2025-03-26 REL PDBe INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_ISSN _citation.pdbx_database_id_PubMed _citation.title _citation_author.identifier_ORCID _citation_author.name _em_admin.last_update DATABASE_REFERENCES citation citation_author em_admin _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation_author.identifier_ORCID _em_admin.last_update PDBe PDBe 2024-03-15 2024-11-13 2024-11-13 2025-03-26 Wellcome Trust 102164/B/15/Z United Kingdom Wellcome Trust 106169/Z/14/Z United Kingdom Structure of human ceramide synthase 6 (CerS6) bound to C16:0 (nanobody Nb02) Pascoa TC Pike ACW Chi G Stefanic S Quigley A Chalk R Mukhopadhyay SMM Venkaya S Dix C Moreira T Tessitore A Cole V Chu A Elkins JM Pautsch A Schnapp G Carpenter EP Sauer DB CERAMIDE, SPHINGOLIPID, COVALENT INTERMEDIATE, MEMBRANE PROTEIN Pascoa TC Pike ACW Tautermann CS Chi G Traub M Quigley A Chalk R Stefanic S Thamm S Pautsch A Carpenter EP Schnapp G Sauer DB Structural basis of the mechanism and inhibition of a human ceramide synthase. Nat.Struct.Mol.Biol. US 32 431 440 2025 39528795 doi:10.1038/s41594-024-01414-3 1545-9985 9eot FULLOVERLAP CerS6-Nb02 complex CerS6-Nb02 complex 0 1 2 Homo sapiens 0.1148 Isoform 2 of Ceramide synthase 6 Homo sapiens 0.042418347999999995 2 Homo sapiens LEVO MAGILAWFWNERFWLPHNVTWADLKNTEEATFPQAEDLYLAFPLAFCIFMVRLIFERFVAKPCAIALNIQANGPQIAPPN AILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKPSTLTRFCESMWRFSFYLYVFTYGVRFLKKTPWLW NTRHCWYNYPYQPLTTDLHYYYILELSFYWSLMFSQFTDIKRKDFGIMFLHHLVSIFLITFSYVNNMARVGTLVLCLHDS ADALLEAAKMANYAKFQKMCDLLFVMFAVVFITTRLGIFPLWVLNTTLFESWEIVGPYPSWWVFNLLLLLVQGLNCFWSY LIVKIACKAVSRGKAGKWNPLHVSKDDRSDAENLYFQ Q6ZMG9 2.3.1.291 Nanobody-02 Vicugna pacos 0.014834367 2 Escherichia coli LEVO QLQFVESGGGLVQAGGSLRLSCAASGRTFSRYAVGWFRQAPGKEREFVASITWNGATTYYADSVKGRFTISRDNAKNTVY LQMNSLKPEDTAVYYCALDLYSYGTRDVADFGSWGKGTRVTVSSHHHHHHEPEA PALMITIC ACID 0.00025642399999999994 2 PLM 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE 0.0007901449999999999 2 PC1 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 2 NAG singleParticle particle 5 7.5 20.0 HEPES 200.0 sodium chloride 0.01 glyco-diosgenin
20 mM HEPES pH 7.5, 200 mM NaCl, and 0.01 % (w/v) GDN
 Quantifoil R1.2/1.3 GOLD 200 CARBON HOLEY GLOW DISCHARGE AIR ETHANE 100 277.15 FEI VITROBOT MARK IV
SEC-purified
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 0.8 2.4 130000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K3 BIOQUANTUM (6k x 4k) 1 14656 1.34 56.36 1 4497470
ab-initio cryoSPARC
 1 C2 FOURIER SPACE 3.02 FSC 0.143 CUT-OFF cryoSPARC 3.3.1 non-uniform refinement 153485 MAXIMUM LIKELIHOOD cryoSPARC 3.3.1 MAXIMUM LIKELIHOOD cryoSPARC 3.3.1 non-uniform refinement 10 RELION 3.1.3 emd_19869.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 324 324 324 0 0 0 324 324 324 283.3921 283.3921 283.3921 90.0 90.0 90.0 X Y Z -4.91982 7.2199874 -0.0016676564 0.10757859 0.8746669 0.8746669 0.8746669 0.6 AUTHOR Sharpened CryoSPARC NU refinement map used for refinement 8QZ6 PDB experimental model RIGID BODY FIT REAL emd_19869_msk_1.map emd_19869_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 324 324 324 0 0 0 324 324 324 283.3921 283.3921 283.3921 90.0 90.0 90.0 X Y Z -0.8008073 1.6756419 -0.0016676562 0.03907831 0.8746669 0.8746669 0.8746669 AUTHOR Final CryoSPARC NU refinement map unsharpened emd_19869_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 324 324 324 0 0 0 324 324 324 283.3921 283.3921 283.3921 90.0 90.0 90.0 X Y Z -0.84493333 1.7127678 0.0014298009 0.05914626 0.8746669 0.8746669 0.8746669 AUTHOR Final CryoSPARC NU refinement halfmap2 emd_19869_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 324 324 324 0 0 0 324 324 324 283.3921 283.3921 283.3921 90.0 90.0 90.0 X Y Z -0.8443906 1.8065555 0.0014251666 0.059179556 0.8746669 0.8746669 0.8746669 AUTHOR Final CryoSPARC NU refinement halfmap1