2026-03-18 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY PDBe PDBe 2026-03-02 2026-03-18 2026-03-18 2026-03-18 Swedish Research Council 2020-04936 Sweden Swedish Research Council 2024-05336 Sweden Knut and Alice Wallenberg Foundation 2018.0042 Sweden Molecular basis of ZPD homopolymerization: cryo-EM structure of a native vertebrate egg coat filament Banjara S Okumura H Jovine L Epidermal growth factor domain, EGF domain, zona pellucida module, zona pellucida domain, ZP module, ZP domain, ZP-N domain, ZP-C domain, interdomain linker, extracellular matrix, glycoprotein, N-glycan, structural protein, protein filament, protein polymerization, fertilization, egg coat Fadini A Li M McCoy AJ Banjara S Okumura H Napier E Fontana P Khan AR Jovine L Terwilliger TC Read RJ Hekstra DR AlQuraishi M AlphaFold as a Prior: Experimental Structure Determination Conditioned on a Pretrained Neural Network To Be Published 0353 Okumura H Kohno Y Iwata Y Mori H Aoki N Sato C Kitajima K Nadano D Matsuda T A newly identified zona pellucida glycoprotein, ZPD, and dimeric ZP1 of chicken egg envelope are involved in sperm activation on sperm-egg interaction. Biochem.J. UK 384 191 199 2004 15264999 doi:10.1042/BJ20040299 1470-8728 0043 BIJOAK Nishio S Okumura H Matsuda T Egg-Coat and Zona Pellucida Proteins of Chicken as a Typical Species of Aves. Curr Top Dev Biol 130 307 329 2018 29853181 doi:10.1016/bs.ctdb.2018.02.008 1557-8933 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 Nishio S Emori C Wiseman B Fahrenkamp D Dioguardi E Zamora-Caballero S Bokhove M Han L Stsiapanava A Algarra B Lu Y Kodani M Bainbridge RE Komondor KM Carlson AE Landreh M de Sanctis D Yasumasu S Ikawa M Jovine L ZP2 cleavage blocks polyspermy by modulating the architecture of the egg coat. Cell 187 1440 1459.e24 2024 38490181 doi:10.1016/j.cell.2024.02.013 1097-4172 EMD-10553 consensus EM volume
Cryo-EM of native human uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament
 EMD-10554 consensus EM volume
Cryo-EM of elastase-treated human uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament
 EMD-13378 consensus EM volume
Full-length cryo-EM structure of the native human uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament
 28yj FULLOVERLAP PDB 6TQK unspecified
Cryo-EM of native human uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament
 PDB 6TQL unspecified
Cryo-EM of elastase-treated human uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament
 PDB 7PFP unspecified
Full-length cryo-EM structure of the native human uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament
 PDB 8BQU unspecified
Molecular basis of ZP3/ZP1 heteropolymerization: crystal structure of a native vertebrate egg coat filament
 PDB 8RKI unspecified
Molecular basis of ZP3/ZP1 heteropolymerization: crystal structure of a native vertebrate egg coat filament fragment
 EMDB EMD-10553 consensus EM volume
Cryo-EM of native human uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament
 EMDB EMD-10554 consensus EM volume
Cryo-EM of elastase-treated human uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament
 EMDB EMD-13378 consensus EM volume
Full-length cryo-EM structure of the native human uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament
 EMDB EMD-56971 associated EM volume
Molecular basis of ZPD homopolymerization: cryo-EM structure of a native vertebrate egg coat filament
 Native chicken ZPD homopolymeric filament Native chicken ZPD homopolymeric filament 0 1 Gallus gallus Ovary Oocyte Zona pellucida (specialized extracellular matrix surrounding the oocyte) Uromodulin Gallus gallus Ovary Oocyte 0.036825234 4 LEVO NKSELVSPHNSRGRFALRAKRSSDACVPNPCQHHGGCQVIEDRPICSCKPGFTGAFCQDVVLKLACEEEHMKMMVRKEVF ELLKIPRELVHLKNQACKVSEREEEGEMFFAATLTGENHTACGSVIQQNSSHVSYSNIIETGREAHRGVISRSFQLEVHF SCVYAYEQVVKMPFALTPVDKLVQFMVREGHFNVSMRLYKTASYLEPYDLLTAAVPITDTLYVMLKIEGQHQLRYFLLSV EDCWATPSADPYQDVLHELIEQGCPHDETVTYLNAIGESTTAKFSFQMFQFVGYPKVFLHCRVRLCLPDGPEPCAKQCPT LWRS Q766V2 singleParticle filament 0.7 7.0 10.0 C8H18N2O4S HEPES NITROGEN TFS KRIOS SPOT SCAN BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 0.7000000000000001 2.8000000000000003 165000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN TFS Selectris 10 FEI FALCON IV (4k x 4k) 19953 2.75 53.0 1 1165059 PHASE FLIPPING AND AMPLITUDE CORRECTION C1 4.6 FSC 0.143 CUT-OFF cryoSPARC EMReady 498339 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD 3 emd_56971.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 375.6032 375.6032 375.6032 90.0 90.0 90.0 X Y Z -0.10123206 0.33351332 -0.0004094335 0.0048670517 0.7336 0.7336 0.7336 0.07 AUTHOR cryoSPARC map AlphaFold in silico model FLEXIBLE FIT
Model building was initiated using a local installation of AlphaFold 3 to predict a minimal filament fragment comprising one full-length subunit (chain A) and two partial subunits (chains B and C). The top-ranked prediction was rigid-body fitted into an initial 8.6 A-resolution map (postprocessed with EMReady2) using UCSF Chimera, followed by flexible fitting with Namdinator. Non-resolved terminal regions were trimmed, and well-defined N-glycan densities were manually built in Coot. The model was refined by real-space refinement in Phenix using NCS constraints and increased non-bonded interaction weights, followed by ADP refinement against the unsharpened map. This model served as a starting point for extension with an additional EGF and ZP-N domain from a fourth subunit (chain D). The extended model was docked into the present 4.6 A-resolution map, manually adjusted, and subjected to flexible fitting using the cryo-EM minimizer from cg2all; subsequently, it was refined using Refmac Servalcat task of CCP-EM Doppio, applying global NCS restraints, ProSMART-derived self-restraints, and increased non-bonded interaction weights. Following additional rounds of manual model rebuilding in Coot and real-space refinement in PHENIX (as described above), with positional refinement performed against a LocScale2-postprocessed map and ADP refinement against the unsharpened map, the model was validated using MolProbity and PHENIX. Note that the EGF domain of chain A (and, to a lesser extent, portions of its ZP-N domain near the postprocessed map boundary and the distal regions of the EGF domains in chains C and D) are weakly defined in the density, consistent with their elevated B-factors. These regions were retained in the model to preserve biological completeness, with their conformations constrained by NCS during refinement.
REAL emd_56971_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 281 98 94 125 204 209 94 98 281 68.958405 71.8928 206.1416 90.0 90.0 90.0 Z Y X -0.092842564 14.575158 0.40901437 1.3497534 0.7336 0.7336 0.7336 AUTHOR EMReady2 postprocessed map, boxed around model emd_56971_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 282 99 94 124 203 206 94 99 282 68.958405 72.6264 206.8752 90.0 90.0 90.0 Z Y X -0.029194938 0.50844264 0.019100754 0.04520331 0.7336 0.7336 0.7336 AUTHOR LocScale-2.0 feature-enhanced map, boxed around model emd_56971_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 375.6032 375.6032 375.6032 90.0 90.0 90.0 X Y Z -0.3696975 0.56632894 -0.00014533717 0.024814444 0.7336 0.7336 0.7336 AUTHOR cryoSPARC half-map 2 emd_56971_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 375.6032 375.6032 375.6032 90.0 90.0 90.0 X Y Z -0.37427804 0.54502344 -0.00014471209 0.024533292 0.7336 0.7336 0.7336 AUTHOR cryoSPARC half-map 1