2026-01-14 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 2024-12-21 2026-01-14 2026-01-14 2026-01-14 German Research Foundation (DFG) INST 216/949-1 FUGG Germany German Research Foundation (DFG) INST 216/512/1 FUGG Germany German Research Foundation (DFG) RTG2550/1 project ID 411422114 Germany The one:one complex of gephyrin and collybistin Burdina N Behrmann E Schwarz G PSD, postsynaptic density, scaffolding protein, inhibitory synapse, LIPID BINDING PROTEIN Burdina N Liebsch F Macha A Behrmann E Schwarz G Structural basis of gephyrin filament formation regulated by collybistin and lipids To Be Published 0353 EMD-52403 consensus EM volume
Dimer of the one:one complex of gephyrin and collybistin
 EMD-52404 consensus EM volume
The four:one complex of gephyrin and collybistin
 EMD-52405 consensus EM volume
Gephyrin E-domain dimer with additional density on the side of the dimer interface
 EMD-52406 consensus EM volume
Gephyrin E-domain dimer with additional density on top of the dimer interface
 EMD-52407 consensus EM volume
Gephyrin (higher oligomer) filament
 EMDB EMD-52403 consensus EM volume
Dimer of the one:one complex of gephyrin and collybistin
 EMDB EMD-52404 consensus EM volume
The four:one complex of gephyrin and collybistin
 EMDB EMD-52405 consensus EM volume
Gephyrin E-domain dimer with additional density on the side of the dimer interface
 EMDB EMD-52406 consensus EM volume
Gephyrin E-domain dimer with additional density on top of the dimer interface
 EMDB EMD-52407 consensus EM volume
Gephyrin (higher oligomer) filament
 EMDB EMD-52402 associated EM volume The one:one complex of gephyrin and collybistin The one:one complex of gephyrin and collybistin 0 1 2 Rattus norvegicus 0.102 Gephyrin dimer 1 1 Rattus norvegicus two copies of collybistin 2 (-SH3) 1 2 Rattus norvegicus Gephyrin Rattus norvegicus Escherichia coli LEVO MRGSHHHHHHGSACELGTMATEGMILTNHDHQIRVGVLTVSDSCFRNLAEDRSGINLKDLVQDPSLLGGTISAYKIVPDEIEEIKETLIDWCDEKELNLILTTGGTGFAPRDVTPEATKEVIEREAPGMALAMLMGSLNVTPLGMLSRPVCGIRGKTLIINLPGSKKGSQECFQFILPALPHAIDLLRDAIVKVKEVHDELEDLPSPPPPLSPPPTTSPHKQTEDKGVQCEEEEEEKKDSGVASTEDSSSSHITAAALAAKIPDSIISRGVQVLPRDTASLSTTPSESPRAQATSRLSTASCPTPKVQSRCSSKENILRASHSAVDITKVARRHRMSPFPLTSMDKAFITVLEMTPVLGTEIINYRDGMGRVLAQDVYAKDNLPPFPASVKDGYAVRAADGPGDRFIIGESQAGEQPTQTVMPGQVMRVTTGAPIPCGADAVVQVEDTELIRESDDGTEELEVRILVQARPGQDIRPIGHDIKRGECVLAKGTHMGPSEIGLLATVGVTEVEVNKFPVVAVMSTGNELLNPEDDLLPGKIRDSNRSTLLATIQEHGYPTINLGIVGDNPDDLLNALNEGISRADVIITSGGVSMGEKDYLKQVLDIDLHAQIHFGRVFMKPGLPTTFATLDIDGVRKIIFALPGNPVSAVVTCNLFVVPALRKMQGILDPRPTIIKARLSCDVKLDPRPEYHRCILTWHHQEPLPWAQSTGNQMSSRLMSMRSANGLLMLPPKTEQYVELHKGEVVDVMVIGRL Q03555-6 2.7.7.75 Collybistin 2 (-SH3) Rattus norvegicus Escherichia coli LEVO MRGSHHHHHHGSACELGTMQWIRGGSGMLWVNQEDGVEEGPSDVQNGHLDPNSDCLCLGRPLQNRDQMRANVINEIMSTERHYIKHLKDICEGYLKQCRKRRDMFSDEQLKVIFGNIEDIYRFQMGFVRDLEKQYNNDDPHLSEIGPCFLEHQDGFWIYSEYCNNHLDACMELSKLMKDSRYQHFFEACRLLQQMIDIAIDGFLLTPVQKICKYPLQLAELLKYTAQDHSDYRYVAAALAVMRNVTQQINERKRRLENIDKIAQWQASVLDWEGDDILDRSSELIYTGEMAWIYQPYGRNQQRVFFLFDHQMVLCKKDLIRRDILYYKGRIDMDKYEVIDIEDGRDDDFNVSMKNAFKLHNKETEEVHLFFAKKLEEKIRWLRAFREERKMVQEDEKIGFEISENQKRQAAMTVRKASKQKVTQRKWHY Q9QX73-2 singleParticle particle 0.333 7.5 25.0 C8H18N2O4S Hepes 250.0 NaCl sodium chloride 2.0 C12H22O11 Sucrose 50.0 C6H14N4O2 Arginine 50.0 C5H10N2O3 Glutamate Quantifoil R1.2/1.3 GOLD 300 GOLD HOLEY GLOW DISCHARGE ETHANE 100 22 FEI VITROBOT MARK IV
the sample was mixed on-grid
 TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 0.5 2.5 96000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN FEI FALCON III (4k x 4k) COUNTING 4096 4096 3 15966 40.0 31.0
Calibrated pixel size: 0.862
 1 445782
after template picking
 cryoSPARC 4.4.1+patch 240110 patch CTF PHASE FLIPPING AND AMPLITUDE CORRECTION
Ab-initio
 1 C1 BACK PROJECTION 3.6 FSC 0.143 CUT-OFF cryoSPARC 4.4.1+patch 240110 Non-uniform refinement 78879 MAXIMUM LIKELIHOOD cryoSPARC 4.4.1+patch 240110 Non-uniform refinement MAXIMUM LIKELIHOOD cryoSPARC 4.4.1+patch 240110 Non-uniform refinement 2 cryoSPARC 4.4.1+patch 240110 Ab-initio emd_52402.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 441.3 441.3 441.3 90.0 90.0 90.0 X Y Z -7.0489364 10.692695000000001 -0.00051935023 0.11811518 1.471 1.471 1.471 1.25 AUTHOR Geph-CB-1:1 complex, combined particles from Folch and non-Folch datasets emd_52402_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 441.344 441.344 441.344 90.0 90.0 90.0 X Y Z -7.425995 9.269114999999999 -0.0001579115 0.1271306 1.724 1.724 1.724 AUTHOR Geph-CB-1:1 complex, particles from non-Folch dataset emd_52402_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 441.3 441.3 441.3 90.0 90.0 90.0 X Y Z -0.0066113686 2.1411376 0.00049142353 0.017541254 1.471 1.471 1.471 AUTHOR Geph-CB-1:1 complex, combined particles from Folch and non-Folch datasets - deepEMhancer, sharpened version emd_52402_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 441.344 441.344 441.344 90.0 90.0 90.0 X Y Z -8.315992 12.222004999999999 -0.00084456574 0.12878798 1.724 1.724 1.724 AUTHOR Geph-CB-1:1 complex, particles from Folch dataset emd_52402_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 441.3 441.3 441.3 90.0 90.0 90.0 X Y Z -2.9867835 6.017716 0.0006087746 0.111729816 1.471 1.471 1.471 AUTHOR Geph-CB-1:1 complex, combined particles from Folch and non-Folch datasets - odd particles emd_52402_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 441.3 441.3 441.3 90.0 90.0 90.0 X Y Z -3.2251863 5.948564 0.0005878532 0.112144284 1.471 1.471 1.471 AUTHOR Geph-CB-1:1 complex, combined particles from Folch and non-Folch datasets - even particles