HEADER RNA BINDING PROTEIN/RNA 21-JUN-24 9IIY TITLE CRYO-EM STRUCTURE OF EFPIWI-PIRNA-TARGET (25-NT, BILOBED) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PIWI; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: RNA (5'- COMPND 7 R(P*UP*AP*GP*CP*AP*GP*AP*UP*CP*GP*GP*UP*UP*GP*UP*AP*UP*AP*GP*AP*CP*G) COMPND 8 -3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: RNA (5'- COMPND 13 R(P*CP*GP*UP*CP*UP*AP*UP*AP*CP*AP*AP*CP*CP*GP*AP*UP*CP*AP*GP*CP*U)- COMPND 14 3'); COMPND 15 CHAIN: C; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: EPHYDATIA FLUVIATILIS; SOURCE 3 ORGANISM_TAXID: 31330; SOURCE 4 GENE: EFPIWIA; SOURCE 5 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 6 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 13 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 17 ORGANISM_COMMON: HUMAN; SOURCE 18 ORGANISM_TAXID: 9606; SOURCE 19 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 20 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS PIWI PROTEIN, PI-RNA, ARGONAUTE, RNA BINDING PROTEIN/RNA, RNA BINDING KEYWDS 2 PROTEIN-RNA COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR Z.Q.LI,Q.K.XU,J.P.WU,E.Z.SHEN REVDAT 5 23-JUL-25 9IIY 1 REMARK REVDAT 4 19-MAR-25 9IIY 1 JRNL REVDAT 3 29-JAN-25 9IIY 1 JRNL REVDAT 2 22-JAN-25 9IIY 1 JRNL REVDAT 1 13-NOV-24 9IIY 0 JRNL AUTH Z.LI,Q.XU,J.ZHONG,Y.ZHANG,T.ZHANG,X.YING,X.LU,X.LI,L.WAN, JRNL AUTH 2 J.XUE,J.HUANG,Y.ZHEN,Z.ZHANG,J.WU,E.Z.SHEN JRNL TITL STRUCTURAL INSIGHTS INTO RNA CLEAVAGE BY PIWI ARGONAUTE. JRNL REF NATURE V. 639 250 2025 JRNL REFN ESSN 1476-4687 JRNL PMID 39814893 JRNL DOI 10.1038/S41586-024-08438-1 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : PHENIX 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) : 3.000 REMARK 3 NUMBER OF PARTICLES : 87581 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 9IIY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 24-JUN-24. REMARK 100 THE DEPOSITION ID IS D_1300048870. 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 : EFPIWI-PIRNA-TARGET (25-NT, REMARK 245 BILOBED) 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 : 8.00 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : TFS FALCON 4I (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 MET A 1 REMARK 465 SER A 2 REMARK 465 GLY A 3 REMARK 465 ARG A 4 REMARK 465 GLY A 5 REMARK 465 GLY A 6 REMARK 465 ARG A 7 REMARK 465 GLY A 8 REMARK 465 ALA A 9 REMARK 465 ALA A 10 REMARK 465 LEU A 11 REMARK 465 LEU A 12 REMARK 465 LYS A 13 REMARK 465 ALA A 14 REMARK 465 LEU A 15 REMARK 465 GLU A 16 REMARK 465 GLN A 17 REMARK 465 PRO A 18 REMARK 465 VAL A 19 REMARK 465 ARG A 20 REMARK 465 ARG A 21 REMARK 465 PRO A 22 REMARK 465 GLY A 23 REMARK 465 GLN A 24 REMARK 465 GLN A 25 REMARK 465 PRO A 26 REMARK 465 VAL A 27 REMARK 465 GLN A 28 REMARK 465 SER A 29 REMARK 465 GLY A 30 REMARK 465 ASP A 31 REMARK 465 GLN A 32 REMARK 465 VAL A 33 REMARK 465 ALA A 34 REMARK 465 GLY A 35 REMARK 465 PRO A 36 REMARK 465 PRO A 37 REMARK 465 SER A 38 REMARK 465 LEU A 39 REMARK 465 THR A 40 REMARK 465 SER A 41 REMARK 465 ALA A 42 REMARK 465 THR A 43 REMARK 465 VAL A 44 REMARK 465 SER A 45 REMARK 465 THR A 46 REMARK 465 VAL A 47 REMARK 465 GLY A 48 REMARK 465 VAL A 49 REMARK 465 VAL A 50 REMARK 465 GLN A 51 REMARK 465 GLN A 52 REMARK 465 HIS A 53 REMARK 465 THR A 54 REMARK 465 VAL A 55 REMARK 465 ALA A 56 REMARK 465 ASP A 57 REMARK 465 VAL A 58 REMARK 465 ASP A 59 REMARK 465 ARG A 60 REMARK 465 CYS A 61 REMARK 465 PRO A 62 REMARK 465 PRO A 63 REMARK 465 LEU A 64 REMARK 465 ALA A 65 REMARK 465 THR A 66 REMARK 465 PRO A 67 REMARK 465 ALA A 68 REMARK 465 SER A 69 REMARK 465 GLY A 70 REMARK 465 GLN A 71 REMARK 465 PRO A 72 REMARK 465 LEU A 73 REMARK 465 THR A 74 REMARK 465 LEU A 75 REMARK 465 HIS A 76 REMARK 465 ARG A 77 REMARK 465 PRO A 78 REMARK 465 LEU A 79 REMARK 465 GLY A 80 REMARK 465 SER A 81 REMARK 465 PRO A 82 REMARK 465 ALA A 83 REMARK 465 VAL A 84 REMARK 465 LEU A 85 REMARK 465 PRO A 86 REMARK 465 LEU A 87 REMARK 465 GLY A 88 REMARK 465 GLY A 89 REMARK 465 ARG A 90 REMARK 465 GLY A 91 REMARK 465 GLY A 92 REMARK 465 ARG A 93 REMARK 465 GLY A 94 REMARK 465 SER A 95 REMARK 465 ARG A 96 REMARK 465 SER A 97 REMARK 465 VAL A 98 REMARK 465 GLU A 99 REMARK 465 PRO A 100 REMARK 465 VAL A 101 REMARK 465 GLU A 102 REMARK 465 PRO A 103 REMARK 465 ARG A 104 REMARK 465 VAL A 105 REMARK 465 ALA A 106 REMARK 465 SER A 107 REMARK 465 GLU A 108 REMARK 465 PRO A 109 REMARK 465 PRO A 110 REMARK 465 SER A 111 REMARK 465 LEU A 112 REMARK 465 ILE A 113 REMARK 465 SER A 114 REMARK 465 PHE A 115 REMARK 465 GLY A 116 REMARK 465 PRO A 117 REMARK 465 SER A 118 REMARK 465 SER A 119 REMARK 465 PRO A 120 REMARK 465 GLU A 121 REMARK 465 ARG A 122 REMARK 465 ALA A 123 REMARK 465 HIS A 124 REMARK 465 THR A 125 REMARK 465 GLU A 126 REMARK 465 THR A 127 REMARK 465 GLU A 128 REMARK 465 ILE A 129 REMARK 465 THR A 130 REMARK 465 PRO A 131 REMARK 465 PRO A 132 REMARK 465 THR A 133 REMARK 465 ALA A 134 REMARK 465 VAL A 135 REMARK 465 SER A 136 REMARK 465 VAL A 137 REMARK 465 GLN A 138 REMARK 465 GLN A 139 REMARK 465 ARG A 140 REMARK 465 PRO A 141 REMARK 465 SER A 142 REMARK 465 SER A 143 REMARK 465 GLN A 144 REMARK 465 THR A 145 REMARK 465 ILE A 146 REMARK 465 SER A 147 REMARK 465 ARG A 148 REMARK 465 GLY A 149 REMARK 465 VAL A 150 REMARK 465 PRO A 151 REMARK 465 ALA A 152 REMARK 465 VAL A 153 REMARK 465 GLY A 154 REMARK 465 ARG A 155 REMARK 465 GLY A 156 REMARK 465 SER A 157 REMARK 465 MET A 158 REMARK 465 LEU A 159 REMARK 465 ARG A 160 REMARK 465 ASP A 161 REMARK 465 PRO A 162 REMARK 465 THR A 163 REMARK 465 SER A 164 REMARK 465 HIS A 165 REMARK 465 VAL A 166 REMARK 465 ARG A 167 REMARK 465 LEU A 168 REMARK 465 PRO A 169 REMARK 465 GLN A 170 REMARK 465 LEU A 171 REMARK 465 TYR A 172 REMARK 465 SER A 173 REMARK 465 SER A 174 REMARK 465 GLY A 175 REMARK 465 GLY A 176 REMARK 465 SER A 177 REMARK 465 PRO A 178 REMARK 465 VAL A 179 REMARK 465 VAL A 180 REMARK 465 GLN A 181 REMARK 465 THR A 182 REMARK 465 ALA A 183 REMARK 465 THR A 184 REMARK 465 ALA A 185 REMARK 465 THR A 186 REMARK 465 PRO A 187 REMARK 465 THR A 188 REMARK 465 VAL A 189 REMARK 465 SER A 190 REMARK 465 PRO A 191 REMARK 465 PRO A 192 REMARK 465 ALA A 193 REMARK 465 LEU A 194 REMARK 465 SER A 195 REMARK 465 PRO A 196 REMARK 465 SER A 197 REMARK 465 PRO A 198 REMARK 465 PRO A 199 REMARK 465 LEU A 200 REMARK 465 LEU A 201 REMARK 465 THR A 202 REMARK 465 GLN A 203 REMARK 465 SER A 204 REMARK 465 PRO A 205 REMARK 465 PRO A 206 REMARK 465 SER A 207 REMARK 465 GLN A 208 REMARK 465 SER A 209 REMARK 465 PRO A 210 REMARK 465 LEU A 211 REMARK 465 PRO A 212 REMARK 465 ILE A 213 REMARK 465 LYS A 214 REMARK 465 ALA A 215 REMARK 465 ILE A 216 REMARK 465 LYS A 217 REMARK 465 ASP A 218 REMARK 465 LEU A 219 REMARK 465 SER A 220 REMARK 465 LEU A 221 REMARK 465 ASN A 222 REMARK 465 VAL A 223 REMARK 465 GLU A 224 REMARK 465 SER A 225 REMARK 465 SER A 226 REMARK 465 MET A 227 REMARK 465 VAL A 228 REMARK 465 SER A 229 REMARK 465 GLN A 230 REMARK 465 ARG A 231 REMARK 465 GLY A 232 REMARK 465 SER A 233 REMARK 465 SER A 234 REMARK 465 GLY A 235 REMARK 465 GLN A 236 REMARK 465 PRO A 237 REMARK 465 VAL A 238 REMARK 465 PRO A 239 REMARK 465 VAL A 240 REMARK 465 SER A 241 REMARK 465 ARG A 488 REMARK 465 PRO A 489 REMARK 465 LYS A 490 REMARK 465 LYS A 491 REMARK 465 LYS A 492 REMARK 465 GLN A 493 REMARK 465 ARG A 494 REMARK 465 GLY A 495 REMARK 465 LYS A 496 REMARK 465 GLN A 497 REMARK 465 ASP A 498 REMARK 465 GLU A 499 REMARK 465 GLY A 500 REMARK 465 ARG A 501 REMARK 465 LYS A 502 REMARK 465 GLU A 503 REMARK 465 VAL A 504 REMARK 465 GLY A 519 REMARK 465 LEU A 520 REMARK 465 THR A 521 REMARK 465 ASP A 522 REMARK 465 ALA A 523 REMARK 465 ALA A 524 REMARK 465 ARG A 525 REMARK 465 SER A 526 REMARK 465 ASP A 527 REMARK 465 PHE A 528 REMARK 465 LYS A 529 REMARK 465 VAL A 530 REMARK 465 MET A 577 REMARK 465 LEU A 578 REMARK 465 ASP A 579 REMARK 465 MET A 580 REMARK 465 GLN A 581 REMARK 465 GLY A 582 REMARK 465 ARG A 583 REMARK 465 ARG A 584 REMARK 465 LEU A 585 REMARK 465 PRO A 586 REMARK 465 PRO A 587 REMARK 465 GLU A 588 REMARK 465 LYS A 589 REMARK 465 ILE A 590 REMARK 465 LEU A 591 REMARK 465 PHE A 592 REMARK 465 LYS A 593 REMARK 465 HIS A 594 REMARK 465 SER A 595 REMARK 465 SER A 596 REMARK 465 ILE A 597 REMARK 465 VAL A 598 REMARK 465 ALA A 599 REMARK 465 ASN A 600 REMARK 465 MET A 601 REMARK 465 GLU A 602 REMARK 465 ALA A 603 REMARK 465 ASP A 604 REMARK 465 TRP A 605 REMARK 465 SER A 606 REMARK 465 GLU A 823 REMARK 465 ARG A 824 REMARK 465 ILE A 825 REMARK 465 ILE A 826 REMARK 465 VAL A 827 REMARK 465 PHE A 828 REMARK 465 ARG A 829 REMARK 465 ASP A 830 REMARK 465 GLY A 831 REMARK 465 VAL A 832 REMARK 465 GLY A 833 REMARK 465 GLU A 834 REMARK 465 GLY A 835 REMARK 465 ARG A 836 REMARK 465 GLU A 837 REMARK 465 GLU A 838 REMARK 465 TYR A 839 REMARK 465 VAL A 840 REMARK 465 SER A 841 REMARK 465 GLU A 842 REMARK 465 PHE A 843 REMARK 465 GLU A 844 REMARK 465 VAL A 845 REMARK 465 PRO A 846 REMARK 465 GLN A 847 REMARK 465 PHE A 848 REMARK 465 ASN A 849 REMARK 465 SER A 850 REMARK 465 CYS A 851 REMARK 465 PHE A 852 REMARK 465 SER A 853 REMARK 465 ILE A 854 REMARK 465 PHE A 855 REMARK 465 GLY A 856 REMARK 465 GLU A 857 REMARK 465 ASN A 858 REMARK 465 TYR A 859 REMARK 465 CYS A 860 REMARK 465 PRO A 861 REMARK 465 LYS A 862 REMARK 465 LEU A 863 REMARK 465 ALA A 864 REMARK 465 VAL A 865 REMARK 465 VAL A 866 REMARK 465 VAL A 867 REMARK 465 VAL A 868 REMARK 465 PRO A 957 REMARK 465 CYS A 958 REMARK 465 ASN A 959 REMARK 465 TYR A 960 REMARK 465 ALA A 961 REMARK 465 HIS A 962 REMARK 465 LYS A 963 REMARK 465 LEU A 964 REMARK 465 ALA A 965 REMARK 465 PHE A 966 REMARK 465 LEU A 967 REMARK 465 VAL A 968 REMARK 465 GLY A 969 REMARK 465 LYS A 970 REMARK 465 SER A 971 REMARK 465 LEU A 972 REMARK 465 HIS A 973 REMARK 465 ARG A 974 REMARK 465 ASP A 975 REMARK 465 PRO A 976 REMARK 465 ALA A 977 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 U C 21 OP1 OP2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OG SER A 916 OP2 G B 6 2.10 REMARK 500 OG1 THR A 402 O CYS A 515 2.18 REMARK 500 O TRP A 745 OH TYR A 946 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 U B 1 P U B 1 OP3 -0.127 REMARK 500 REMARK 500 REMARK: NULL 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 U B 12 O3' - P - OP2 ANGL. DEV. = -20.9 DEGREES REMARK 500 U B 12 O3' - P - OP1 ANGL. DEV. = -24.2 DEGREES REMARK 500 U B 12 OP1 - P - OP2 ANGL. DEV. = 10.7 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 GLU A 266 -62.02 -92.99 REMARK 500 ASP A 289 30.81 -141.55 REMARK 500 ILE A 299 -50.04 -128.02 REMARK 500 GLN A 302 -65.35 -121.58 REMARK 500 LEU A 304 -167.10 -164.97 REMARK 500 SER A 322 -165.57 -162.83 REMARK 500 VAL A 324 -62.67 -128.27 REMARK 500 ASP A 325 -175.04 -171.22 REMARK 500 ASN A 414 -173.13 -172.79 REMARK 500 PRO A 451 44.67 -76.10 REMARK 500 LEU A 510 114.83 -163.02 REMARK 500 THR A 538 39.97 -143.60 REMARK 500 VAL A 540 65.27 -157.17 REMARK 500 GLU A 608 52.27 -91.54 REMARK 500 GLU A 667 48.55 -81.66 REMARK 500 SER A 668 -36.83 -131.02 REMARK 500 PRO A 679 -9.65 -57.00 REMARK 500 PRO A 750 47.32 -91.24 REMARK 500 GLU A 794 114.14 -160.80 REMARK 500 LYS A 870 31.69 -140.43 REMARK 500 ARG A 879 48.60 -82.75 REMARK 500 SER A 907 10.51 -141.08 REMARK 500 ILE A 923 -61.71 -94.22 REMARK 500 TYR A 946 52.38 -90.53 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-60609 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF EFPIWI-PIRNA-TARGET (25-NT, BILOBED) DBREF 9IIY A 1 987 UNP D5MRY8 D5MRY8_9METZ 1 987 DBREF 9IIY B 1 22 PDB 9IIY 9IIY 1 22 DBREF 9IIY C 1 21 PDB 9IIY 9IIY 1 21 SEQRES 1 A 987 MET SER GLY ARG GLY GLY ARG GLY ALA ALA LEU LEU LYS SEQRES 2 A 987 ALA LEU GLU GLN PRO VAL ARG ARG PRO GLY GLN GLN PRO SEQRES 3 A 987 VAL GLN SER GLY ASP GLN VAL ALA GLY PRO PRO SER LEU SEQRES 4 A 987 THR SER ALA THR VAL SER THR VAL GLY VAL VAL GLN GLN SEQRES 5 A 987 HIS THR VAL ALA ASP VAL ASP ARG CYS PRO PRO LEU ALA SEQRES 6 A 987 THR PRO ALA SER GLY GLN PRO LEU THR LEU HIS ARG PRO SEQRES 7 A 987 LEU GLY SER PRO ALA VAL LEU PRO LEU GLY GLY ARG GLY SEQRES 8 A 987 GLY ARG GLY SER ARG SER VAL GLU PRO VAL GLU PRO ARG SEQRES 9 A 987 VAL ALA SER GLU PRO PRO SER LEU ILE SER PHE GLY PRO SEQRES 10 A 987 SER SER PRO GLU ARG ALA HIS THR GLU THR GLU ILE THR SEQRES 11 A 987 PRO PRO THR ALA VAL SER VAL GLN GLN ARG PRO SER SER SEQRES 12 A 987 GLN THR ILE SER ARG GLY VAL PRO ALA VAL GLY ARG GLY SEQRES 13 A 987 SER MET LEU ARG ASP PRO THR SER HIS VAL ARG LEU PRO SEQRES 14 A 987 GLN LEU TYR SER SER GLY GLY SER PRO VAL VAL GLN THR SEQRES 15 A 987 ALA THR ALA THR PRO THR VAL SER PRO PRO ALA LEU SER SEQRES 16 A 987 PRO SER PRO PRO LEU LEU THR GLN SER PRO PRO SER GLN SEQRES 17 A 987 SER PRO LEU PRO ILE LYS ALA ILE LYS ASP LEU SER LEU SEQRES 18 A 987 ASN VAL GLU SER SER MET VAL SER GLN ARG GLY SER SER SEQRES 19 A 987 GLY GLN PRO VAL PRO VAL SER ALA ASN TYR LEU PRO LEU SEQRES 20 A 987 LYS GLY ASN MET ASP GLY VAL PHE LYS TYR ALA VAL GLY SEQRES 21 A 987 PHE ASN PRO PRO VAL GLU ASP ILE ARG SER ARG SER GLN SEQRES 22 A 987 LEU LEU ASN GLU HIS LYS GLU LEU ILE GLY LEU THR ARG SEQRES 23 A 987 VAL PHE ASP GLY SER THR LEU TYR VAL PRO LYS ARG ILE SEQRES 24 A 987 CYS GLU GLN ARG LEU ASP LEU MET SER THR ARG GLN THR SEQRES 25 A 987 ASP GLY ALA SER ILE LYS VAL THR ILE SER LEU VAL ASP SEQRES 26 A 987 SER VAL LYS ASN ARG ASP VAL VAL GLN LEU MET ASN VAL SEQRES 27 A 987 ILE PHE LYS ARG ILE LEU ARG SER LEU LYS LEU GLN ARG SEQRES 28 A 987 ILE GLY ARG ASP TYR TYR ASP ALA ASN SER PRO LEU GLU SEQRES 29 A 987 VAL PRO GLN HIS LYS MET GLN LEU TRP PRO GLY TYR VAL SEQRES 30 A 987 THR ALA ILE ASN ARG HIS GLU GLY GLY LEU MET LEU VAL SEQRES 31 A 987 LEU ASP VAL SER HIS ARG VAL MET LYS THR ASP THR ALA SEQRES 32 A 987 LEU ASP PHE LEU TYR GLU LEU TYR HIS PHE ASN GLN ASP SEQRES 33 A 987 LYS PHE ARG GLU GLU ALA PHE LYS GLN LEU VAL GLY SER SEQRES 34 A 987 VAL VAL LEU THR ARG TYR ASN ASN ARG THR TYR GLU ILE SEQRES 35 A 987 ASP ASP ILE ALA TRP ASP LYS ASN PRO ARG CYS ALA PHE SEQRES 36 A 987 GLN ASP HIS ALA GLY SER GLN ILE THR PHE VAL ASP TYR SEQRES 37 A 987 TYR LYS ARG ALA TYR ASP LEU ASP ILE THR ASP LEU GLU SEQRES 38 A 987 GLN PRO LEU LEU ILE HIS ARG PRO LYS LYS LYS GLN ARG SEQRES 39 A 987 GLY LYS GLN ASP GLU GLY ARG LYS GLU VAL GLU GLU MET SEQRES 40 A 987 VAL CYS LEU VAL PRO GLU LEU CYS ALA MET THR GLY LEU SEQRES 41 A 987 THR ASP ALA ALA ARG SER ASP PHE LYS VAL MET LYS ASP SEQRES 42 A 987 LEU ALA VAL HIS THR ARG VAL PRO PRO GLU LYS ARG ALA SEQRES 43 A 987 GLU SER PHE ARG LYS PHE ILE GLN ARG LEU ASN THR THR SEQRES 44 A 987 LYS GLU ALA SER GLU LEU LEU HIS SER TRP GLY LEU VAL SEQRES 45 A 987 LEU ASP SER ARG MET LEU ASP MET GLN GLY ARG ARG LEU SEQRES 46 A 987 PRO PRO GLU LYS ILE LEU PHE LYS HIS SER SER ILE VAL SEQRES 47 A 987 ALA ASN MET GLU ALA ASP TRP SER ARG GLU CYS LEU LYS SEQRES 48 A 987 GLU HIS VAL ILE SER ALA VAL SER LEU LEU ASP TRP ALA SEQRES 49 A 987 VAL LEU PHE VAL ARG LYS ASP GLN GLY LYS ALA THR ASP SEQRES 50 A 987 PHE VAL ASN MET LEU SER LYS VAL CYS PRO PRO ILE GLY SEQRES 51 A 987 MET GLU VAL HIS GLU PRO LYS MET VAL GLU VAL VAL ASN SEQRES 52 A 987 ASP ARG THR GLU SER TYR LEU ARG ALA LEU ARG GLU LEU SEQRES 53 A 987 ILE ALA PRO ARG LEU GLN MET VAL VAL ILE VAL PHE PRO SEQRES 54 A 987 THR SER ARG ASP ASP ARG TYR SER ALA VAL LYS LYS LEU SEQRES 55 A 987 CYS CYS ILE GLU SER PRO ILE PRO SER GLN VAL LEU ILE SEQRES 56 A 987 ALA ARG THR ILE THR GLN GLN GLN LYS LEU ARG SER VAL SEQRES 57 A 987 ALA GLN LYS VAL ALA LEU GLN MET ASN ALA LYS LEU GLY SEQRES 58 A 987 GLY GLU LEU TRP ALA VAL GLU ILE PRO LEU LYS SER CYS SEQRES 59 A 987 MET VAL VAL GLY ILE ASP VAL TYR HIS ASP LYS SER TYR SEQRES 60 A 987 GLY ASN LYS SER ILE ALA GLY PHE VAL ALA SER THR ASN SEQRES 61 A 987 PRO SER PHE THR ARG TRP TYR SER ARG THR ALA MET GLN SEQRES 62 A 987 GLU GLN SER GLN GLU LEU ILE HIS GLU LEU LYS LEU CYS SEQRES 63 A 987 MET GLN ALA ALA LEU LYS LYS TYR ASN GLU MET ASN GLN SEQRES 64 A 987 SER LEU PRO GLU ARG ILE ILE VAL PHE ARG ASP GLY VAL SEQRES 65 A 987 GLY GLU GLY ARG GLU GLU TYR VAL SER GLU PHE GLU VAL SEQRES 66 A 987 PRO GLN PHE ASN SER CYS PHE SER ILE PHE GLY GLU ASN SEQRES 67 A 987 TYR CYS PRO LYS LEU ALA VAL VAL VAL VAL GLN LYS ARG SEQRES 68 A 987 ILE THR THR ARG ILE PHE GLY ARG SER GLY HIS SER TYR SEQRES 69 A 987 ASP ASN PRO PRO PRO GLY VAL ILE VAL ASP HIS THR ILE SEQRES 70 A 987 THR LYS SER TYR ASP PHE TYR LEU VAL SER GLN HIS VAL SEQRES 71 A 987 ARG GLN GLY THR VAL SER PRO THR TYR TYR ARG VAL ILE SEQRES 72 A 987 TYR ASP LYS SER GLY LEU LYS PRO ASP HIS LEU GLN ARG SEQRES 73 A 987 LEU THR TYR LYS LEU THR HIS MET TYR TYR ASN TRP PRO SEQRES 74 A 987 GLY THR ILE ARG THR PRO ALA PRO CYS ASN TYR ALA HIS SEQRES 75 A 987 LYS LEU ALA PHE LEU VAL GLY LYS SER LEU HIS ARG ASP SEQRES 76 A 987 PRO ALA HIS GLU LEU SER ASP ARG LEU PHE PHE LEU SEQRES 1 B 22 U A G C A G A U C G G U U SEQRES 2 B 22 G U A U A G A C G SEQRES 1 C 21 C G U C U A U A C A A C C SEQRES 2 C 21 G A U C A G C U HELIX 1 AA1 ASP A 267 GLN A 273 1 7 HELIX 2 AA2 ASP A 331 LYS A 348 1 18 HELIX 3 AA3 PRO A 366 LYS A 369 5 4 HELIX 4 AA4 THR A 402 ASN A 414 1 13 HELIX 5 AA5 GLN A 415 LEU A 426 1 12 HELIX 6 AA6 THR A 464 TYR A 473 1 10 HELIX 7 AA7 VAL A 511 GLU A 513 5 3 HELIX 8 AA8 ASP A 533 HIS A 537 5 5 HELIX 9 AA9 ARG A 545 THR A 559 1 15 HELIX 10 AB1 THR A 559 GLY A 570 1 12 HELIX 11 AB2 VAL A 628 GLN A 632 5 5 HELIX 12 AB3 THR A 636 CYS A 646 1 11 HELIX 13 AB4 PRO A 647 GLY A 650 5 4 HELIX 14 AB5 ARG A 671 LEU A 676 1 6 HELIX 15 AB6 ARG A 692 LYS A 701 1 10 HELIX 16 AB7 ALA A 716 THR A 720 1 5 HELIX 17 AB8 LYS A 724 LEU A 740 1 17 HELIX 18 AB9 GLU A 798 LEU A 803 1 6 HELIX 19 AC1 LEU A 803 GLN A 819 1 17 HELIX 20 AC2 LYS A 930 HIS A 943 1 14 SHEET 1 AA1 4 ASN A 381 ARG A 382 0 SHEET 2 AA1 4 LEU A 387 VAL A 390 -1 O MET A 388 N ASN A 381 SHEET 3 AA1 4 TYR A 244 GLY A 249 -1 N LEU A 245 O LEU A 389 SHEET 4 AA1 4 LEU A 571 LEU A 573 -1 O VAL A 572 N LYS A 248 SHEET 1 AA2 2 LYS A 256 TYR A 257 0 SHEET 2 AA2 2 LEU A 293 TYR A 294 -1 O LEU A 293 N TYR A 257 SHEET 1 AA3 2 LEU A 306 THR A 309 0 SHEET 2 AA3 2 SER A 316 VAL A 319 -1 O ILE A 317 N SER A 308 SHEET 1 AA4 2 LEU A 349 ILE A 352 0 SHEET 2 AA4 2 ASP A 355 ASP A 358 -1 O TYR A 357 N GLN A 350 SHEET 1 AA5 3 LEU A 363 VAL A 365 0 SHEET 2 AA5 3 MET A 370 TRP A 373 -1 O LEU A 372 N LEU A 363 SHEET 3 AA5 3 ARG A 396 MET A 398 -1 O ARG A 396 N TRP A 373 SHEET 1 AA6 3 THR A 439 GLU A 441 0 SHEET 2 AA6 3 VAL A 430 THR A 433 -1 N VAL A 431 O TYR A 440 SHEET 3 AA6 3 CYS A 515 ALA A 516 -1 O ALA A 516 N LEU A 432 SHEET 1 AA7 2 PHE A 455 GLN A 456 0 SHEET 2 AA7 2 GLN A 462 ILE A 463 -1 N ILE A 463 O PHE A 455 SHEET 1 AA8 3 ALA A 624 VAL A 625 0 SHEET 2 AA8 3 VAL A 684 PHE A 688 1 O VAL A 685 N ALA A 624 SHEET 3 AA8 3 GLN A 712 ILE A 715 1 O LEU A 714 N ILE A 686 SHEET 1 AA9 2 GLY A 758 ILE A 759 0 SHEET 2 AA9 2 PHE A 775 VAL A 776 -1 O VAL A 776 N GLY A 758 SHEET 1 AB1 2 TYR A 904 LEU A 905 0 SHEET 2 AB1 2 THR A 918 TYR A 919 -1 O THR A 918 N LEU A 905 CISPEP 1 ASN A 262 PRO A 263 0 -5.59 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 MASTER 572 0 0 20 25 0 0 6 5943 3 0 80 END