an inhibitor of viral hemagglutination present in urine. Proc. Soc. Exp. Biol. Med. 74 106 108 1950 15430405 0037-9727 Delain E Thiery JP Coulard D Joliviene A Hartman L Etude chimique et ultrastructurale de la glycoproteine de Tamm et Horsfall ou uromucoide. Biol. Cellulaire 39 31 42 1980 Pennica D Kohr WJ Kuang WJ Glaister D Aggarwal BB Chen EY Goeddel DV Identification of human uromodulin as the Tamm-Horsfall urinary glycoprotein. Science US 236 83 88 1987 3453112 doi:10.1126/science.3453112 0036-8075 0038 SCIEAS Jovine L Qi H Williams Z Litscher E Wassarman PM The ZP domain is a conserved module for polymerization of extracellular proteins. Nat. Cell Biol. UK 4 457 461 2002 12021773 doi:10.1038/ncb802 1465-7392 Serafini-Cessi F Malagolini N Cavallone D Tamm-Horsfall glycoprotein: biology and clinical relevance. Am. J. Kidney Dis. 42 658 676 2003 14520616 doi:10.1016/s0272-6386(03)00829-1 1523-6838 Jovine L Qi H Williams Z Litscher ES Wassarman PM A duplicated motif controls assembly of zona pellucida domain proteins. Proc. Natl. Acad. Sci. U.S.A. US 101 5922 5927 2004 15079052 doi:10.1073/pnas.0401600101 0027-8424 0040 PNASA6 Jovine L Darie CC Litscher ES Wassarman PM Zona pellucida domain proteins. Annu. Rev. Biochem. US 74 83 114 2005 15952882 doi:10.1146/annurev.biochem.74.082803.133039 0066-4154 0413 ARBOAW Schaeffer C Santambrogio S Perucca S Casari G Rampoldi L Analysis of uromodulin polymerization provides new insights into the mechanisms regulating ZP domain-mediated protein assembly. Mol. Biol. Cell US 20 589 599 2009 19005207 doi:10.1091/mbc.e08-08-0876 1939-4586 Han L Monne M Okumura H Schwend T Cherry AL Flot D Matsuda T Jovine L Insights into egg coat assembly and egg-sperm interaction from the X-ray structure of full-length ZP3. Cell 143 404 415 2010 20970175 doi:10.1016/j.cell.2010.09.041 1097-4172 Rampoldi L Scolari F Amoroso A Ghiggeri G Devuyst O The rediscovery of uromodulin (Tamm-Horsfall protein): from tubulointerstitial nephropathy to chronic kidney disease. Kidney Int. 80 338 347 2011 21654721 doi:10.1038/ki.2011.134 1523-1755 Brunati M Perucca S Han L Cattaneo A Consolato F Andolfo A Schaeffer C Olinger E Peng J Santambrogio S Perrier R Li S Bokhove M Bachi A Hummler E Devuyst O Wu Q Jovine L Rampoldi L The serine protease hepsin mediates urinary secretion and polymerisation of Zona Pellucida domain protein uromodulin. Elife US 4 e08887 2015 26673890 doi:10.7554/eLife.08887 2050-084X Bokhove M Nishimura K Brunati M Han L de Sanctis D Rampoldi L Jovine L A structured interdomain linker directs self-polymerization of human uromodulin. Proc. Natl. Acad. Sci. U.S.A. US 113 1552 1557 2016 26811476 doi:10.1073/pnas.1519803113 1091-6490 0040 PNASA6 Bokhove M Jovine L Structure of zona pellucida module proteins. Curr. Top. Dev. Biol. 130 413 442 2018 29853186 doi:10.1016/bs.ctdb.2018.02.007 1557-8933 Stsiapanava A Xu C Brunati M Zamora-Caballero S Schaeffer C Han L Carroni M Yasumasu S Rampoldi L Wu B Jovine L Cryo-EM structure of native human uromodulin, a zona pellucida module polymer. bioRxiv US 2020 doi:10.1101/2020.05.28.119206 2692-8205 EMD-10554 other EM volume
Cryo-EM of elastase-treated human uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament.
 6tqk FULLOVERLAP Uromodulin (UMOD)/Tamm-Horsfall protein (THP) Uromodulin (UMOD)/Tamm-Horsfall protein (THP) 0 1 Homo sapiens Uromodulin Homo sapiens 0.061498816 3 LEVO DTSEARWCSECHSNATCTEDEAVTTCTCQEGFTGDGLTCVDLDECAIPGAHNCSANSSCVNTPGSFSCVCPEGFRLSPGL GCTDVDECAEPGLSHCHALATCVNVVGSYLCVCPAGYRGDGWHCECSPGSCGPGLDCVPEGDALVCADPCQAHRTLDEYW RSTEYGEGYACDTDLRGWYRFVGQGGARMAETCVPVLRCNTAAPMWLNGTHPSSDEGIVSRKACAHWSGHCCLWDASVQV KACAGGYYVYNLTAPPECHLAYCTDPSSVEGTCEECSIDEDCKSNNGRWHCQCKQDFNITDISLLEHRLECGANDMKVSL GKCQLKSLGFDKVFMYLSDSRCSGFNDRDNRDWVSVVTPARDGPCGTVLTRNETHATYSNTLYLADEIIIRDLNIKINFA CSYPLDMKVSLKTALQPMVSALNIRVGGTGMFTVRMALFQTPSYTQPYQGSSVTLSTEAFLYVGTMLDGGDLSRFALLMT NCYATPSSNATDPLKYFIIQDRCPHTRDSTIQVVENGESSQGRFSVQMFRFAGNYDLVYLHCEVYLCDTMNEKCKPTCSG TRF P07911 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 2 NAG helical filament 0.85 7.0 Quantifoil R2/2 GOLD 300 CARBON HOLEY GLOW DISCHARGE AIR ETHANE 294 FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 1.4000000000000001 3.5 130000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20 GATAN K2 QUANTUM (4k x 4k) COUNTING 1 2300 6.0 40.0 1 62.5 180 C1 3.35 OTHER RELION 3.0.5 PHENIX phenix.resolve_cryo_em
PHENIX ResolveCryoEM FSCref=0.5
288403 412322
Featureless Gaussian cylinder
 NOT APPLICABLE RELION 3.0.5 emd_10553.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 213 103 93 0 74 79 93 103 213 98.579994 109.17999 225.77998 90.0 90.0 90.0 Z Y X -28.094010999999998 45.33775 0.00000000003902 1.0 1.06 1.06 1.06 1.8 AUTHOR Density-modified cryo-em map of native uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament core (estimated resolution 3.35 A). 4WRN A 296-429 PDB experimental model 4WRN A 466-587 PDB experimental model FLEXIBLE FIT REAL 115.879999999999995 emd_10553_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 249 139 101 0 56 75 101 139 249 107.06 147.34 263.93997 90.0 90.0 90.0 Z Y X -19.290028 31.652906000000002 0.000000000003553 1.0 1.06 1.06 1.06 AUTHOR Density-modified cryo-em map of native uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament (estimated resolution 3.76 A). emd_10553_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 250 250 250 0 0 0 250 250 250 265.0 265.0 265.0 90.0 90.0 90.0 X Y Z -0.017465917 0.047251932 0.00038221708 0.0018355391 1.06 1.06 1.06 AUTHOR Unsharpened cryo-EM map of native uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament. emd_10553_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 250 250 250 0 0 0 250 250 250 265.0 265.0 265.0 90.0 90.0 90.0 X Y Z -0.01935318 0.048054844 0.00035852945 0.001892752 1.06 1.06 1.06 AUTHOR Unsharpened cryo-EM half map of native uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament. emd_10553_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 250 250 250 0 0 0 250 250 250 265.0 265.0 265.0 90.0 90.0 90.0 X Y Z -0.016860858 0.04750516 0.0003634315 0.001894014 1.06 1.06 1.06 AUTHOR Unsharpened cryo-EM half map of native uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament.