HEADER RNA BINDING PROTEIN/RNA 21-JUN-24 9IJ1 TITLE CRYO-EM STRUCTURE OF MILI-PIRNA-TARGET (22-NT, BILOBED) 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 (5'- COMPND 12 R(P*CP*AP*AP*GP*UP*UP*UP*CP*CP*AP*UP*GP*UP*UP*GP*AP*UP*GP*GP*UP*A)- COMPND 13 3'); COMPND 14 CHAIN: C; COMPND 15 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 16-JUL-25 9IJ1 1 REMARK REVDAT 4 19-MAR-25 9IJ1 1 JRNL REVDAT 3 29-JAN-25 9IJ1 1 JRNL REVDAT 2 22-JAN-25 9IJ1 1 JRNL REVDAT 1 13-NOV-24 9IJ1 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. 3.20 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) : 3.200 REMARK 3 NUMBER OF PARTICLES : 122269 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 9IJ1 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_1300048883. 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 (22-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 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 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 LEU A 484 REMARK 465 LEU A 485 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 ILE A 664 CG1 CG2 CD1 REMARK 470 LYS A 714 CG CD CE NZ REMARK 470 A C 21 OP1 OP2 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 LEU A 228 CA - CB - CG ANGL. DEV. = 14.0 DEGREES REMARK 500 MET A 512 CG - SD - CE ANGL. DEV. = 10.4 DEGREES REMARK 500 MET A 613 CA - CB - CG ANGL. DEV. = 12.2 DEGREES REMARK 500 LEU A 657 CA - CB - CG ANGL. DEV. = 14.8 DEGREES REMARK 500 LEU A 786 CA - CB - CG ANGL. DEV. = 14.9 DEGREES REMARK 500 U B 1 C3' - O3' - P ANGL. DEV. = 7.2 DEGREES REMARK 500 U B 2 O3' - P - OP2 ANGL. DEV. = 7.5 DEGREES REMARK 500 C B 11 C5 - C6 - N1 ANGL. DEV. = 3.7 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 ASN A 227 -55.76 -120.97 REMARK 500 LEU A 228 -8.06 77.61 REMARK 500 ASN A 422 17.21 59.86 REMARK 500 PRO A 468 -167.50 -72.59 REMARK 500 LYS A 588 30.75 -99.27 REMARK 500 ALA A 612 35.63 -143.09 REMARK 500 ILE A 647 -68.47 61.32 REMARK 500 THR A 649 -18.28 72.41 REMARK 500 LEU A 657 -70.01 -82.48 REMARK 500 LEU A 658 41.66 35.64 REMARK 500 TRP A 728 147.44 -172.21 REMARK 500 ASN A 840 46.34 37.23 REMARK 500 THR A 880 -166.19 -78.57 REMARK 500 PHE A 970 47.37 -90.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 MET A 498 THR A 499 144.46 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 MG A1001 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 743 OD1 REMARK 620 2 ASP A 743 OD2 45.1 REMARK 620 3 ASP A 813 OD2 76.1 64.0 REMARK 620 4 U C 13 OP1 110.5 154.8 109.5 REMARK 620 5 U C 13 OP2 167.0 135.1 116.4 70.1 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-60612 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF MILI-PIRNA-TARGET (22-NT, BILOBED) DBREF 9IJ1 A 1 971 UNP Q8CDG1 PIWL2_MOUSE 1 971 DBREF 9IJ1 B 1 26 PDB 9IJ1 9IJ1 1 26 DBREF 9IJ1 C 1 21 PDB 9IJ1 9IJ1 1 21 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 21 C A A G U U U C C A U G U SEQRES 2 C 21 U G A U G G U A HET OMC B 26 21 HET MG A1001 1 HETNAM OMC O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 2 OMC C10 H16 N3 O8 P FORMUL 4 MG MG 2+ HELIX 1 AA1 CYS A 251 ASP A 261 1 11 HELIX 2 AA2 SER A 314 LEU A 316 5 3 HELIX 3 AA3 CYS A 317 LYS A 330 1 14 HELIX 4 AA4 VAL A 388 ASN A 399 1 12 HELIX 5 AA5 PHE A 403 LEU A 411 1 9 HELIX 6 AA6 PHE A 450 TYR A 458 1 9 HELIX 7 AA7 PRO A 502 LYS A 507 1 6 HELIX 8 AA8 ALA A 511 ASN A 520 1 10 HELIX 9 AA9 SER A 522 GLN A 539 1 18 HELIX 10 AB1 ASN A 540 ARG A 549 1 10 HELIX 11 AB2 TRP A 586 VAL A 590 5 5 HELIX 12 AB3 ALA A 612 GLU A 624 1 13 HELIX 13 AB4 LYS A 625 GLY A 628 5 4 HELIX 14 AB5 THR A 649 LEU A 658 1 10 HELIX 15 AB6 GLY A 659 ILE A 664 5 6 HELIX 16 AB7 ARG A 675 GLN A 689 1 15 HELIX 17 AB8 LEU A 717 LEU A 723 1 7 HELIX 18 AB9 SER A 785 ASN A 801 1 17 HELIX 19 AC1 GLN A 819 TYR A 826 1 8 HELIX 20 AC2 GLU A 827 PHE A 835 1 9 HELIX 21 AC3 GLU A 836 PHE A 838 5 3 HELIX 22 AC4 SER A 914 HIS A 927 1 14 HELIX 23 AC5 PRO A 939 ILE A 955 1 17 HELIX 24 AC6 ALA A 961 CYS A 965 5 5 SHEET 1 AA1 5 ALA A 271 PHE A 272 0 SHEET 2 AA1 5 ILE A 276 LEU A 279 -1 O TYR A 278 N ALA A 271 SHEET 3 AA1 5 VAL A 238 VAL A 243 -1 N TYR A 241 O LEU A 277 SHEET 4 AA1 5 GLU A 299 LEU A 310 -1 O THR A 307 N GLN A 240 SHEET 5 AA1 5 VAL A 286 GLN A 292 -1 N VAL A 287 O ILE A 304 SHEET 1 AA2 2 LYS A 335 VAL A 337 0 SHEET 2 AA2 2 ASN A 340 TYR A 342 -1 O TYR A 342 N LYS A 335 SHEET 1 AA3 6 MET A 348 LEU A 350 0 SHEET 2 AA3 6 LEU A 355 PRO A 359 -1 O ILE A 357 N MET A 348 SHEET 3 AA3 6 HIS A 380 SER A 387 -1 O ILE A 383 N GLN A 356 SHEET 4 AA3 6 SER A 496 THR A 499 -1 O MET A 498 N ASP A 386 SHEET 5 AA3 6 ILE A 415 THR A 418 -1 N ILE A 417 O PHE A 497 SHEET 6 AA3 6 THR A 424 ARG A 426 -1 O TYR A 425 N VAL A 416 SHEET 1 AA4 2 ALA A 362 THR A 368 0 SHEET 2 AA4 2 GLY A 371 ASP A 377 -1 O ASP A 377 N ALA A 362 SHEET 1 AA5 3 ASP A 429 ASP A 431 0 SHEET 2 AA5 3 LEU A 469 HIS A 472 -1 O LEU A 469 N ASP A 431 SHEET 3 AA5 3 ILE A 489 LEU A 491 -1 O ILE A 489 N HIS A 472 SHEET 1 AA6 2 SER A 439 VAL A 441 0 SHEET 2 AA6 2 GLU A 447 THR A 449 -1 O ILE A 448 N PHE A 440 SHEET 1 AA7 3 SER A 577 VAL A 579 0 SHEET 2 AA7 3 ARG A 570 ASN A 572 -1 N ILE A 571 O PHE A 578 SHEET 3 AA7 3 GLY A 729 VAL A 730 -1 O GLY A 729 N ASN A 572 SHEET 1 AA8 2 ALA A 605 TYR A 608 0 SHEET 2 AA8 2 ALA A 638 GLU A 641 1 O ALA A 638 N LEU A 606 SHEET 1 AA9 2 VAL A 668 ILE A 671 0 SHEET 2 AA9 2 GLN A 695 ASN A 698 1 O ILE A 697 N CYS A 669 SHEET 1 AB1 6 LEU A 737 ILE A 740 0 SHEET 2 AB1 6 LYS A 807 ASP A 813 1 O VAL A 809 N ILE A 740 SHEET 3 AB1 6 LYS A 844 GLN A 851 1 O VAL A 846 N VAL A 810 SHEET 4 AB1 6 PRO A 901 ASN A 909 -1 O ILE A 905 N VAL A 849 SHEET 5 AB1 6 VAL A 885 LEU A 890 -1 N VAL A 885 O CYS A 906 SHEET 6 AB1 6 VAL A 874 VAL A 875 -1 N VAL A 875 O TYR A 888 SHEET 1 AB2 3 ASP A 743 TYR A 745 0 SHEET 2 AB2 3 VAL A 755 PHE A 758 -1 O VAL A 755 N TYR A 745 SHEET 3 AB2 3 ARG A 772 PHE A 775 -1 O ARG A 772 N PHE A 758 SHEET 1 AB3 2 LEU A 860 ALA A 861 0 SHEET 2 AB3 2 PHE A 866 VAL A 867 -1 O VAL A 867 N LEU A 860 LINK O3' U B 25 P OMC B 26 1555 1555 1.61 LINK OD1 ASP A 743 MG MG A1001 1555 1555 2.87 LINK OD2 ASP A 743 MG MG A1001 1555 1555 2.84 LINK OD2 ASP A 813 MG MG A1001 1555 1555 2.69 LINK MG MG A1001 OP1 U C 13 1555 1555 2.10 LINK MG MG A1001 OP2 U C 13 1555 1555 2.33 CISPEP 1 SER A 246 PRO A 247 0 2.36 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 6063 LEU A 971 HETATM 6593 N1 OMC B 26 59.190 58.409 109.886 1.00264.95 N HETATM 6594 C2 OMC B 26 58.807 59.689 110.365 1.00264.36 C HETATM 6595 N3 OMC B 26 59.603 60.738 110.068 1.00264.10 N HETATM 6596 C4 OMC B 26 60.704 60.602 109.360 1.00264.06 C HETATM 6597 C5 OMC B 26 61.125 59.334 108.860 1.00264.12 C HETATM 6598 C6 OMC B 26 60.330 58.290 109.156 1.00264.61 C HETATM 6599 O2 OMC B 26 57.792 59.851 111.025 1.00263.73 O HETATM 6600 N4 OMC B 26 61.436 61.686 109.109 1.00264.00 N HETATM 6601 C1' OMC B 26 58.441 57.160 110.115 1.00264.74 C HETATM 6602 C2' OMC B 26 58.460 56.665 111.560 1.00264.62 C HETATM 6603 O2' OMC B 26 59.635 55.938 111.850 1.00264.54 O HETATM 6604 CM2 OMC B 26 59.800 55.666 113.222 1.00264.14 C HETATM 6605 C3' OMC B 26 57.176 55.845 111.615 1.00264.43 C HETATM 6606 C4' OMC B 26 56.232 56.648 110.725 1.00264.44 C HETATM 6607 O4' OMC B 26 57.079 57.376 109.793 1.00264.43 O HETATM 6608 O3' OMC B 26 57.403 54.563 111.032 1.00264.44 O HETATM 6609 C5' OMC B 26 55.345 57.627 111.454 1.00264.46 C HETATM 6610 O5' OMC B 26 54.143 57.892 110.737 1.00265.05 O HETATM 6611 P OMC B 26 53.967 59.241 109.907 1.00265.51 P HETATM 6612 OP1 OMC B 26 52.471 59.524 109.800 1.00264.70 O HETATM 6613 OP2 OMC B 26 54.893 60.290 110.505 1.00264.23 O TER 6614 OMC B 26 TER 7058 A C 21 HETATM 7059 MG MG A1001 81.927 84.064 75.572 1.00 79.86 MG CONECT 4221 7059 CONECT 4222 7059 CONECT 4795 7059 CONECT 6581 6611 CONECT 6593 6594 6598 6601 CONECT 6594 6593 6595 6599 CONECT 6595 6594 6596 CONECT 6596 6595 6597 6600 CONECT 6597 6596 6598 CONECT 6598 6593 6597 CONECT 6599 6594 CONECT 6600 6596 CONECT 6601 6593 6602 6607 CONECT 6602 6601 6603 6605 CONECT 6603 6602 6604 CONECT 6604 6603 CONECT 6605 6602 6606 6608 CONECT 6606 6605 6607 6609 CONECT 6607 6601 6606 CONECT 6608 6605 CONECT 6609 6606 6610 CONECT 6610 6609 6611 CONECT 6611 6581 6610 6612 6613 CONECT 6612 6611 CONECT 6613 6611 CONECT 6868 7059 CONECT 6869 7059 CONECT 7059 4221 4222 4795 6868 CONECT 7059 6869 MASTER 432 0 2 24 38 0 0 6 7056 3 29 79 END