HEADER TRANSFERASE 11-MAY-26 26QS TITLE CRYO-EM STRUCTURE OF HUMAN UGCG BOUND TO UDP-GLUCOSE 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, 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 26QS 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. 2.88 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) : 2.880 REMARK 3 NUMBER OF PARTICLES : 162423 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 26QS 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_1300074126. 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 : FEI FALCON IV (4K 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 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 VAL A 13 CG1 CG2 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 PRO A 64 -9.73 -59.29 REMARK 500 LYS A 206 58.60 -95.28 REMARK 500 VAL A 310 -62.67 -94.35 REMARK 500 THR A 377 49.36 36.30 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-80832 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF HUMAN UGCG BOUND TO UDP-GLUCOSE DBREF 26QS A 1 391 UNP Q16739 CEGT_HUMAN 1 391 SEQRES 1 A 391 MET ALA LEU LEU ASP LEU ALA LEU GLU GLY MET ALA VAL SEQRES 2 A 391 PHE GLY PHE VAL LEU PHE LEU VAL LEU TRP LEU MET HIS SEQRES 3 A 391 PHE MET ALA ILE ILE TYR THR ARG LEU HIS LEU ASN LYS SEQRES 4 A 391 LYS ALA THR ASP LYS GLN PRO TYR SER LYS LEU PRO GLY SEQRES 5 A 391 VAL SER LEU LEU LYS PRO LEU LYS GLY VAL ASP PRO ASN SEQRES 6 A 391 LEU ILE ASN ASN LEU GLU THR PHE PHE GLU LEU ASP TYR SEQRES 7 A 391 PRO LYS TYR GLU VAL LEU LEU CYS VAL GLN ASP HIS ASP SEQRES 8 A 391 ASP PRO ALA ILE ASP VAL CYS LYS LYS LEU LEU GLY LYS SEQRES 9 A 391 TYR PRO ASN VAL ASP ALA ARG LEU PHE ILE GLY GLY LYS SEQRES 10 A 391 LYS VAL GLY ILE ASN PRO LYS ILE ASN ASN LEU MET PRO SEQRES 11 A 391 GLY TYR GLU VAL ALA LYS TYR ASP LEU ILE TRP ILE CYS SEQRES 12 A 391 ASP SER GLY ILE ARG VAL ILE PRO ASP THR LEU THR ASP SEQRES 13 A 391 MET VAL ASN GLN MET THR GLU LYS VAL GLY LEU VAL HIS SEQRES 14 A 391 GLY LEU PRO TYR VAL ALA ASP ARG GLN GLY PHE ALA ALA SEQRES 15 A 391 THR LEU GLU GLN VAL TYR PHE GLY THR SER HIS PRO ARG SEQRES 16 A 391 TYR TYR ILE SER ALA ASN VAL THR GLY PHE LYS CYS VAL SEQRES 17 A 391 THR GLY MET SER CYS LEU MET ARG LYS ASP VAL LEU ASP SEQRES 18 A 391 GLN ALA GLY GLY LEU ILE ALA PHE ALA GLN TYR ILE ALA SEQRES 19 A 391 GLU ASP TYR PHE MET ALA LYS ALA ILE ALA ASP ARG GLY SEQRES 20 A 391 TRP ARG PHE ALA MET SER THR GLN VAL ALA MET GLN ASN SEQRES 21 A 391 SER GLY SER TYR SER ILE SER GLN PHE GLN SER ARG MET SEQRES 22 A 391 ILE ARG TRP THR LYS LEU ARG ILE ASN MET LEU PRO ALA SEQRES 23 A 391 THR ILE ILE CYS GLU PRO ILE SER GLU CYS PHE VAL ALA SEQRES 24 A 391 SER LEU ILE ILE GLY TRP ALA ALA HIS HIS VAL PHE ARG SEQRES 25 A 391 TRP ASP ILE MET VAL PHE PHE MET CYS HIS CYS LEU ALA SEQRES 26 A 391 TRP PHE ILE PHE ASP TYR ILE GLN LEU ARG GLY VAL GLN SEQRES 27 A 391 GLY GLY THR LEU CYS PHE SER LYS LEU ASP TYR ALA VAL SEQRES 28 A 391 ALA TRP PHE ILE ARG GLU SER MET THR ILE TYR ILE PHE SEQRES 29 A 391 LEU SER ALA LEU TRP ASP PRO THR ILE SER TRP ARG THR SEQRES 30 A 391 GLY ARG TYR ARG LEU ARG CYS GLY GLY THR ALA GLU GLU SEQRES 31 A 391 ILE HET UPG A 401 36 HETNAM UPG URIDINE-5'-DIPHOSPHATE-GLUCOSE HETSYN UPG URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE HETSYN 2 UPG ESTER FORMUL 2 UPG C15 H24 N2 O17 P2 HELIX 1 AA1 MET A 1 HIS A 36 1 36 HELIX 2 AA2 PRO A 46 LEU A 50 5 5 HELIX 3 AA3 ASN A 65 GLU A 75 1 11 HELIX 4 AA4 ASP A 92 TYR A 105 1 14 HELIX 5 AA5 ASN A 122 VAL A 134 1 13 HELIX 6 AA6 ASP A 152 GLN A 160 1 9 HELIX 7 AA7 GLY A 179 GLY A 204 1 26 HELIX 8 AA8 LYS A 217 ALA A 223 1 7 HELIX 9 AA9 GLY A 224 PHE A 229 1 6 HELIX 10 AB1 ALA A 234 ARG A 246 1 13 HELIX 11 AB2 SER A 265 LEU A 284 1 20 HELIX 12 AB3 PRO A 285 CYS A 290 5 6 HELIX 13 AB4 GLU A 291 SER A 294 5 4 HELIX 14 AB5 GLU A 295 PHE A 311 1 17 HELIX 15 AB6 ASP A 314 GLY A 339 1 26 HELIX 16 AB7 SER A 345 LEU A 368 1 24 SHEET 1 AA1 7 ALA A 110 ILE A 114 0 SHEET 2 AA1 7 TYR A 81 VAL A 87 1 N LEU A 85 O PHE A 113 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 LEU A 139 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 VAL A 165 HIS A 169 -1 N VAL A 168 O LEU A 214 SHEET 7 AA1 7 ARG A 249 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 SHEET 1 AA3 2 SER A 374 TRP A 375 0 SHEET 2 AA3 2 GLY A 378 ARG A 379 -1 O GLY A 378 N TRP A 375 SSBOND 1 CYS A 296 CYS A 323 1555 1555 2.04 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 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 2337 2564 CONECT 2564 2337 CONECT 3130 3131 3135 3138 CONECT 3131 3130 3132 3136 CONECT 3132 3131 3133 CONECT 3133 3132 3134 3137 CONECT 3134 3133 3135 CONECT 3135 3130 3134 CONECT 3136 3131 CONECT 3137 3133 CONECT 3138 3130 3139 3143 CONECT 3139 3138 3140 3141 CONECT 3140 3139 CONECT 3141 3139 3142 3144 CONECT 3142 3141 3143 3145 CONECT 3143 3138 3142 CONECT 3144 3141 CONECT 3145 3142 3146 CONECT 3146 3145 3147 CONECT 3147 3146 3148 3149 3150 CONECT 3148 3147 CONECT 3149 3147 CONECT 3150 3147 3151 CONECT 3151 3150 3152 3153 3154 CONECT 3152 3151 CONECT 3153 3151 CONECT 3154 3151 3155 CONECT 3155 3154 3156 3164 CONECT 3156 3155 3157 3161 CONECT 3157 3156 3158 3162 CONECT 3158 3157 3159 3163 CONECT 3159 3158 3160 3164 CONECT 3160 3159 3165 CONECT 3161 3156 CONECT 3162 3157 CONECT 3163 3158 CONECT 3164 3155 3159 CONECT 3165 3160 MASTER 124 0 1 16 12 0 0 6 3164 1 38 31 END