2025-11-05 REL PDBe INITIAL_RELEASE REPOSITORY PDBe PDBe 2025-08-18 2025-11-05 2025-11-05 2025-11-05 German Research Foundation (DFG) CR 937/2-1 Germany Mouse otoferlin (216-1931) in the lipid-free Ca2+-bound state, "open" conformation (class 1) Cretu C Moser T Ferlin, otoferlin, multi-C2 domain, Ca2+-binding, membrane fusion, MEMBRANE PROTEIN Chen H Cretu C Trebilcock A Evdokimova N Babai N Feldmann L Leidner F Benseler F Mutschall S Esch K Szabo CZK Pena V Pape C Grubmuller H Strenzke N Brose N Wichmann C Preobraschenski J Moser T Structure and function of otoferlin, a synaptic protein of sensory hair cells essential for hearing. Sci Adv US 11 eady8532 eady8532 2025 41091875 doi:10.1126/sciadv.ady8532 2375-2548 9seg FULLOVERLAP PDB 9QE2 unspecified
lipid-bound otoferlin (216-1931)
 PDB 9SE5 unspecified PDB 9SEA unspecified EMDB EMD-54809 associated EM volume
Mouse otoferlin (216-1931) in the lipid-free Ca2+-bound state, "open" conformation (class 1)
 Lipid-free mouse otoferlin (216-1931) in the Ca2+-bound state, "open" conformation (class 1) Lipid-free mouse otoferlin (216-1931) in the Ca2+-bound state, "open" conformation (class 1) 0 1 Mus musculus 0.188 Otoferlin Mus musculus 0.200417609
Mouse otoferlin (residues 216-1931) cloned in-frame with a twin-StrepII affinity tag and an HRV3C protease cleavage site
1 Spodoptera frugiperda LEVO MASWSHPQFEKGGGSGGGSGGGSWSHPQFEKLEVLFQGPGSGDKDCEQSNAMEDLDHLAIQLGDGLDPDSVSLASVTALT SNVSNKRSKPDIKMEPSAGRPMDYQVSITVIEARQLVGLNMDPVVCVEVGDDKKYTSMKESTNCPYYNEYFVFDFHVSPD VMFDKIIKISVIHSKNLLRSGTLVGSFKMDVGTVYSQPEHQFHHKWAILSDPDDISAGLKGYVKCDVAVVGKGDNIKTPH KANETDEDDIEGNLLLPEGVPPERQWARFYVKIYRAEGLPRMNTSLMANVKKAFIGENKDLVDPYVQVFFAGQKGKTSVQ KSSYEPLWNEQVVFTDLFPPLCKRMKVQIRDSDKVNDVAIGTHFIDLRKISNDGDKGFLPTLGPAWVNMYGSTRNYTLLD EHQDLNEGLGEGVSFRARLMLGLAVEILDTSNPELTSSTEVQVEQATPVSESCTGRMEEFFLFGAFLEASMIDRKNGDKP ITFEVTIGNYGNEVDGMSRPLRPRPRKEPGDEEEVDLIQNSSDDEGDEAGDLASVSSTPPMRPQITDRNYFHLPYLERKP CIYIKSWWPDQRRRLYNANIMDHIADKLEEGLNDVQEMIKTEKSYPERRLRGVLEELSCGCHRFLSLSDKDQGRSSRTRL DRERLKSCMRELESMGQQAKSLRAQVKRHTVRDKLRSCQNFLQKLRFLADEPQHSIPDVFIWMMSNNKRIAYARVPSKDL LFSIVEEELGKDCAKVKTLFLKLPGKRGFGSAGWTVQAKLELYLWLGLSKQRKDFLCGLPCGFEEVKAAQGLGLHSFPPI SLVYTKKQAFQLRAHMYQARSLFAADSSGLSDPFARVFFINQSQCTEVLNETLCPTWDQMLVFDNLELYGEAHELRDDPP IIVIEIYDQDSMGKADFMGRTFAKPLVKMADEAYCPPRFPPQLEYYQIYRGSATAGDLLAAFELLQIGPSGKADLPPING PVDMDRGPIMPVPVGIRPVLSKYRVEVLFWGLRDLKRVNLAQVDRPRVDIECAGKGVQSSLIHNYKKNPNFNTLVKWFEV DLPENELLHPPLNIRVVDCRAFGRYTLVGSHAVSSLRRFIYRPPDRSAPNWNTTGEVVVSMEPEEPVKKLETMVKLDATS DAVVKVDVAEDEKERKKKKKKGPSEEPEEEEPDESMLDWWSKYFASIDTMKEQLRQHETSGTDLEEKEEMESAEGLKGPM KSKEKSRAAKEEKKKKNQSPGPGQGSEAPEKKKAKIDELKVYPKELESEFDSFEDWLHTFNLLRGKTGDDEDGSTEEERI VGRFKGSLCVYKVPLPEDVSREAGYDPTYGMFQGIPSNDPINVLVRIYVVRATDLHPADINGKADPYIAIKLGKTDIRDK ENYISKQLNPVFGKSFDIEASFPMESMLTVAVYDWDLVGTDDLIGETKIDLENRFYSKHRATCGIAQTYSIHGYNIWRDP MKPSQILTRLCKEGKVDGPHFGPHGRVRVANRVFTGPSEIEDENGQRKPTDEHVALSALRHWEDIPRVGCRLVPEHVETR PLLNPDKPGIEQGRLELWVDMFPMDMPAPGTPLDISPRKPKKYELRVIVWNTDEVVLEDDDFFTGEKSSDIFVRGWLKGQ QEDKQDTDVHYHSLTGEGNFNWRYLFPFDYLAAEEKIVMSKKESMFSWDETEYKIPARLTLQIWDADHFSADDFLGAIEL DLNRFPRGAKTAKQCTMEMATGEVDVPLVSIFKQKRVKGWWPLLARNENDEFELTGKVEAELHLLTAEEAEKNPVGLARN EPDPLEK A0A0R4J1K2 CALCIUM ION 4.0078e-05 7 CA singleParticle particle 0.42 7.5 25.0 HEPES 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid 150.0 KCl potassium chloride 1.25 C3H8O3 glycerol 0.5 TCEP tris(2-carboxyethyl)phosphine 0.5 CaCl2 calcium chloride Quantifoil R1.2/1.3 COPPER 200 CARBON HOLEY PLASMA CLEANING AIR
Harrick Plasma cleaner, medium settings, in air
 ETHANE-PROPANE 100 277.15 FEI VITROBOT MARK IV
Prior to vitrification, the Ca2+-bound lipid-free otoferlin (216-1931) was crosslinked with glutaraldehyde in batch and purified by size-exclusion chromatography
 TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 1.1 2.3000000000000003 165000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN TFS Selectris 10 EPU v.3.6 FEI FALCON IV (4k x 4k) 1 12269 2.46 38.13
11981 exposures were selected after curation
 1 5201261 cryoSPARC v.4.7 PHASE FLIPPING AND AMPLITUDE CORRECTION
Ab-initio
 1 C1 2.91 FSC 0.143 CUT-OFF cryoSPARC v.4.7 189916 MAXIMUM LIKELIHOOD cryoSPARC v.4.7 MAXIMUM LIKELIHOOD cryoSPARC v.4.7 6 cryoSPARC v.4.7 emd_54809.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 259.2 259.2 259.2 90.0 90.0 90.0 X Y Z -0.102543294 0.16002807 -0.0001457397 0.0036650875 0.72 0.72 0.72 0.012 AUTHOR Calcium-bound lipid-free otoferlin, overall map (class 1) 9QE2 Other experimental model
lipid-bound otoferlin (216-1931)
 OTHER UCSF ChimeraX v.1.8 REAL emd_54809_msk_1.map emd_54809_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 259.2 259.2 259.2 90.0 90.0 90.0 X Y Z -0.13854504 0.20380601 0.000048302958 0.011045549 0.72 0.72 0.72 AUTHOR Calcium-bound lipid-free otoferlin, half map B (class 1) emd_54809_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 259.2 259.2 259.2 90.0 90.0 90.0 X Y Z -0.1360125 0.18731809 0.000047224028 0.01103104 0.72 0.72 0.72 AUTHOR Calcium-bound lipid-free otoferlin, half map A (class 1)