HEADER RNA BINDING PROTEIN/RNA 21-JUN-24 9IJ3 TITLE CRYO-EM STRUCTURE OF MILI-PIRNA-TARGET (26-NT) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PIWI-LIKE PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.26.-; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: RNA (26-MER); COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: RNA (25-MER); COMPND 12 CHAIN: C; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: PIWIL2, MILI; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 14 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 16 MOL_ID: 3; SOURCE 17 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 18 ORGANISM_COMMON: HUMAN; SOURCE 19 ORGANISM_TAXID: 9606; SOURCE 20 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 21 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 22 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 9IJ3 1 REMARK REVDAT 4 19-MAR-25 9IJ3 1 JRNL REVDAT 3 29-JAN-25 9IJ3 1 JRNL REVDAT 2 22-JAN-25 9IJ3 1 JRNL REVDAT 1 13-NOV-24 9IJ3 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. 2.60 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) : 2.600 REMARK 3 NUMBER OF PARTICLES : 139074 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 9IJ3 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_1300048884. 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 : MILI-PIRNA-TARGET (26-NT) 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 ASP A 2 REMARK 465 PRO A 3 REMARK 465 VAL A 4 REMARK 465 ARG A 5 REMARK 465 PRO A 6 REMARK 465 LEU A 7 REMARK 465 PHE A 8 REMARK 465 ARG A 9 REMARK 465 GLY A 10 REMARK 465 PRO A 11 REMARK 465 THR A 12 REMARK 465 PRO A 13 REMARK 465 VAL A 14 REMARK 465 HIS A 15 REMARK 465 PRO A 16 REMARK 465 SER A 17 REMARK 465 GLN A 18 REMARK 465 CYS A 19 REMARK 465 VAL A 20 REMARK 465 ARG A 21 REMARK 465 MET A 22 REMARK 465 PRO A 23 REMARK 465 GLY A 24 REMARK 465 CYS A 25 REMARK 465 TRP A 26 REMARK 465 PRO A 27 REMARK 465 GLN A 28 REMARK 465 ALA A 29 REMARK 465 PRO A 30 REMARK 465 ARG A 31 REMARK 465 PRO A 32 REMARK 465 LEU A 33 REMARK 465 GLU A 34 REMARK 465 PRO A 35 REMARK 465 ALA A 36 REMARK 465 TRP A 37 REMARK 465 GLY A 38 REMARK 465 ARG A 39 REMARK 465 ALA A 40 REMARK 465 GLY A 41 REMARK 465 PRO A 42 REMARK 465 ALA A 43 REMARK 465 GLY A 44 REMARK 465 ARG A 45 REMARK 465 GLY A 46 REMARK 465 LEU A 47 REMARK 465 VAL A 48 REMARK 465 PHE A 49 REMARK 465 ARG A 50 REMARK 465 LYS A 51 REMARK 465 PRO A 52 REMARK 465 GLU A 53 REMARK 465 ASP A 54 REMARK 465 SER A 55 REMARK 465 SER A 56 REMARK 465 PRO A 57 REMARK 465 PRO A 58 REMARK 465 LEU A 59 REMARK 465 GLN A 60 REMARK 465 PRO A 61 REMARK 465 VAL A 62 REMARK 465 GLN A 63 REMARK 465 LYS A 64 REMARK 465 ASP A 65 REMARK 465 SER A 66 REMARK 465 VAL A 67 REMARK 465 GLY A 68 REMARK 465 LEU A 69 REMARK 465 VAL A 70 REMARK 465 SER A 71 REMARK 465 MET A 72 REMARK 465 PHE A 73 REMARK 465 ARG A 74 REMARK 465 GLY A 75 REMARK 465 MET A 76 REMARK 465 GLY A 77 REMARK 465 LEU A 78 REMARK 465 ASP A 79 REMARK 465 THR A 80 REMARK 465 ALA A 81 REMARK 465 PHE A 82 REMARK 465 ARG A 83 REMARK 465 PRO A 84 REMARK 465 PRO A 85 REMARK 465 SER A 86 REMARK 465 LYS A 87 REMARK 465 ARG A 88 REMARK 465 GLU A 89 REMARK 465 VAL A 90 REMARK 465 PRO A 91 REMARK 465 PRO A 92 REMARK 465 LEU A 93 REMARK 465 GLY A 94 REMARK 465 ARG A 95 REMARK 465 GLY A 96 REMARK 465 VAL A 97 REMARK 465 LEU A 98 REMARK 465 GLY A 99 REMARK 465 ARG A 100 REMARK 465 GLY A 101 REMARK 465 LEU A 102 REMARK 465 SER A 103 REMARK 465 ALA A 104 REMARK 465 ASN A 105 REMARK 465 MET A 106 REMARK 465 VAL A 107 REMARK 465 ARG A 108 REMARK 465 LYS A 109 REMARK 465 ASP A 110 REMARK 465 ARG A 111 REMARK 465 GLU A 112 REMARK 465 GLU A 113 REMARK 465 PRO A 114 REMARK 465 ARG A 115 REMARK 465 SER A 116 REMARK 465 SER A 117 REMARK 465 LEU A 118 REMARK 465 PRO A 119 REMARK 465 ASP A 120 REMARK 465 PRO A 121 REMARK 465 SER A 122 REMARK 465 VAL A 123 REMARK 465 LEU A 124 REMARK 465 ALA A 125 REMARK 465 ALA A 126 REMARK 465 GLY A 127 REMARK 465 ASP A 128 REMARK 465 SER A 129 REMARK 465 LYS A 130 REMARK 465 LEU A 131 REMARK 465 ALA A 132 REMARK 465 GLU A 133 REMARK 465 ALA A 134 REMARK 465 SER A 135 REMARK 465 VAL A 136 REMARK 465 GLY A 137 REMARK 465 TRP A 138 REMARK 465 SER A 139 REMARK 465 ARG A 140 REMARK 465 MET A 141 REMARK 465 LEU A 142 REMARK 465 GLY A 143 REMARK 465 ARG A 144 REMARK 465 GLY A 145 REMARK 465 SER A 146 REMARK 465 SER A 147 REMARK 465 GLU A 148 REMARK 465 VAL A 149 REMARK 465 SER A 150 REMARK 465 LEU A 151 REMARK 465 LEU A 152 REMARK 465 PRO A 153 REMARK 465 LEU A 154 REMARK 465 GLY A 155 REMARK 465 ARG A 156 REMARK 465 ALA A 157 REMARK 465 ALA A 158 REMARK 465 SER A 159 REMARK 465 SER A 160 REMARK 465 ILE A 161 REMARK 465 GLY A 162 REMARK 465 ARG A 163 REMARK 465 GLY A 164 REMARK 465 MET A 165 REMARK 465 ASP A 166 REMARK 465 LYS A 167 REMARK 465 PRO A 168 REMARK 465 PRO A 169 REMARK 465 SER A 170 REMARK 465 ALA A 171 REMARK 465 PHE A 172 REMARK 465 GLY A 173 REMARK 465 LEU A 174 REMARK 465 THR A 175 REMARK 465 ALA A 176 REMARK 465 ARG A 177 REMARK 465 ASP A 178 REMARK 465 PRO A 179 REMARK 465 PRO A 180 REMARK 465 ARG A 181 REMARK 465 LEU A 182 REMARK 465 PRO A 183 REMARK 465 GLN A 184 REMARK 465 PRO A 185 REMARK 465 PRO A 186 REMARK 465 ALA A 187 REMARK 465 LEU A 188 REMARK 465 SER A 189 REMARK 465 PRO A 190 REMARK 465 THR A 191 REMARK 465 SER A 192 REMARK 465 LEU A 193 REMARK 465 HIS A 194 REMARK 465 SER A 195 REMARK 465 ALA A 196 REMARK 465 ASP A 197 REMARK 465 PRO A 198 REMARK 465 PRO A 199 REMARK 465 PRO A 200 REMARK 465 VAL A 201 REMARK 465 LEU A 202 REMARK 465 THR A 203 REMARK 465 MET A 204 REMARK 465 GLU A 205 REMARK 465 ARG A 206 REMARK 465 LYS A 207 REMARK 465 GLU A 208 REMARK 465 LYS A 209 REMARK 465 GLU A 210 REMARK 465 LEU A 211 REMARK 465 LEU A 212 REMARK 465 VAL A 213 REMARK 465 LYS A 214 REMARK 465 GLN A 215 REMARK 465 GLY A 216 REMARK 465 SER A 217 REMARK 465 LYS A 218 REMARK 465 GLY A 219 REMARK 465 THR A 220 REMARK 465 GLN A 478 REMARK 465 ASN A 479 REMARK 465 ASN A 480 REMARK 465 HIS A 481 REMARK 465 GLY A 482 REMARK 465 MET A 483 REMARK 465 SER A 749 REMARK 465 ARG A 750 REMARK 465 MET A 777 REMARK 465 PRO A 778 REMARK 465 HIS A 779 REMARK 465 GLN A 780 REMARK 465 GLU A 781 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 GLU A 236 CG CD OE1 OE2 REMARK 470 GLN A 263 CG CD OE1 NE2 REMARK 470 LYS A 513 CG CD CE NZ REMARK 470 LEU A 788 CG CD1 CD2 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 CE LYS A 252 OP1 U C 11 2.12 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 -0.128 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 ILE A 357 CG1 - CB - CG2 ANGL. DEV. = -15.9 DEGREES REMARK 500 ASP A 429 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 LEU A 451 CA - CB - CG ANGL. DEV. = 14.0 DEGREES REMARK 500 LEU A 619 CA - CB - CG ANGL. DEV. = 15.0 DEGREES REMARK 500 A B 9 O5' - P - OP2 ANGL. DEV. = 7.2 DEGREES REMARK 500 C B 11 C5 - C6 - N1 ANGL. DEV. = 3.1 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 LEU A 226 -77.38 66.00 REMARK 500 ASN A 227 -132.15 52.88 REMARK 500 ASN A 235 -168.91 -127.34 REMARK 500 GLU A 236 -168.32 -117.35 REMARK 500 ALA A 237 66.27 60.74 REMARK 500 SER A 346 39.42 -97.18 REMARK 500 ARG A 354 24.28 49.23 REMARK 500 ASN A 422 28.47 43.29 REMARK 500 ASP A 465 50.04 -94.10 REMARK 500 ASP A 466 25.00 -143.55 REMARK 500 GLU A 476 160.78 66.08 REMARK 500 LEU A 485 -61.74 61.63 REMARK 500 LYS A 486 36.61 -99.12 REMARK 500 THR A 591 49.19 -86.98 REMARK 500 PRO A 600 85.14 -69.69 REMARK 500 TRP A 639 38.24 -98.86 REMARK 500 VAL A 688 -58.35 -122.50 REMARK 500 GLN A 736 63.85 60.18 REMARK 500 LYS A 787 -137.44 40.13 REMARK 500 GLU A 806 -54.98 -121.67 REMARK 500 PRO A 829 42.43 -85.03 REMARK 500 HIS A 842 75.38 53.82 REMARK 500 HIS A 865 -166.59 -162.84 REMARK 500 THR A 878 -12.21 71.49 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A1001 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 743 OD1 REMARK 620 2 ASP A 813 OD2 82.0 REMARK 620 3 U C 17 OP1 158.3 118.4 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-60614 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF MILI-PIRNA-TARGET (26-NT) DBREF 9IJ3 A 1 971 UNP Q8CDG1 PIWL2_MOUSE 1 971 DBREF 9IJ3 B 1 26 PDB 9IJ3 9IJ3 1 26 DBREF 9IJ3 C 1 25 PDB 9IJ3 9IJ3 1 25 SEQRES 1 A 971 MET ASP PRO VAL ARG PRO LEU PHE ARG GLY PRO THR PRO SEQRES 2 A 971 VAL HIS PRO SER GLN CYS VAL ARG MET PRO GLY CYS TRP SEQRES 3 A 971 PRO GLN ALA PRO ARG PRO LEU GLU PRO ALA TRP GLY ARG SEQRES 4 A 971 ALA GLY PRO ALA GLY ARG GLY LEU VAL PHE ARG LYS PRO SEQRES 5 A 971 GLU ASP SER SER PRO PRO LEU GLN PRO VAL GLN LYS ASP SEQRES 6 A 971 SER VAL GLY LEU VAL SER MET PHE ARG GLY MET GLY LEU SEQRES 7 A 971 ASP THR ALA PHE ARG PRO PRO SER LYS ARG GLU VAL PRO SEQRES 8 A 971 PRO LEU GLY ARG GLY VAL LEU GLY ARG GLY LEU SER ALA SEQRES 9 A 971 ASN MET VAL ARG LYS ASP ARG GLU GLU PRO ARG SER SER SEQRES 10 A 971 LEU PRO ASP PRO SER VAL LEU ALA ALA GLY ASP SER LYS SEQRES 11 A 971 LEU ALA GLU ALA SER VAL GLY TRP SER ARG MET LEU GLY SEQRES 12 A 971 ARG GLY SER SER GLU VAL SER LEU LEU PRO LEU GLY ARG SEQRES 13 A 971 ALA ALA SER SER ILE GLY ARG GLY MET ASP LYS PRO PRO SEQRES 14 A 971 SER ALA PHE GLY LEU THR ALA ARG ASP PRO PRO ARG LEU SEQRES 15 A 971 PRO GLN PRO PRO ALA LEU SER PRO THR SER LEU HIS SER SEQRES 16 A 971 ALA ASP PRO PRO PRO VAL LEU THR MET GLU ARG LYS GLU SEQRES 17 A 971 LYS GLU LEU LEU VAL LYS GLN GLY SER LYS GLY THR PRO SEQRES 18 A 971 GLN SER LEU GLY LEU ASN LEU ILE LYS ILE GLN CYS HIS SEQRES 19 A 971 ASN GLU ALA VAL TYR GLN TYR HIS VAL THR PHE SER PRO SEQRES 20 A 971 SER VAL GLU CYS LYS SER MET ARG PHE GLY MET LEU LYS SEQRES 21 A 971 ASP HIS GLN SER VAL THR GLY ASN VAL THR ALA PHE ASP SEQRES 22 A 971 GLY SER ILE LEU TYR LEU PRO VAL LYS LEU GLN GLN VAL SEQRES 23 A 971 VAL GLU LEU LYS SER GLN ARG LYS THR ASP ASP ALA GLU SEQRES 24 A 971 ILE SER ILE LYS ILE GLN LEU THR LYS ILE LEU GLU PRO SEQRES 25 A 971 CYS SER ASP LEU CYS ILE PRO PHE TYR ASN VAL VAL PHE SEQRES 26 A 971 ARG ARG VAL MET LYS LEU LEU ASP MET LYS LEU VAL GLY SEQRES 27 A 971 ARG ASN PHE TYR ASP PRO THR SER ALA MET VAL LEU GLN SEQRES 28 A 971 GLN HIS ARG LEU GLN ILE TRP PRO GLY TYR ALA ALA SER SEQRES 29 A 971 ILE ARG ARG THR ASP GLY GLY LEU PHE LEU LEU ALA ASP SEQRES 30 A 971 VAL SER HIS LYS VAL ILE ARG ASN ASP SER VAL LEU ASP SEQRES 31 A 971 VAL MET HIS ALA ILE TYR GLN GLN ASN LYS GLU HIS PHE SEQRES 32 A 971 GLN ASP GLU CYS SER LYS LEU LEU VAL GLY SER ILE VAL SEQRES 33 A 971 ILE THR ARG TYR ASN ASN ARG THR TYR ARG ILE ASP ASP SEQRES 34 A 971 VAL ASP TRP ASN LYS THR PRO LYS ASP SER PHE VAL MET SEQRES 35 A 971 SER ASP GLY LYS GLU ILE THR PHE LEU GLU TYR TYR SER SEQRES 36 A 971 LYS ASN TYR GLY ILE THR VAL LYS GLU ASP ASP GLN PRO SEQRES 37 A 971 LEU LEU ILE HIS ARG PRO SER GLU ARG GLN ASN ASN HIS SEQRES 38 A 971 GLY MET LEU LEU LYS GLY GLU ILE LEU LEU LEU PRO GLU SEQRES 39 A 971 LEU SER PHE MET THR GLY ILE PRO GLU LYS MET LYS LYS SEQRES 40 A 971 ASP PHE ARG ALA MET LYS ASP LEU THR GLN GLN ILE ASN SEQRES 41 A 971 LEU SER PRO LYS GLN HIS HIS GLY ALA LEU GLU CYS LEU SEQRES 42 A 971 LEU GLN ARG ILE SER GLN ASN GLU THR ALA SER ASN GLU SEQRES 43 A 971 LEU THR ARG TRP GLY LEU SER LEU HIS LYS ASP VAL HIS SEQRES 44 A 971 LYS ILE GLU GLY ARG LEU LEU PRO MET GLU ARG ILE ASN SEQRES 45 A 971 LEU ARG ASN THR SER PHE VAL THR SER GLU ASP LEU ASN SEQRES 46 A 971 TRP VAL LYS GLU VAL THR ARG ASP ALA SER ILE LEU THR SEQRES 47 A 971 ILE PRO MET HIS PHE TRP ALA LEU PHE TYR PRO LYS ARG SEQRES 48 A 971 ALA MET ASP GLN ALA ARG GLU LEU VAL ASN MET LEU GLU SEQRES 49 A 971 LYS ILE ALA GLY PRO ILE GLY MET ARG ILE SER PRO PRO SEQRES 50 A 971 ALA TRP VAL GLU LEU LYS ASP ASP ARG ILE GLU THR TYR SEQRES 51 A 971 ILE ARG THR ILE GLN SER LEU LEU GLY VAL GLU GLY LYS SEQRES 52 A 971 ILE GLN MET VAL VAL CYS ILE ILE MET GLY THR ARG ASP SEQRES 53 A 971 ASP LEU TYR GLY ALA ILE LYS LYS LEU CYS CYS VAL GLN SEQRES 54 A 971 SER PRO VAL PRO SER GLN VAL ILE ASN VAL ARG THR ILE SEQRES 55 A 971 GLY GLN PRO THR ARG LEU ARG SER VAL ALA GLN LYS ILE SEQRES 56 A 971 LEU LEU GLN MET ASN CYS LYS LEU GLY GLY GLU LEU TRP SEQRES 57 A 971 GLY VAL ASP ILE PRO LEU LYS GLN LEU MET VAL ILE GLY SEQRES 58 A 971 MET ASP VAL TYR HIS ASP PRO SER ARG GLY MET ARG SER SEQRES 59 A 971 VAL VAL GLY PHE VAL ALA SER ILE ASN LEU THR LEU THR SEQRES 60 A 971 LYS TRP TYR SER ARG VAL VAL PHE GLN MET PRO HIS GLN SEQRES 61 A 971 GLU ILE VAL ASP SER LEU LYS LEU CYS LEU VAL GLY SER SEQRES 62 A 971 LEU LYS LYS TYR TYR GLU VAL ASN HIS CYS LEU PRO GLU SEQRES 63 A 971 LYS ILE VAL VAL TYR ARG ASP GLY VAL SER ASP GLY GLN SEQRES 64 A 971 LEU LYS THR VAL ALA ASN TYR GLU ILE PRO GLN LEU GLN SEQRES 65 A 971 LYS CYS PHE GLU ALA PHE ASP ASN TYR HIS PRO LYS MET SEQRES 66 A 971 VAL VAL PHE VAL VAL GLN LYS LYS ILE SER THR ASN LEU SEQRES 67 A 971 TYR LEU ALA ALA PRO ASP HIS PHE VAL THR PRO SER PRO SEQRES 68 A 971 GLY THR VAL VAL ASP HIS THR ILE THR SER CYS GLU TRP SEQRES 69 A 971 VAL ASP PHE TYR LEU LEU ALA HIS HIS VAL ARG GLN GLY SEQRES 70 A 971 CYS GLY ILE PRO THR HIS TYR ILE CYS VAL LEU ASN THR SEQRES 71 A 971 ALA ASN LEU SER PRO ASP HIS MET GLN ARG LEU THR PHE SEQRES 72 A 971 LYS LEU CYS HIS MET TYR TRP ASN TRP PRO GLY THR ILE SEQRES 73 A 971 ARG VAL PRO ALA PRO CYS LYS TYR ALA HIS LYS LEU ALA SEQRES 74 A 971 PHE LEU SER GLY GLN ILE LEU HIS HIS GLU PRO ALA ILE SEQRES 75 A 971 GLN LEU CYS GLY ASN LEU PHE PHE LEU SEQRES 1 B 26 U U A C C A U C A A C A U SEQRES 2 B 26 G G A A A C U U G G C U OMC SEQRES 1 C 25 G A G C C A A G U U U C C SEQRES 2 C 25 A U G U U G A U G G U A HET OMC B 26 21 HET MN A1001 1 HETNAM OMC O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE HETNAM MN MANGANESE (II) ION FORMUL 2 OMC C10 H16 N3 O8 P FORMUL 4 MN MN 2+ HELIX 1 AA1 CYS A 251 HIS A 262 1 12 HELIX 2 AA2 HIS A 262 GLY A 267 1 6 HELIX 3 AA3 SER A 314 LEU A 316 5 3 HELIX 4 AA4 CYS A 317 LEU A 331 1 15 HELIX 5 AA5 PRO A 344 ALA A 347 5 4 HELIX 6 AA6 SER A 387 ASN A 399 1 13 HELIX 7 AA7 HIS A 402 VAL A 412 1 11 HELIX 8 AA8 PHE A 450 ASN A 457 1 8 HELIX 9 AA9 PRO A 502 ASP A 508 1 7 HELIX 10 AB1 ASP A 508 ILE A 519 1 12 HELIX 11 AB2 SER A 522 ASN A 540 1 19 HELIX 12 AB3 ASN A 540 TRP A 550 1 11 HELIX 13 AB4 PRO A 609 ARG A 611 5 3 HELIX 14 AB5 ALA A 612 GLY A 628 1 17 HELIX 15 AB6 ARG A 646 GLU A 661 1 16 HELIX 16 AB7 ARG A 675 VAL A 688 1 14 HELIX 17 AB8 VAL A 699 GLY A 703 1 5 HELIX 18 AB9 LEU A 708 LEU A 723 1 16 HELIX 19 AC1 LEU A 788 HIS A 802 1 15 HELIX 20 AC2 GLN A 819 ASN A 825 1 7 HELIX 21 AC3 GLU A 827 GLN A 832 1 6 HELIX 22 AC4 LYS A 833 ALA A 837 5 5 HELIX 23 AC5 SER A 914 MET A 928 1 15 HELIX 24 AC6 PRO A 939 ILE A 955 1 17 SHEET 1 AA1 3 LEU A 224 GLY A 225 0 SHEET 2 AA1 3 TYR A 859 ALA A 861 -1 O TYR A 859 N GLY A 225 SHEET 3 AA1 3 PHE A 866 VAL A 867 -1 O VAL A 867 N LEU A 860 SHEET 1 AA2 2 GLN A 232 CYS A 233 0 SHEET 2 AA2 2 SER A 553 LEU A 554 -1 O SER A 553 N CYS A 233 SHEET 1 AA3 5 ALA A 271 PHE A 272 0 SHEET 2 AA3 5 ILE A 276 TYR A 278 -1 O TYR A 278 N ALA A 271 SHEET 3 AA3 5 GLN A 240 SER A 246 -1 N TYR A 241 O LEU A 277 SHEET 4 AA3 5 GLU A 299 ILE A 304 -1 O LYS A 303 N THR A 244 SHEET 5 AA3 5 VAL A 287 GLN A 292 -1 N VAL A 287 O ILE A 304 SHEET 1 AA4 4 LYS A 335 VAL A 337 0 SHEET 2 AA4 4 ASN A 340 TYR A 342 -1 O TYR A 342 N LYS A 335 SHEET 3 AA4 4 PRO A 359 TYR A 361 -1 O TYR A 361 N PHE A 341 SHEET 4 AA4 4 VAL A 378 HIS A 380 -1 O SER A 379 N GLY A 360 SHEET 1 AA5 3 VAL A 349 LEU A 350 0 SHEET 2 AA5 3 LEU A 355 GLN A 356 -1 O LEU A 355 N LEU A 350 SHEET 3 AA5 3 ILE A 383 ARG A 384 -1 O ILE A 383 N GLN A 356 SHEET 1 AA6 2 SER A 364 THR A 368 0 SHEET 2 AA6 2 GLY A 371 LEU A 375 -1 O LEU A 375 N SER A 364 SHEET 1 AA7 3 ARG A 423 ARG A 426 0 SHEET 2 AA7 3 ILE A 415 THR A 418 -1 N THR A 418 O ARG A 423 SHEET 3 AA7 3 SER A 496 MET A 498 -1 O PHE A 497 N ILE A 417 SHEET 1 AA8 3 ASP A 429 ASP A 431 0 SHEET 2 AA8 3 LEU A 469 ILE A 471 -1 O LEU A 469 N ASP A 431 SHEET 3 AA8 3 LEU A 490 LEU A 491 -1 O LEU A 491 N LEU A 470 SHEET 1 AA9 2 SER A 439 VAL A 441 0 SHEET 2 AA9 2 GLU A 447 THR A 449 -1 O ILE A 448 N PHE A 440 SHEET 1 AB1 9 ARG A 564 LEU A 565 0 SHEET 2 AB1 9 THR A 873 VAL A 875 -1 O VAL A 874 N ARG A 564 SHEET 3 AB1 9 VAL A 885 LEU A 890 -1 O TYR A 888 N VAL A 875 SHEET 4 AB1 9 THR A 902 ASN A 909 -1 O TYR A 904 N PHE A 887 SHEET 5 AB1 9 VAL A 846 GLN A 851 -1 N GLN A 851 O HIS A 903 SHEET 6 AB1 9 LYS A 807 ARG A 812 1 N VAL A 810 O VAL A 846 SHEET 7 AB1 9 LEU A 737 TYR A 745 1 N ILE A 740 O VAL A 809 SHEET 8 AB1 9 VAL A 755 SER A 761 -1 O VAL A 755 N TYR A 745 SHEET 9 AB1 9 TRP A 769 PHE A 775 -1 O TYR A 770 N ALA A 760 SHEET 1 AB2 3 SER A 577 PHE A 578 0 SHEET 2 AB2 3 ILE A 571 ASN A 572 -1 N ILE A 571 O PHE A 578 SHEET 3 AB2 3 GLY A 729 VAL A 730 -1 O GLY A 729 N ASN A 572 SHEET 1 AB3 2 VAL A 667 ILE A 671 0 SHEET 2 AB3 2 SER A 694 ASN A 698 1 O ILE A 697 N ILE A 671 LINK O3' U B 25 P OMC B 26 1555 1555 1.61 LINK OD1 ASP A 743 MN MN A1001 1555 1555 1.97 LINK OD2 ASP A 813 MN MN A1001 1555 1555 2.43 LINK MN MN A1001 OP1 U C 17 1555 1555 2.59 CISPEP 1 SER A 246 PRO A 247 0 -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 TER 5922 LEU A 971 HETATM 6452 N1 OMC B 26 92.977 122.424 115.775 1.00 47.88 N HETATM 6453 C2 OMC B 26 92.530 121.149 116.177 1.00 47.28 C HETATM 6454 N3 OMC B 26 93.444 120.286 116.668 1.00 46.56 N HETATM 6455 C4 OMC B 26 94.715 120.611 116.773 1.00 46.78 C HETATM 6456 C5 OMC B 26 95.204 121.892 116.376 1.00 48.78 C HETATM 6457 C6 OMC B 26 94.289 122.749 115.888 1.00 48.90 C HETATM 6458 O2 OMC B 26 91.349 120.859 116.075 1.00 46.68 O HETATM 6459 N4 OMC B 26 95.562 119.708 117.266 1.00 46.85 N HETATM 6460 C1' OMC B 26 92.062 123.436 115.230 1.00 47.40 C HETATM 6461 C2' OMC B 26 91.873 124.650 116.138 1.00 47.17 C HETATM 6462 O2' OMC B 26 90.876 124.424 117.113 1.00 45.81 O HETATM 6463 CM2 OMC B 26 91.392 124.040 118.366 1.00 44.52 C HETATM 6464 C3' OMC B 26 91.535 125.738 115.127 1.00 47.10 C HETATM 6465 C4' OMC B 26 92.416 125.368 113.940 1.00 48.18 C HETATM 6466 O4' OMC B 26 92.621 123.931 114.026 1.00 46.13 O HETATM 6467 O3' OMC B 26 90.163 125.630 114.751 1.00 46.79 O HETATM 6468 C5' OMC B 26 93.759 126.054 113.895 1.00 47.55 C HETATM 6469 O5' OMC B 26 94.577 125.533 112.852 1.00 49.67 O HETATM 6470 P OMC B 26 96.155 125.410 113.029 1.00 51.44 P HETATM 6471 OP1 OMC B 26 96.749 126.810 112.942 1.00 46.74 O HETATM 6472 OP2 OMC B 26 96.435 124.553 114.260 1.00 46.57 O TER 6473 OMC B 26 TER 7007 A C 25 HETATM 7008 MN MN A1001 89.135 92.211 78.402 1.00 5.68 MN CONECT 4143 7008 CONECT 4654 7008 CONECT 6440 6470 CONECT 6452 6453 6457 6460 CONECT 6453 6452 6454 6458 CONECT 6454 6453 6455 CONECT 6455 6454 6456 6459 CONECT 6456 6455 6457 CONECT 6457 6452 6456 CONECT 6458 6453 CONECT 6459 6455 CONECT 6460 6452 6461 6466 CONECT 6461 6460 6462 6464 CONECT 6462 6461 6463 CONECT 6463 6462 CONECT 6464 6461 6465 6467 CONECT 6465 6464 6466 6468 CONECT 6466 6460 6465 CONECT 6467 6464 CONECT 6468 6465 6469 CONECT 6469 6468 6470 CONECT 6470 6440 6469 6471 6472 CONECT 6471 6470 CONECT 6472 6470 CONECT 6815 7008 CONECT 7008 4143 4654 6815 MASTER 453 0 2 24 41 0 0 6 7005 3 26 79 END