HEADER TRANSFERASE 11-MAY-26 26QJ TITLE CRYO-EM STRUCTURE OF HUMAN UGCG BOUND TO MIGLUSTAT COMPND MOL_ID: 1; COMPND 2 MOLECULE: CERAMIDE GLUCOSYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GLCT-1,GLUCOSYLCERAMIDE SYNTHASE,GCS,GLYCOSYLCERAMIDE COMPND 5 SYNTHASE,UDP-GLUCOSE CERAMIDE GLUCOSYLTRANSFERASE,UDP-GLUCOSE:N- COMPND 6 ACYLSPHINGOSINE D-GLUCOSYLTRANSFERASE; COMPND 7 EC: 2.4.1.80; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: UGCG; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS CERAMIDE GLUCOSYLTRANSFERASE; UGCG;MIGLUSTAT, TRANSFERASE EXPDTA ELECTRON MICROSCOPY AUTHOR C.WU,S.JIN,J.XU,J.J.WANG,X.GUO,Y.LI,Z.CAO,M.JIANG,Q.YUAN,W.HU,C.LI, AUTHOR 2 Y.XU,M.W.WANG,Y.JIANG,H.E.XU REVDAT 1 02-SEP-26 26QJ 0 JRNL AUTH C.WU,S.JIN,J.XU,J.J.WANG,X.GUO,Y.LI,Z.CAO,M.JIANG,Q.YUAN, JRNL AUTH 2 W.HU,C.LI,Y.XU,M.W.WANG,Y.JIANG,H.E.XU JRNL TITL PRIMATE-SPECIFIC REGULATION OF THE HUMAN GLYCOSPHINGOLIPID JRNL TITL 2 GATEKEEPER UGCG JRNL REF NATURE 2026 JRNL REFN ESSN 1476-4687 JRNL DOI 10.1038/S41586-026-10927-4 REMARK 2 REMARK 2 RESOLUTION. 3.34 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, PHENIX, CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 3.340 REMARK 3 NUMBER OF PARTICLES : 156456 REMARK 3 CTF CORRECTION METHOD : NONE REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 26QJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 15-MAY-26. REMARK 100 THE DEPOSITION ID IS D_1300074123. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : CERAMIDE GLUCOSYLTRANSFERASE REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TALOS ARCTICA REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 5000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5000.00 REMARK 245 ILLUMINATION MODE : OTHER REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : OTHER REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 LYS A 40 REMARK 465 ALA A 41 REMARK 465 THR A 42 REMARK 465 ASP A 43 REMARK 465 LYS A 44 REMARK 465 GLN A 45 REMARK 465 GLY A 385 REMARK 465 GLY A 386 REMARK 465 THR A 387 REMARK 465 ALA A 388 REMARK 465 GLU A 389 REMARK 465 GLU A 390 REMARK 465 ILE A 391 REMARK 465 LEU A 392 REMARK 465 ASP A 393 REMARK 465 VAL A 394 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 376 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 379 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 381 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 383 CG CD NE CZ NH1 NH2 REMARK 470 CYS A 384 SG REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 177 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 356 NE - CZ - NH2 ANGL. DEV. = 3.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LEU A 3 -83.82 -125.42 REMARK 500 LYS A 60 108.72 -168.51 REMARK 500 ASP A 77 71.28 -101.46 REMARK 500 THR A 191 -79.83 -112.69 REMARK 500 ALA A 223 32.33 -92.54 REMARK 500 ASN A 260 40.99 -140.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-80827 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF HUMAN UGCG BOUND TO MIGLUSTAT DBREF 26QJ A 1 394 UNP Q16739 CEGT_HUMAN 1 394 SEQRES 1 A 394 MET ALA LEU LEU ASP LEU ALA LEU GLU GLY MET ALA VAL SEQRES 2 A 394 PHE GLY PHE VAL LEU PHE LEU VAL LEU TRP LEU MET HIS SEQRES 3 A 394 PHE MET ALA ILE ILE TYR THR ARG LEU HIS LEU ASN LYS SEQRES 4 A 394 LYS ALA THR ASP LYS GLN PRO TYR SER LYS LEU PRO GLY SEQRES 5 A 394 VAL SER LEU LEU LYS PRO LEU LYS GLY VAL ASP PRO ASN SEQRES 6 A 394 LEU ILE ASN ASN LEU GLU THR PHE PHE GLU LEU ASP TYR SEQRES 7 A 394 PRO LYS TYR GLU VAL LEU LEU CYS VAL GLN ASP HIS ASP SEQRES 8 A 394 ASP PRO ALA ILE ASP VAL CYS LYS LYS LEU LEU GLY LYS SEQRES 9 A 394 TYR PRO ASN VAL ASP ALA ARG LEU PHE ILE GLY GLY LYS SEQRES 10 A 394 LYS VAL GLY ILE ASN PRO LYS ILE ASN ASN LEU MET PRO SEQRES 11 A 394 GLY TYR GLU VAL ALA LYS TYR ASP LEU ILE TRP ILE CYS SEQRES 12 A 394 ASP SER GLY ILE ARG VAL ILE PRO ASP THR LEU THR ASP SEQRES 13 A 394 MET VAL ASN GLN MET THR GLU LYS VAL GLY LEU VAL HIS SEQRES 14 A 394 GLY LEU PRO TYR VAL ALA ASP ARG GLN GLY PHE ALA ALA SEQRES 15 A 394 THR LEU GLU GLN VAL TYR PHE GLY THR SER HIS PRO ARG SEQRES 16 A 394 TYR TYR ILE SER ALA ASN VAL THR GLY PHE LYS CYS VAL SEQRES 17 A 394 THR GLY MET SER CYS LEU MET ARG LYS ASP VAL LEU ASP SEQRES 18 A 394 GLN ALA GLY GLY LEU ILE ALA PHE ALA GLN TYR ILE ALA SEQRES 19 A 394 GLU ASP TYR PHE MET ALA LYS ALA ILE ALA ASP ARG GLY SEQRES 20 A 394 TRP ARG PHE ALA MET SER THR GLN VAL ALA MET GLN ASN SEQRES 21 A 394 SER GLY SER TYR SER ILE SER GLN PHE GLN SER ARG MET SEQRES 22 A 394 ILE ARG TRP THR LYS LEU ARG ILE ASN MET LEU PRO ALA SEQRES 23 A 394 THR ILE ILE CYS GLU PRO ILE SER GLU CYS PHE VAL ALA SEQRES 24 A 394 SER LEU ILE ILE GLY TRP ALA ALA HIS HIS VAL PHE ARG SEQRES 25 A 394 TRP ASP ILE MET VAL PHE PHE MET CYS HIS CYS LEU ALA SEQRES 26 A 394 TRP PHE ILE PHE ASP TYR ILE GLN LEU ARG GLY VAL GLN SEQRES 27 A 394 GLY GLY THR LEU CYS PHE SER LYS LEU ASP TYR ALA VAL SEQRES 28 A 394 ALA TRP PHE ILE ARG GLU SER MET THR ILE TYR ILE PHE SEQRES 29 A 394 LEU SER ALA LEU TRP ASP PRO THR ILE SER TRP ARG THR SEQRES 30 A 394 GLY ARG TYR ARG LEU ARG CYS GLY GLY THR ALA GLU GLU SEQRES 31 A 394 ILE LEU ASP VAL HET CLR A 401 28 HET NBV A 402 15 HETNAM CLR CHOLESTEROL HETNAM NBV (2R,3R,4R,5S)-1-BUTYL-2-(HYDROXYMETHYL)PIPERIDINE-3,4, HETNAM 2 NBV 5-TRIOL FORMUL 2 CLR C27 H46 O FORMUL 3 NBV C10 H21 N O4 HELIX 1 AA1 LEU A 3 LEU A 37 1 35 HELIX 2 AA2 ASN A 65 GLU A 75 1 11 HELIX 3 AA3 PRO A 93 TYR A 105 1 13 HELIX 4 AA4 ASN A 122 ALA A 135 1 14 HELIX 5 AA5 ASP A 152 GLN A 160 1 9 HELIX 6 AA6 GLY A 179 THR A 191 1 13 HELIX 7 AA7 THR A 191 GLY A 204 1 14 HELIX 8 AA8 LYS A 217 GLN A 222 1 6 HELIX 9 AA9 LEU A 226 ALA A 230 5 5 HELIX 10 AB1 ALA A 234 ALA A 242 1 9 HELIX 11 AB2 ILE A 243 ARG A 246 5 4 HELIX 12 AB3 SER A 265 LEU A 284 1 20 HELIX 13 AB4 ALA A 286 GLU A 291 1 6 HELIX 14 AB5 PRO A 292 SER A 294 5 3 HELIX 15 AB6 GLU A 295 ARG A 312 1 18 HELIX 16 AB7 ASP A 314 GLY A 339 1 26 HELIX 17 AB8 SER A 345 ASP A 370 1 26 SHEET 1 AA1 7 ARG A 111 ILE A 114 0 SHEET 2 AA1 7 TYR A 81 VAL A 87 1 N VAL A 83 O ARG A 111 SHEET 3 AA1 7 VAL A 53 LEU A 59 1 N LEU A 55 O LEU A 84 SHEET 4 AA1 7 LEU A 139 CYS A 143 1 O TRP A 141 N SER A 54 SHEET 5 AA1 7 SER A 212 ARG A 216 -1 O MET A 215 N ILE A 140 SHEET 6 AA1 7 LEU A 167 HIS A 169 -1 N VAL A 168 O LEU A 214 SHEET 7 AA1 7 PHE A 250 MET A 252 1 O ALA A 251 N HIS A 169 SHEET 1 AA2 3 ILE A 147 ARG A 148 0 SHEET 2 AA2 3 ALA A 257 GLN A 259 -1 O MET A 258 N ARG A 148 SHEET 3 AA2 3 PRO A 172 VAL A 174 1 N TYR A 173 O GLN A 259 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 CONECT 3014 3015 3023 CONECT 3015 3014 3016 CONECT 3016 3015 3017 3041 CONECT 3017 3016 3018 CONECT 3018 3017 3019 3023 CONECT 3019 3018 3020 CONECT 3020 3019 3021 CONECT 3021 3020 3022 3027 CONECT 3022 3021 3023 3024 CONECT 3023 3014 3018 3022 3032 CONECT 3024 3022 3025 CONECT 3025 3024 3026 CONECT 3026 3025 3027 3030 3031 CONECT 3027 3021 3026 3028 CONECT 3028 3027 3029 CONECT 3029 3028 3030 CONECT 3030 3026 3029 3033 CONECT 3031 3026 CONECT 3032 3023 CONECT 3033 3030 3034 3035 CONECT 3034 3033 CONECT 3035 3033 3036 CONECT 3036 3035 3037 CONECT 3037 3036 3038 CONECT 3038 3037 3039 3040 CONECT 3039 3038 CONECT 3040 3038 CONECT 3041 3016 CONECT 3042 3043 CONECT 3043 3042 3044 CONECT 3044 3043 3045 3051 CONECT 3045 3044 3046 3047 CONECT 3046 3045 CONECT 3047 3045 3048 3049 CONECT 3048 3047 CONECT 3049 3047 3050 3052 CONECT 3050 3049 CONECT 3051 3044 3052 3053 CONECT 3052 3049 3051 CONECT 3053 3051 3054 CONECT 3054 3053 3055 CONECT 3055 3054 3056 CONECT 3056 3055 MASTER 173 0 2 17 10 0 0 6 3055 1 43 31 END