HEADER MEMBRANE PROTEIN 13-MAR-26 29IN TITLE STRUCTURAL BASIS OF AUTOANTIBODY BINDING IN IGLON5 DISEASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: IGLON FAMILY MEMBER 5; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: ANTIBODY LIGHT CHAIN; COMPND 7 CHAIN: L; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: ANTIBODY HEAVY CHAIN; COMPND 11 CHAIN: H; COMPND 12 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: IGLON5; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 13 MOL_ID: 3; SOURCE 14 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 15 ORGANISM_TAXID: 9606; SOURCE 16 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS AUTOANTIBODIES, NEURONAL ADHESION MOLECULE, IGCAM, IGLON, MEMBRANE KEYWDS 2 PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR L.PEREZ REVDAT 1 02-SEP-26 29IN 0 JRNL AUTH L.PEREZ JRNL TITL STRUCTURAL BASIS OF AUTOANTIBODY BINDING IN IGLON5 DISEASE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, CRYOSPARC, CRYOSPARC, REMARK 3 MOTIONCORR2, UCSF CHIMERA, PHENIX, REMARK 3 CRYOSPARC, CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 6DLE REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : 73.920 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) : 3.500 REMARK 3 NUMBER OF PARTICLES : 702836 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 29IN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-MAR-26. REMARK 100 THE DEPOSITION ID IS D_1292155205. 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 : IGLON5 DIMER WITH 2 FABS REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 1.20 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.00 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 : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2400.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : OTHER REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 3700.00 REMARK 245 ILLUMINATION MODE : OTHER 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, L, H 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 HIS A 130 CG ND1 CD2 CE1 NE2 REMARK 470 VAL A 131 CG1 CG2 REMARK 470 ARG A 134 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 153 CG CD1 CD2 REMARK 470 ARG A 159 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 161 CG CD OE1 OE2 REMARK 470 LEU A 169 CG CD1 CD2 REMARK 470 ARG A 170 CG CD NE CZ NH1 NH2 REMARK 470 PHE A 173 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU A 176 CG CD OE1 OE2 REMARK 470 GLU A 178 CG CD OE1 OE2 REMARK 470 ARG A 187 CG CD NE CZ NH1 NH2 REMARK 470 VAL A 201 CG1 CG2 REMARK 470 ASN A 202 CG OD1 ND2 REMARK 470 SER A 203 OG REMARK 470 ARG A 208 CZ NH1 NH2 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 160 -157.67 -76.40 REMARK 500 THR L 10 50.28 -119.57 REMARK 500 GLU L 17 -173.91 -175.68 REMARK 500 ALA L 51 -9.11 71.47 REMARK 500 PRO L 80 2.80 -66.21 REMARK 500 THR L 172 -169.77 -125.57 REMARK 500 SER H 30 7.21 -68.51 REMARK 500 SER H 65 48.28 -93.21 REMARK 500 ALA H 88 -169.76 -164.33 REMARK 500 SER H 130 30.40 -95.48 REMARK 500 ASP H 144 62.29 63.81 REMARK 500 SER H 203 47.43 -92.08 REMARK 500 ASN H 204 46.61 34.24 REMARK 500 ASP H 217 57.95 -93.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-57080 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-57198 RELATED DB: EMDB REMARK 900 STRUCTURAL BASIS OF AUTOANTIBODY BINDING IN IGLON5 DISEASE DBREF 29IN A 129 216 UNP A6NGN9 IGLO5_HUMAN 129 216 DBREF 29IN L 1 214 PDB 29IN 29IN 1 214 DBREF 29IN H 1 218 PDB 29IN 29IN 1 218 SEQRES 1 A 88 VAL HIS VAL PRO ALA ARG ILE VAL ASN ILE SER SER PRO SEQRES 2 A 88 VAL THR VAL ASN GLU GLY GLY ASN VAL ASN LEU LEU CYS SEQRES 3 A 88 LEU ALA VAL GLY ARG PRO GLU PRO THR VAL THR TRP ARG SEQRES 4 A 88 GLN LEU ARG ASP GLY PHE THR SER GLU GLY GLU ILE LEU SEQRES 5 A 88 GLU ILE SER ASP ILE GLN ARG GLY GLN ALA GLY GLU TYR SEQRES 6 A 88 GLU CYS VAL THR HIS ASN GLY VAL ASN SER ALA PRO ASP SEQRES 7 A 88 SER ARG ARG VAL LEU VAL THR VAL ASN TYR SEQRES 1 L 216 GLU ILE VAL LEU THR GLN SER PRO GLY THR LEU SER LEU SEQRES 2 L 216 SER PRO GLY GLU ARG ALA THR LEU SER CYS ARG ALA SER SEQRES 3 L 216 GLN SER VAL SER SER ASN TYR LEU ALA TRP TYR GLN GLN SEQRES 4 L 216 LYS PRO GLY GLN PRO PRO ARG LEU LEU ILE TYR GLY ALA SEQRES 5 L 216 SER SER ARG ALA ALA GLY ILE ALA ASP ARG PHE ARG GLY SEQRES 6 L 216 SER GLY SER GLY THR ASP PHE THR LEU THR ILE SER ARG SEQRES 7 L 216 LEU GLU PRO GLU ASP PHE ALA VAL TYR LEU CYS GLN LEU SEQRES 8 L 216 TYR VAL THR SER GLN GLY TYR THR PHE GLY PRO GLY THR SEQRES 9 L 216 ARG VAL ASP VAL LYS ARG THR VAL ALA ALA PRO SER VAL SEQRES 10 L 216 PHE ILE PHE PRO PRO SER ASP GLU GLN LEU LYS SER GLY SEQRES 11 L 216 THR ALA SER VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO SEQRES 12 L 216 ARG GLU ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU SEQRES 13 L 216 GLN SER GLY ASN SER GLN GLU SER VAL THR GLU GLN ASP SEQRES 14 L 216 SER LYS ASP SER THR TYR SER LEU SER SER THR LEU THR SEQRES 15 L 216 LEU SER LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR ALA SEQRES 16 L 216 CYS GLU VAL THR HIS GLN GLY LEU ARG SER PRO VAL THR SEQRES 17 L 216 LYS SER PHE ASN ARG GLY GLU CYS SEQRES 1 H 228 GLN LEU ARG LEU GLN GLU SER GLY PRO GLY LEU LEU LYS SEQRES 2 H 228 PRO SER GLU THR LEU SER LEU THR CYS THR VAL SER GLY SEQRES 3 H 228 GLY SER ILE SER ASP SER ASN HIS TYR TRP GLY TRP ILE SEQRES 4 H 228 ARG GLN PRO PRO GLY LYS GLY LEU GLU TRP ILE GLY SER SEQRES 5 H 228 ILE TYR PHE SER GLY SER THR TYR TYR ASN PRO SER LEU SEQRES 6 H 228 ARG SER ARG VAL THR ILE SER ILE ALA THR SER ASN ASN SEQRES 7 H 228 GLN PHE SER LEU ARG LEU PRO SER LEU THR ALA ALA ASP SEQRES 8 H 228 THR ALA VAL TYR TYR CYS ALA ARG ASP VAL ARG ARG MET SEQRES 9 H 228 PHE GLY ALA THR CYS PHE ASP TYR TRP GLY GLN GLY ALA SEQRES 10 H 228 VAL VAL THR ILE SER SER ALA SER THR LYS GLY PRO SER SEQRES 11 H 228 VAL PHE PRO LEU ALA PRO SER SER LYS SER THR SER GLY SEQRES 12 H 228 GLY THR ALA ALA LEU GLY CYS LEU VAL LYS ASP TYR PHE SEQRES 13 H 228 PRO GLU PRO VAL THR VAL SER TRP ASN SER GLY ALA LEU SEQRES 14 H 228 THR SER GLY VAL HIS THR PHE PRO ALA VAL LEU GLN SER SEQRES 15 H 228 SER GLY LEU TYR SER LEU SER SER VAL VAL THR VAL PRO SEQRES 16 H 228 SER SER SER LEU GLY THR GLN THR TYR ILE CYS ASN VAL SEQRES 17 H 228 ASN HIS LYS PRO SER ASN THR LYS VAL ASP LYS LYS VAL SEQRES 18 H 228 GLU PRO LYS SER CYS ASP LYS HELIX 1 AA1 GLN A 186 ALA A 190 5 5 HELIX 2 AA2 SER L 121 GLY L 128 1 8 HELIX 3 AA3 LYS L 183 HIS L 189 1 7 HELIX 4 AA4 LEU H 63 VAL H 67 5 5 HELIX 5 AA5 THR H 83 THR H 87 5 5 HELIX 6 AA6 SER H 156 ALA H 158 5 3 HELIX 7 AA7 SER H 187 LEU H 189 5 3 SHEET 1 AA1 3 ARG A 134 ILE A 138 0 SHEET 2 AA1 3 VAL A 150 VAL A 157 -1 O VAL A 157 N ARG A 134 SHEET 3 AA1 3 ILE A 179 ILE A 182 -1 O LEU A 180 N LEU A 152 SHEET 1 AA2 5 VAL A 142 ASN A 145 0 SHEET 2 AA2 5 ARG A 208 ASN A 215 1 O THR A 213 N VAL A 144 SHEET 3 AA2 5 GLY A 191 HIS A 198 -1 N TYR A 193 O VAL A 210 SHEET 4 AA2 5 THR A 163 GLN A 168 -1 N THR A 165 O VAL A 196 SHEET 5 AA2 5 THR A 174 GLU A 176 -1 O SER A 175 N TRP A 166 SHEET 1 AA3 4 THR L 5 GLN L 6 0 SHEET 2 AA3 4 CYS L 23 ARG L 24 -1 O ARG L 24 N THR L 5 SHEET 3 AA3 4 ASP L 70 SER L 76 -1 O PHE L 71 N CYS L 23 SHEET 4 AA3 4 ARG L 18 THR L 20 -1 N ALA L 19 O ILE L 75 SHEET 1 AA4 4 THR L 5 GLN L 6 0 SHEET 2 AA4 4 CYS L 23 ARG L 24 -1 O ARG L 24 N THR L 5 SHEET 3 AA4 4 ASP L 70 SER L 76 -1 O PHE L 71 N CYS L 23 SHEET 4 AA4 4 ARG L 63 SER L 67 -1 N SER L 67 O ASP L 70 SHEET 1 AA5 2 SER L 12 LEU L 13 0 SHEET 2 AA5 2 ASP L 105 VAL L 106 1 O ASP L 105 N LEU L 13 SHEET 1 AA6 5 SER L 53 ARG L 54 0 SHEET 2 AA6 5 ARG L 45 TYR L 49 -1 N TYR L 49 O SER L 53 SHEET 3 AA6 5 ALA L 34 GLN L 38 -1 N TRP L 35 O LEU L 47 SHEET 4 AA6 5 VAL L 85 VAL L 92 -1 O VAL L 85 N GLN L 38 SHEET 5 AA6 5 GLY L 95A THR L 97 -1 O THR L 97 N LEU L 90 SHEET 1 AA7 4 SER L 114 PHE L 118 0 SHEET 2 AA7 4 THR L 129 PHE L 139 -1 O VAL L 133 N PHE L 118 SHEET 3 AA7 4 TYR L 173 SER L 182 -1 O LEU L 175 N LEU L 136 SHEET 4 AA7 4 GLN L 160 VAL L 163 -1 N GLN L 160 O THR L 178 SHEET 1 AA8 3 ALA L 144 VAL L 150 0 SHEET 2 AA8 3 VAL L 191 HIS L 198 -1 O GLU L 195 N GLN L 147 SHEET 3 AA8 3 VAL L 205 ASN L 210 -1 O PHE L 209 N TYR L 192 SHEET 1 AA9 4 ARG H 3 SER H 7 0 SHEET 2 AA9 4 THR H 17 SER H 25 -1 O THR H 21 N SER H 7 SHEET 3 AA9 4 GLN H 77 PRO H 82A-1 O LEU H 82 N LEU H 18 SHEET 4 AA9 4 THR H 68 ALA H 72 -1 N SER H 70 O SER H 79 SHEET 1 AB1 5 THR H 57 TYR H 59 0 SHEET 2 AB1 5 GLU H 46 ILE H 51 -1 N SER H 50 O TYR H 58 SHEET 3 AB1 5 HIS H 34 GLN H 39 -1 N ARG H 38 O GLU H 46 SHEET 4 AB1 5 ALA H 88 ARG H 97 -1 O ALA H 93 N GLY H 35B SHEET 5 AB1 5 THR H 100C CYS H 100D-1 O CYS H 100D N VAL H 96 SHEET 1 AB2 5 THR H 57 TYR H 59 0 SHEET 2 AB2 5 GLU H 46 ILE H 51 -1 N SER H 50 O TYR H 58 SHEET 3 AB2 5 HIS H 34 GLN H 39 -1 N ARG H 38 O GLU H 46 SHEET 4 AB2 5 ALA H 88 ARG H 97 -1 O ALA H 93 N GLY H 35B SHEET 5 AB2 5 ALA H 107 VAL H 109 -1 O ALA H 107 N TYR H 90 SHEET 1 AB3 4 SER H 120 LEU H 124 0 SHEET 2 AB3 4 THR H 135 TYR H 145 -1 O LYS H 143 N SER H 120 SHEET 3 AB3 4 TYR H 176 PRO H 185 -1 O SER H 180 N CYS H 140 SHEET 4 AB3 4 HIS H 164 THR H 165 -1 N HIS H 164 O VAL H 181 SHEET 1 AB4 4 SER H 120 LEU H 124 0 SHEET 2 AB4 4 THR H 135 TYR H 145 -1 O LYS H 143 N SER H 120 SHEET 3 AB4 4 TYR H 176 PRO H 185 -1 O SER H 180 N CYS H 140 SHEET 4 AB4 4 VAL H 169 LEU H 170 -1 N VAL H 169 O SER H 177 SHEET 1 AB5 3 VAL H 150 TRP H 154 0 SHEET 2 AB5 3 TYR H 194 HIS H 200 -1 O ASN H 197 N SER H 153 SHEET 3 AB5 3 THR H 205 VAL H 211 -1 O THR H 205 N HIS H 200 SSBOND 1 CYS A 154 CYS A 195 1555 1555 2.03 SSBOND 2 CYS L 23 CYS L 88 1555 1555 2.03 SSBOND 3 CYS L 134 CYS L 194 1555 1555 2.03 SSBOND 4 CYS L 214 CYS H 216 1555 1555 2.03 SSBOND 5 CYS H 22 CYS H 92 1555 1555 2.04 SSBOND 6 CYS H 140 CYS H 196 1555 1555 2.03 CISPEP 1 ARG A 159 PRO A 160 0 1.67 CISPEP 2 GLU H 148 PRO H 149 0 -2.62 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 172 456 CONECT 456 172 CONECT 772 1282 CONECT 1282 772 CONECT 1634 2113 CONECT 2113 1634 CONECT 2269 3964 CONECT 2435 3020 CONECT 3020 2435 CONECT 3394 3808 CONECT 3808 3394 CONECT 3964 2269 MASTER 155 0 0 7 55 0 0 6 3979 3 12 42 END