HEADER MEMBRANE PROTEIN 09-DEC-25 9TK9 TITLE STRUCTURE OF HUMAN CLN8 IN THE PRESENCE OF DOCOSAHEXAENOATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN CLN8; COMPND 3 CHAIN: B; COMPND 4 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: CLN8, C8ORF61; SOURCE 6 EXPRESSION_SYSTEM: SACCHAROMYCES CEREVISIAE; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4932 KEYWDS BIS(MONOACYLGLYCERO)PHOSPHATE, BATTEN DISEASE, KEYWDS 2 GLYCEROPHOSPHOGLYCEROL, LYSOPHOSPHATIDYLGLYCEROL, ACYLTRANSFERASE, KEYWDS 3 NEURODEGENERATION, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR D.LACABANNE,P.K.SHEOKAND,J.J.RUPRECHT,K.PETKEVICIUS REVDAT 1 29-JUL-26 9TK9 0 JRNL AUTH P.K.SHEOKAND,D.LACABANNE,A.M.JAMES,J.J.RUPRECHT, JRNL AUTH 2 J.VAN DER KLEIJ,J.MULLER-NIVA,M.H.SALO,N.JUNEJA,J.JENKINS, JRNL AUTH 3 C.SHUN YU,M.A.PRATT,M.S.KING,J.M.WEIMER,A.KOULMAN, JRNL AUTH 4 R.HINTTALA,F.M.SANTORELLI,M.P.MURPHY,E.R.S.KUNJI, JRNL AUTH 5 K.PETKEVICUS JRNL TITL STEREOSPECIFIC GPG ACYLATION BY CLN8 DRIVES BMP BIOSYNTHESIS JRNL TITL 2 AND UNDERPINS BATTEN DISEASE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.73 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : WARP, EPU, WARP, CRYOSPARC, 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) : 2.730 REMARK 3 NUMBER OF PARTICLES : 360847 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 9TK9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-MAY-26. REMARK 100 THE DEPOSITION ID IS D_1292152872. 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 : CLN8 DIMER 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 : 7.40 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : TFS FALCON 4I (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 600.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1800.00 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) : 5025.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 262.44000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 262.44000 REMARK 350 BIOMT3 2 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 MET B 1 REMARK 465 ASN B 2 REMARK 465 PRO B 3 REMARK 465 ALA B 4 REMARK 465 SER B 5 REMARK 465 ASP B 6 REMARK 465 GLY B 7 REMARK 465 GLY B 8 REMARK 465 THR B 9 REMARK 465 SER B 10 REMARK 465 GLU B 11 REMARK 465 SER B 12 REMARK 465 ILE B 13 REMARK 465 VAL B 261 REMARK 465 ASP B 262 REMARK 465 TRP B 263 REMARK 465 ASN B 264 REMARK 465 PHE B 265 REMARK 465 ALA B 266 REMARK 465 GLN B 267 REMARK 465 PRO B 268 REMARK 465 GLU B 269 REMARK 465 ALA B 270 REMARK 465 LYS B 271 REMARK 465 SER B 272 REMARK 465 ARG B 273 REMARK 465 PRO B 274 REMARK 465 GLU B 275 REMARK 465 GLY B 276 REMARK 465 ASN B 277 REMARK 465 GLY B 278 REMARK 465 GLN B 279 REMARK 465 LEU B 280 REMARK 465 LEU B 281 REMARK 465 ARG B 282 REMARK 465 LYS B 283 REMARK 465 LYS B 284 REMARK 465 ARG B 285 REMARK 465 PRO B 286 REMARK 465 ASP B 287 REMARK 465 ALA B 288 REMARK 465 ALA B 289 REMARK 465 ILE B 290 REMARK 465 GLU B 291 REMARK 465 GLY B 292 REMARK 465 ARG B 293 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-56021 RELATED DB: EMDB REMARK 900 STRUCTURE OF HUMAN CLN8 IN THE PRESENCE OF DOCOSAHEXAENOATE DBREF 9TK9 B 1 286 UNP Q9UBY8 CLN8_HUMAN 1 286 SEQADV 9TK9 ASP B 287 UNP Q9UBY8 EXPRESSION TAG SEQADV 9TK9 ALA B 288 UNP Q9UBY8 EXPRESSION TAG SEQADV 9TK9 ALA B 289 UNP Q9UBY8 EXPRESSION TAG SEQADV 9TK9 ILE B 290 UNP Q9UBY8 EXPRESSION TAG SEQADV 9TK9 GLU B 291 UNP Q9UBY8 EXPRESSION TAG SEQADV 9TK9 GLY B 292 UNP Q9UBY8 EXPRESSION TAG SEQADV 9TK9 ARG B 293 UNP Q9UBY8 EXPRESSION TAG SEQRES 1 B 293 MET ASN PRO ALA SER ASP GLY GLY THR SER GLU SER ILE SEQRES 2 B 293 PHE ASP LEU ASP TYR ALA SER TRP GLY ILE ARG SER THR SEQRES 3 B 293 LEU MET VAL ALA GLY PHE VAL PHE TYR LEU GLY VAL PHE SEQRES 4 B 293 VAL VAL CYS HIS GLN LEU SER SER SER LEU ASN ALA THR SEQRES 5 B 293 TYR ARG SER LEU VAL ALA ARG GLU LYS VAL PHE TRP ASP SEQRES 6 B 293 LEU ALA ALA THR ARG ALA VAL PHE GLY VAL GLN SER THR SEQRES 7 B 293 ALA ALA GLY LEU TRP ALA LEU LEU GLY ASP PRO VAL LEU SEQRES 8 B 293 HIS ALA ASP LYS ALA ARG GLY GLN GLN ASN TRP CYS TRP SEQRES 9 B 293 PHE HIS ILE THR THR ALA THR GLY PHE PHE CYS PHE GLU SEQRES 10 B 293 ASN VAL ALA VAL HIS LEU SER ASN LEU ILE PHE ARG THR SEQRES 11 B 293 PHE ASP LEU PHE LEU VAL ILE HIS HIS LEU PHE ALA PHE SEQRES 12 B 293 LEU GLY PHE LEU GLY CYS LEU VAL ASN LEU GLN ALA GLY SEQRES 13 B 293 HIS TYR LEU ALA MET THR THR LEU LEU LEU GLU MET SER SEQRES 14 B 293 THR PRO PHE THR CYS VAL SER TRP MET LEU LEU LYS ALA SEQRES 15 B 293 GLY TRP SER GLU SER LEU PHE TRP LYS LEU ASN GLN TRP SEQRES 16 B 293 LEU MET ILE HIS MET PHE HIS CYS ARG MET VAL LEU THR SEQRES 17 B 293 TYR HIS MET TRP TRP VAL CYS PHE TRP HIS TRP ASP GLY SEQRES 18 B 293 LEU VAL SER SER LEU TYR LEU PRO HIS LEU THR LEU PHE SEQRES 19 B 293 LEU VAL GLY LEU ALA LEU LEU THR LEU ILE ILE ASN PRO SEQRES 20 B 293 TYR TRP THR HIS LYS LYS THR GLN GLN LEU LEU ASN PRO SEQRES 21 B 293 VAL ASP TRP ASN PHE ALA GLN PRO GLU ALA LYS SER ARG SEQRES 22 B 293 PRO GLU GLY ASN GLY GLN LEU LEU ARG LYS LYS ARG PRO SEQRES 23 B 293 ASP ALA ALA ILE GLU GLY ARG HET HXA B 301 24 HET COA B 302 48 HETNAM HXA DOCOSA-4,7,10,13,16,19-HEXAENOIC ACID HETNAM COA COENZYME A FORMUL 2 HXA C22 H32 O2 FORMUL 3 COA C21 H36 N7 O16 P3 S FORMUL 4 HOH *16(H2 O) HELIX 1 AA1 SER B 20 ASN B 50 1 31 HELIX 2 AA2 ASN B 50 LEU B 56 1 7 HELIX 3 AA3 VAL B 57 LEU B 86 1 30 HELIX 4 AA4 ASP B 88 ASP B 94 1 7 HELIX 5 AA5 TRP B 102 PHE B 128 1 27 HELIX 6 AA6 ASP B 132 ASN B 152 1 21 HELIX 7 AA7 HIS B 157 LEU B 166 1 10 HELIX 8 AA8 SER B 169 GLY B 183 1 15 HELIX 9 AA9 SER B 187 HIS B 218 1 32 HELIX 10 AB1 HIS B 218 LEU B 226 1 9 HELIX 11 AB2 TYR B 227 ILE B 244 1 18 HELIX 12 AB3 ILE B 244 ASN B 259 1 16 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 MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 2 -1.000000 0.000000 0.000000 262.44000 MTRIX2 2 0.000000 -1.000000 0.000000 262.44000 MTRIX3 2 0.000000 0.000000 1.000000 0.00000 CONECT 2022 2023 2024 2025 CONECT 2023 2022 CONECT 2024 2022 CONECT 2025 2022 2026 CONECT 2026 2025 2027 CONECT 2027 2026 2028 CONECT 2028 2027 2029 CONECT 2029 2028 2030 CONECT 2030 2029 2031 CONECT 2031 2030 2032 CONECT 2032 2031 2033 CONECT 2033 2032 2034 CONECT 2034 2033 2035 CONECT 2035 2034 2036 CONECT 2036 2035 2037 CONECT 2037 2036 2038 CONECT 2038 2037 2039 CONECT 2039 2038 2040 CONECT 2040 2039 2041 CONECT 2041 2040 2042 CONECT 2042 2041 2043 CONECT 2043 2042 2044 CONECT 2044 2043 2045 CONECT 2045 2044 CONECT 2046 2047 2051 CONECT 2047 2046 2048 CONECT 2048 2047 2049 CONECT 2049 2048 2050 2055 CONECT 2050 2049 2051 2053 CONECT 2051 2046 2050 2052 CONECT 2052 2051 CONECT 2053 2050 2054 CONECT 2054 2053 2055 CONECT 2055 2049 2054 2056 CONECT 2056 2055 2057 2066 CONECT 2057 2056 2058 2059 CONECT 2058 2057 CONECT 2059 2057 2060 2065 CONECT 2060 2059 2061 CONECT 2061 2060 2062 2063 2064 CONECT 2062 2061 CONECT 2063 2061 CONECT 2064 2061 CONECT 2065 2059 2066 2067 CONECT 2066 2056 2065 CONECT 2067 2065 2068 CONECT 2068 2067 2069 CONECT 2069 2068 2070 2071 2072 CONECT 2070 2069 CONECT 2071 2069 CONECT 2072 2069 2073 CONECT 2073 2072 2074 2075 2076 CONECT 2074 2073 CONECT 2075 2073 CONECT 2076 2073 2078 CONECT 2077 2078 2079 2080 2081 CONECT 2078 2076 2077 CONECT 2079 2077 CONECT 2080 2077 CONECT 2081 2077 2082 2083 CONECT 2082 2081 CONECT 2083 2081 2084 2085 CONECT 2084 2083 CONECT 2085 2083 2086 CONECT 2086 2085 2087 CONECT 2087 2086 2088 CONECT 2088 2087 2089 2090 CONECT 2089 2088 CONECT 2090 2088 2091 CONECT 2091 2090 2092 CONECT 2092 2091 2093 CONECT 2093 2092 MASTER 155 0 2 12 0 0 0 12 2108 1 72 23 END