HEADER PROTEIN FIBRIL 05-FEB-26 10SH TITLE THE CRYOEM STRUCTURE OF T12 TYPE2 NANOFIBER COMPND MOL_ID: 1; COMPND 2 MOLECULE: T12 TYPE 2 NANOFIBER; COMPND 3 CHAIN: D, H, J, K, L, O, P, R, S, T, Y, Z, 8; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: HYPIVIGGSK(NH2) SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS NANOFIBER, PROTEIN FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR H.ZHANG,Y.YANG REVDAT 1 17-JUN-26 10SH 0 JRNL AUTH J.M.GODBE,H.ZHANG,A.K.SHARMA,K.N.ERNST,Z.JING,M.R.DYER, JRNL AUTH 2 J.L.PRIOR,E.TEUBNER,B.MANION,R.TANG,Y.YANG,M.SHOKEEN JRNL TITL TAILORING AVIDITY THROUGH MORPHOLOGY: STRUCTURE-AVIDITY JRNL TITL 2 RELATIONSHIP IN CD38-BINDING NANOFIBER RADIOTRACERS. JRNL REF ACS APPL BIO MATER V. 9 4242 2026 JRNL REFN ISSN 2576-6422 JRNL PMID 42011845 JRNL DOI 10.1021/ACSABM.6C00348 REMARK 2 REMARK 2 RESOLUTION. 2.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, REFMAC, SERVALCAT 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) : 2.970 REMARK 3 NUMBER OF PARTICLES : 35 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING ONLY REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 10SH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-FEB-26. REMARK 100 THE DEPOSITION ID IS D_1000304895. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : HELICAL REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : FILAMENT REMARK 245 PARTICLE TYPE : HELICAL REMARK 245 NAME OF SAMPLE : T12 TYPE2 NANOFIBER 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 : TFS TALOS REMARK 245 DETECTOR TYPE : FEI FALCON I (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 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) : 5000.00 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: 13-MERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: 13-MERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, H, J, K, L, O, P, R, S, T, REMARK 350 AND CHAINS: Y, Z, 8 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 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 J 4 81.18 -69.54 REMARK 500 TYR P 3 58.96 -143.03 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-75435 RELATED DB: EMDB REMARK 900 THE CRYOEM STRUCTURE OF T12 TYPE2 NANOFIBER DBREF 10SH D 2 12 PDB 10SH 10SH 2 12 DBREF 10SH H 2 12 PDB 10SH 10SH 2 12 DBREF 10SH J 2 12 PDB 10SH 10SH 2 12 DBREF 10SH K 2 12 PDB 10SH 10SH 2 12 DBREF 10SH L 2 12 PDB 10SH 10SH 2 12 DBREF 10SH O 2 12 PDB 10SH 10SH 2 12 DBREF 10SH P 2 12 PDB 10SH 10SH 2 12 DBREF 10SH R 2 12 PDB 10SH 10SH 2 12 DBREF 10SH S 2 12 PDB 10SH 10SH 2 12 DBREF 10SH T 2 12 PDB 10SH 10SH 2 12 DBREF 10SH Y 2 12 PDB 10SH 10SH 2 12 DBREF 10SH Z 2 12 PDB 10SH 10SH 2 12 DBREF 10SH 8 2 12 PDB 10SH 10SH 2 12 SEQRES 1 D 11 HIS TYR PRO ILE VAL ILE GLY GLY SER LYS NH2 SEQRES 1 H 11 HIS TYR PRO ILE VAL ILE GLY GLY SER LYS NH2 SEQRES 1 J 11 HIS TYR PRO ILE VAL ILE GLY GLY SER LYS NH2 SEQRES 1 K 11 HIS TYR PRO ILE VAL ILE GLY GLY SER LYS NH2 SEQRES 1 L 11 HIS TYR PRO ILE VAL ILE GLY GLY SER LYS NH2 SEQRES 1 O 11 HIS TYR PRO ILE VAL ILE GLY GLY SER LYS NH2 SEQRES 1 P 11 HIS TYR PRO ILE VAL ILE GLY GLY SER LYS NH2 SEQRES 1 R 11 HIS TYR PRO ILE VAL ILE GLY GLY SER LYS NH2 SEQRES 1 S 11 HIS TYR PRO ILE VAL ILE GLY GLY SER LYS NH2 SEQRES 1 T 11 HIS TYR PRO ILE VAL ILE GLY GLY SER LYS NH2 SEQRES 1 Y 11 HIS TYR PRO ILE VAL ILE GLY GLY SER LYS NH2 SEQRES 1 Z 11 HIS TYR PRO ILE VAL ILE GLY GLY SER LYS NH2 SEQRES 1 8 11 HIS TYR PRO ILE VAL ILE GLY GLY SER LYS NH2 HET NH2 D 12 1 HET NH2 H 12 1 HET NH2 J 12 1 HET NH2 K 12 1 HET NH2 L 12 1 HET NH2 O 12 1 HET NH2 P 12 1 HET NH2 R 12 1 HET NH2 S 12 1 HET NH2 T 12 1 HET NH2 Y 12 1 HET NH2 Z 12 1 HET NH2 8 12 1 HET DAO D 101 13 HET DAO H 101 13 HET DAO J 101 13 HET DAO K 101 13 HET DAO L 101 13 HET DAO O 101 13 HET DAO P 101 13 HET DAO R 101 13 HET DAO S 101 13 HET DAO T 101 13 HET DAO Y 101 13 HET DAO Z 101 13 HET DAO 8 101 13 HETNAM NH2 AMINO GROUP HETNAM DAO LAURIC ACID FORMUL 1 NH2 13(H2 N) FORMUL 14 DAO 13(C12 H24 O2) LINK C LYS D 11 N NH2 D 12 1555 1555 1.24 LINK NZ LYS D 11 C1 DAO D 101 1555 1555 1.34 LINK C LYS H 11 N NH2 H 12 1555 1555 1.24 LINK NZ LYS H 11 C1 DAO H 101 1555 1555 1.34 LINK C LYS J 11 N NH2 J 12 1555 1555 1.24 LINK NZ LYS J 11 C1 DAO J 101 1555 1555 1.34 LINK C LYS K 11 N NH2 K 12 1555 1555 1.26 LINK NZ LYS K 11 C1 DAO K 101 1555 1555 1.34 LINK C LYS L 11 N NH2 L 12 1555 1555 1.30 LINK NZ LYS L 11 C1 DAO L 101 1555 1555 1.34 LINK C LYS O 11 N NH2 O 12 1555 1555 1.25 LINK NZ LYS O 11 C1 DAO O 101 1555 1555 1.34 LINK C LYS P 11 N NH2 P 12 1555 1555 1.27 LINK NZ LYS P 11 C1 DAO P 101 1555 1555 1.35 LINK C LYS R 11 N NH2 R 12 1555 1555 1.24 LINK NZ LYS R 11 C1 DAO R 101 1555 1555 1.34 LINK C LYS S 11 N NH2 S 12 1555 1555 1.27 LINK NZ LYS S 11 C1 DAO S 101 1555 1555 1.35 LINK C LYS T 11 N NH2 T 12 1555 1555 1.27 LINK NZ LYS T 11 C1 DAO T 101 1555 1555 1.34 LINK C LYS Y 11 N NH2 Y 12 1555 1555 1.25 LINK NZ LYS Y 11 C1 DAO Y 101 1555 1555 1.34 LINK C LYS Z 11 N NH2 Z 12 1555 1555 1.25 LINK NZ LYS Z 11 C1 DAO Z 101 1555 1555 1.34 LINK C LYS 8 11 N NH2 8 12 1555 1555 1.25 LINK NZ LYS 8 11 C1 DAO 8 101 1555 1555 1.34 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 0.999334 -0.036487 0.000000 3.69030 MTRIX2 2 0.036487 0.999334 0.000000 -3.55800 MTRIX3 2 0.000000 0.000000 1.000000 -14.25000 MTRIX1 3 0.999704 -0.024327 0.000000 2.44580 MTRIX2 3 0.024327 0.999704 0.000000 -2.38700 MTRIX3 3 0.000000 0.000000 1.000000 -9.50000 MTRIX1 4 0.999926 -0.012165 0.000000 1.21560 MTRIX2 4 0.012165 0.999926 0.000000 -1.20090 MTRIX3 4 0.000000 0.000000 1.000000 -4.75000 MTRIX1 5 0.999926 0.012165 0.000000 -1.20090 MTRIX2 5 -0.012165 0.999926 0.000000 1.21560 MTRIX3 5 0.000000 0.000000 1.000000 4.75000 MTRIX1 6 0.999704 0.024327 0.000000 -2.38700 MTRIX2 6 -0.024327 0.999704 0.000000 2.44580 MTRIX3 6 0.000000 0.000000 1.000000 9.50000 CONECT 69 76 CONECT 75 1003 CONECT 76 69 CONECT 146 153 CONECT 152 1016 CONECT 153 146 CONECT 223 230 CONECT 229 1029 CONECT 230 223 CONECT 300 307 CONECT 306 1042 CONECT 307 300 CONECT 377 384 CONECT 383 1055 CONECT 384 377 CONECT 454 461 CONECT 460 1068 CONECT 461 454 CONECT 531 538 CONECT 537 1081 CONECT 538 531 CONECT 608 615 CONECT 614 1094 CONECT 615 608 CONECT 685 692 CONECT 691 1107 CONECT 692 685 CONECT 762 769 CONECT 768 1120 CONECT 769 762 CONECT 839 846 CONECT 845 1133 CONECT 846 839 CONECT 916 923 CONECT 922 1146 CONECT 923 916 CONECT 993 1000 CONECT 999 1159 CONECT 1000 993 CONECT 1002 1003 CONECT 1003 75 1002 1004 CONECT 1004 1003 1005 CONECT 1005 1004 1006 CONECT 1006 1005 1007 CONECT 1007 1006 1008 CONECT 1008 1007 1009 CONECT 1009 1008 1010 CONECT 1010 1009 1011 CONECT 1011 1010 1012 CONECT 1012 1011 1013 CONECT 1013 1012 1014 CONECT 1014 1013 CONECT 1015 1016 CONECT 1016 152 1015 1017 CONECT 1017 1016 1018 CONECT 1018 1017 1019 CONECT 1019 1018 1020 CONECT 1020 1019 1021 CONECT 1021 1020 1022 CONECT 1022 1021 1023 CONECT 1023 1022 1024 CONECT 1024 1023 1025 CONECT 1025 1024 1026 CONECT 1026 1025 1027 CONECT 1027 1026 CONECT 1028 1029 CONECT 1029 229 1028 1030 CONECT 1030 1029 1031 CONECT 1031 1030 1032 CONECT 1032 1031 1033 CONECT 1033 1032 1034 CONECT 1034 1033 1035 CONECT 1035 1034 1036 CONECT 1036 1035 1037 CONECT 1037 1036 1038 CONECT 1038 1037 1039 CONECT 1039 1038 1040 CONECT 1040 1039 CONECT 1041 1042 CONECT 1042 306 1041 1043 CONECT 1043 1042 1044 CONECT 1044 1043 1045 CONECT 1045 1044 1046 CONECT 1046 1045 1047 CONECT 1047 1046 1048 CONECT 1048 1047 1049 CONECT 1049 1048 1050 CONECT 1050 1049 1051 CONECT 1051 1050 1052 CONECT 1052 1051 1053 CONECT 1053 1052 CONECT 1054 1055 CONECT 1055 383 1054 1056 CONECT 1056 1055 1057 CONECT 1057 1056 1058 CONECT 1058 1057 1059 CONECT 1059 1058 1060 CONECT 1060 1059 1061 CONECT 1061 1060 1062 CONECT 1062 1061 1063 CONECT 1063 1062 1064 CONECT 1064 1063 1065 CONECT 1065 1064 1066 CONECT 1066 1065 CONECT 1067 1068 CONECT 1068 460 1067 1069 CONECT 1069 1068 1070 CONECT 1070 1069 1071 CONECT 1071 1070 1072 CONECT 1072 1071 1073 CONECT 1073 1072 1074 CONECT 1074 1073 1075 CONECT 1075 1074 1076 CONECT 1076 1075 1077 CONECT 1077 1076 1078 CONECT 1078 1077 1079 CONECT 1079 1078 CONECT 1080 1081 CONECT 1081 537 1080 1082 CONECT 1082 1081 1083 CONECT 1083 1082 1084 CONECT 1084 1083 1085 CONECT 1085 1084 1086 CONECT 1086 1085 1087 CONECT 1087 1086 1088 CONECT 1088 1087 1089 CONECT 1089 1088 1090 CONECT 1090 1089 1091 CONECT 1091 1090 1092 CONECT 1092 1091 CONECT 1093 1094 CONECT 1094 614 1093 1095 CONECT 1095 1094 1096 CONECT 1096 1095 1097 CONECT 1097 1096 1098 CONECT 1098 1097 1099 CONECT 1099 1098 1100 CONECT 1100 1099 1101 CONECT 1101 1100 1102 CONECT 1102 1101 1103 CONECT 1103 1102 1104 CONECT 1104 1103 1105 CONECT 1105 1104 CONECT 1106 1107 CONECT 1107 691 1106 1108 CONECT 1108 1107 1109 CONECT 1109 1108 1110 CONECT 1110 1109 1111 CONECT 1111 1110 1112 CONECT 1112 1111 1113 CONECT 1113 1112 1114 CONECT 1114 1113 1115 CONECT 1115 1114 1116 CONECT 1116 1115 1117 CONECT 1117 1116 1118 CONECT 1118 1117 CONECT 1119 1120 CONECT 1120 768 1119 1121 CONECT 1121 1120 1122 CONECT 1122 1121 1123 CONECT 1123 1122 1124 CONECT 1124 1123 1125 CONECT 1125 1124 1126 CONECT 1126 1125 1127 CONECT 1127 1126 1128 CONECT 1128 1127 1129 CONECT 1129 1128 1130 CONECT 1130 1129 1131 CONECT 1131 1130 CONECT 1132 1133 CONECT 1133 845 1132 1134 CONECT 1134 1133 1135 CONECT 1135 1134 1136 CONECT 1136 1135 1137 CONECT 1137 1136 1138 CONECT 1138 1137 1139 CONECT 1139 1138 1140 CONECT 1140 1139 1141 CONECT 1141 1140 1142 CONECT 1142 1141 1143 CONECT 1143 1142 1144 CONECT 1144 1143 CONECT 1145 1146 CONECT 1146 922 1145 1147 CONECT 1147 1146 1148 CONECT 1148 1147 1149 CONECT 1149 1148 1150 CONECT 1150 1149 1151 CONECT 1151 1150 1152 CONECT 1152 1151 1153 CONECT 1153 1152 1154 CONECT 1154 1153 1155 CONECT 1155 1154 1156 CONECT 1156 1155 1157 CONECT 1157 1156 CONECT 1158 1159 CONECT 1159 999 1158 1160 CONECT 1160 1159 1161 CONECT 1161 1160 1162 CONECT 1162 1161 1163 CONECT 1163 1162 1164 CONECT 1164 1163 1165 CONECT 1165 1164 1166 CONECT 1166 1165 1167 CONECT 1167 1166 1168 CONECT 1168 1167 1169 CONECT 1169 1168 1170 CONECT 1170 1169 MASTER 118 0 26 0 0 0 0 24 1157 13 208 13 END