HEADER RNA BINDING PROTEIN/RNA 24-FEB-25 9NHB TITLE CRYO-EM STRUCTURE OF SIWI-PIRNA-TARGET(25-NT)-GTSF1 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: PIWI-LIKE PROTEIN SIWI; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.26.-; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: PIRNA; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: TARGET RNA (25-NT); COMPND 12 CHAIN: C; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 4; COMPND 15 MOLECULE: GTSF1; COMPND 16 CHAIN: E; COMPND 17 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOMBYX MORI; SOURCE 3 ORGANISM_COMMON: DOMESTIC SILKWORM; SOURCE 4 ORGANISM_TAXID: 7091; SOURCE 5 GENE: SIWI; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630; SOURCE 16 MOL_ID: 4; SOURCE 17 ORGANISM_SCIENTIFIC: BOMBYX MORI; SOURCE 18 ORGANISM_COMMON: DOMESTIC SILKWORM; SOURCE 19 ORGANISM_TAXID: 7091; SOURCE 20 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SIWI, GTSF1, RNA BINDING PROTEIN, RNA BINDING PROTEIN-RNA COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR S.SARKAR,L.F.R.GEBERT,I.J.MACRAE REVDAT 2 01-OCT-25 9NHB 1 JRNL REVDAT 1 17-SEP-25 9NHB 0 JRNL AUTH D.DE,S.SARKAR,L.F.R.GEBERT,T.WIRYAMAN,T.A.ANZELON,I.J.MACRAE JRNL TITL A CONSERVED PIWI SILENCING COMPLEX DETECTS PIRNA-TARGET JRNL TITL 2 ENGAGEMENT. JRNL REF MOL.CELL V. 85 3275 2025 JRNL REFN ISSN 1097-2765 JRNL PMID 40912244 JRNL DOI 10.1016/J.MOLCEL.2025.08.010 REMARK 2 REMARK 2 RESOLUTION. 3.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : UCSF CHIMERAX, PHENIX, COOT, UCSF REMARK 3 CHIMERAX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 5GUH REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE FIT 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) : 3.700 REMARK 3 NUMBER OF PARTICLES : 161717 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 9NHB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-FEB-25. REMARK 100 THE DEPOSITION ID IS D_1000293313. 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 : SIWI-PIRNA-TARGET(25-NT)-GTSF1 REMARK 245 COMPLEX REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.89 REMARK 245 SAMPLE SUPPORT DETAILS : 15 MA 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 : 4687 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TALOS ARCTICA REMARK 245 DETECTOR TYPE : GATAN K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3000.00 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 : OTHER REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 200 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, E 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 GLU A 3 REMARK 465 PRO A 4 REMARK 465 ARG A 5 REMARK 465 GLY A 6 REMARK 465 ARG A 7 REMARK 465 GLY A 8 REMARK 465 ARG A 9 REMARK 465 ALA A 10 REMARK 465 ARG A 11 REMARK 465 GLY A 12 REMARK 465 ARG A 13 REMARK 465 ALA A 14 REMARK 465 GLY A 15 REMARK 465 ARG A 16 REMARK 465 GLY A 17 REMARK 465 GLY A 18 REMARK 465 ASP A 19 REMARK 465 GLY A 20 REMARK 465 GLY A 21 REMARK 465 GLY A 22 REMARK 465 PRO A 23 REMARK 465 ALA A 24 REMARK 465 PRO A 25 REMARK 465 ARG A 26 REMARK 465 ARG A 27 REMARK 465 PRO A 28 REMARK 465 GLY A 29 REMARK 465 GLU A 30 REMARK 465 GLN A 31 REMARK 465 ALA A 32 REMARK 465 GLY A 33 REMARK 465 PRO A 34 REMARK 465 SER A 35 REMARK 465 GLN A 36 REMARK 465 GLN A 37 REMARK 465 SER A 38 REMARK 465 MET A 39 REMARK 465 PRO A 40 REMARK 465 PRO A 41 REMARK 465 GLY A 42 REMARK 465 PRO A 43 REMARK 465 ARG A 44 REMARK 465 PRO A 45 REMARK 465 GLN A 46 REMARK 465 PRO A 47 REMARK 465 PRO A 48 REMARK 465 SER A 49 REMARK 465 GLY A 50 REMARK 465 TRP A 51 REMARK 465 GLY A 52 REMARK 465 PRO A 53 REMARK 465 GLN A 54 REMARK 465 SER A 55 REMARK 465 SER A 56 REMARK 465 VAL A 57 REMARK 465 PRO A 58 REMARK 465 PRO A 59 REMARK 465 VAL A 60 REMARK 465 ARG A 61 REMARK 465 ALA A 62 REMARK 465 GLY A 63 REMARK 465 VAL A 64 REMARK 465 PRO A 65 REMARK 465 THR A 66 REMARK 465 PRO A 67 REMARK 465 THR A 68 REMARK 465 ALA A 69 REMARK 465 GLN A 70 REMARK 465 ALA A 71 REMARK 465 GLY A 72 REMARK 465 ARG A 73 REMARK 465 ALA A 74 REMARK 465 SER A 75 REMARK 465 HIS A 76 REMARK 465 ARG A 77 REMARK 465 VAL A 78 REMARK 465 THR A 79 REMARK 465 PRO A 80 REMARK 465 THR A 81 REMARK 465 THR A 82 REMARK 465 HIS A 83 REMARK 465 GLU A 84 REMARK 465 HIS A 85 REMARK 465 PRO A 86 REMARK 465 GLY A 87 REMARK 465 ASP A 88 REMARK 465 ILE A 89 REMARK 465 ASP A 90 REMARK 465 VAL A 91 REMARK 465 GLN A 92 REMARK 465 GLN A 93 REMARK 465 ARG A 94 REMARK 465 MET A 95 REMARK 465 GLN A 96 REMARK 465 LYS A 97 REMARK 465 LEU A 98 REMARK 465 GLU A 99 REMARK 465 LEU A 100 REMARK 465 GLY A 101 REMARK 465 PRO A 102 REMARK 465 HIS A 103 REMARK 465 SER A 104 REMARK 465 SER A 105 REMARK 465 GLY A 106 REMARK 465 GLY A 107 REMARK 465 GLY A 108 REMARK 465 ASP A 109 REMARK 465 ALA A 110 REMARK 465 SER A 111 REMARK 465 SER A 112 REMARK 465 VAL A 113 REMARK 465 VAL A 114 REMARK 465 GLY A 115 REMARK 465 ARG A 116 REMARK 465 GLY A 117 REMARK 465 SER A 118 REMARK 465 ARG A 119 REMARK 465 ARG A 120 REMARK 465 GLY A 121 REMARK 465 GLY A 122 REMARK 465 GLY A 123 REMARK 465 ARG A 124 REMARK 465 VAL A 125 REMARK 465 LEU A 126 REMARK 465 PRO A 127 REMARK 465 GLU A 128 REMARK 465 THR A 129 REMARK 465 ILE A 130 REMARK 465 SER A 131 REMARK 465 ILE A 132 REMARK 465 LEU A 133 REMARK 465 ARG A 134 REMARK 465 THR A 135 REMARK 465 ARG A 136 REMARK 465 PRO A 137 REMARK 465 GLU A 138 REMARK 465 ALA A 139 REMARK 465 VAL A 140 REMARK 465 THR A 141 REMARK 465 HIS A 213 REMARK 465 PRO A 214 REMARK 465 ASP A 215 REMARK 465 PRO A 216 REMARK 465 MET A 217 REMARK 465 PRO A 413 REMARK 465 GLU A 414 REMARK 465 SER A 705 REMARK 465 GLY A 706 REMARK 465 GLU A 707 REMARK 465 U B 24 REMARK 465 A2M B 25 REMARK 465 U C 1 REMARK 465 A C 2 REMARK 465 A C 26 REMARK 465 A C 27 REMARK 465 MET E 1 REMARK 465 GLU E 2 REMARK 465 VAL E 3 REMARK 465 THR E 4 REMARK 465 ILE E 5 REMARK 465 ALA E 6 REMARK 465 ASN E 7 REMARK 465 PRO E 8 REMARK 465 LYS E 9 REMARK 465 PRO E 10 REMARK 465 ASN E 11 REMARK 465 GLN E 12 REMARK 465 MET E 13 REMARK 465 ILE E 14 REMARK 465 THR E 15 REMARK 465 CYS E 16 REMARK 465 PRO E 17 REMARK 465 TYR E 18 REMARK 465 GLU E 19 REMARK 465 LYS E 20 REMARK 465 ALA E 21 REMARK 465 HIS E 22 REMARK 465 ILE E 23 REMARK 465 VAL E 24 REMARK 465 GLU E 25 REMARK 465 HIS E 26 REMARK 465 TYR E 27 REMARK 465 ARG E 28 REMARK 465 MET E 29 REMARK 465 HIS E 30 REMARK 465 ILE E 31 REMARK 465 HIS E 32 REMARK 465 LEU E 33 REMARK 465 GLN E 34 REMARK 465 LYS E 35 REMARK 465 CYS E 36 REMARK 465 ARG E 37 REMARK 465 LYS E 38 REMARK 465 GLN E 39 REMARK 465 HIS E 40 REMARK 465 PRO E 41 REMARK 465 ALA E 42 REMARK 465 CYS E 43 REMARK 465 ASN E 44 REMARK 465 LYS E 45 REMARK 465 VAL E 46 REMARK 465 GLN E 47 REMARK 465 CYS E 48 REMARK 465 PRO E 49 REMARK 465 PHE E 50 REMARK 465 ASP E 51 REMARK 465 ALA E 52 REMARK 465 THR E 53 REMARK 465 HIS E 54 REMARK 465 VAL E 55 REMARK 465 VAL E 56 REMARK 465 ASN E 57 REMARK 465 ASP E 58 REMARK 465 VAL E 59 REMARK 465 GLU E 60 REMARK 465 LEU E 61 REMARK 465 ASP E 62 REMARK 465 PHE E 63 REMARK 465 HIS E 64 REMARK 465 VAL E 65 REMARK 465 THR E 66 REMARK 465 VAL E 67 REMARK 465 CYS E 68 REMARK 465 PRO E 69 REMARK 465 LYS E 70 REMARK 465 ARG E 71 REMARK 465 HIS E 72 REMARK 465 MET E 73 REMARK 465 LEU E 74 REMARK 465 ASP E 75 REMARK 465 THR E 76 REMARK 465 GLN E 77 REMARK 465 LEU E 78 REMARK 465 TYR E 79 REMARK 465 ILE E 80 REMARK 465 THR E 81 REMARK 465 ASP E 82 REMARK 465 ASP E 83 REMARK 465 GLU E 84 REMARK 465 TYR E 85 REMARK 465 ARG E 86 REMARK 465 PRO E 87 REMARK 465 THR E 88 REMARK 465 VAL E 89 REMARK 465 GLU E 90 REMARK 465 VAL E 91 REMARK 465 HIS E 92 REMARK 465 ALA E 93 REMARK 465 THR E 94 REMARK 465 PRO E 95 REMARK 465 VAL E 96 REMARK 465 LEU E 97 REMARK 465 PRO E 98 REMARK 465 SER E 99 REMARK 465 ASP E 100 REMARK 465 ASP E 105 REMARK 465 GLU E 106 REMARK 465 THR E 107 REMARK 465 SER E 108 REMARK 465 THR E 109 REMARK 465 SER E 110 REMARK 465 TYR E 111 REMARK 465 ILE E 112 REMARK 465 PRO E 113 REMARK 465 ASP E 114 REMARK 465 PRO E 115 REMARK 465 SER E 116 REMARK 465 LYS E 117 REMARK 465 LYS E 118 REMARK 465 GLY E 119 REMARK 465 ALA E 120 REMARK 465 HIS E 121 REMARK 465 ILE E 122 REMARK 465 ILE E 123 REMARK 465 THR E 124 REMARK 465 LYS E 125 REMARK 465 ALA E 126 REMARK 465 LYS E 127 REMARK 465 GLY E 128 REMARK 465 LEU E 129 REMARK 465 THR E 130 REMARK 465 ARG E 131 REMARK 465 SER E 132 REMARK 465 GLU E 133 REMARK 465 ARG E 134 REMARK 465 GLN E 135 REMARK 465 SER E 136 REMARK 465 LEU E 137 REMARK 465 ARG E 138 REMARK 465 LYS E 139 REMARK 465 GLU E 140 REMARK 465 LEU E 141 REMARK 465 ILE E 142 REMARK 465 LYS E 143 REMARK 465 THR E 144 REMARK 465 TYR E 145 REMARK 465 ARG E 146 REMARK 465 PRO E 147 REMARK 465 LEU E 148 REMARK 465 GLU E 149 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 OD2 ASP A 690 OG1 THR A 694 2.18 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 -0.109 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 ARG A 356 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 440 NE - CZ - NH2 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG A 520 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 606 NE - CZ - NH2 ANGL. DEV. = 4.3 DEGREES REMARK 500 TYR A 669 CB - CG - CD2 ANGL. DEV. = -3.8 DEGREES REMARK 500 G B 2 C3' - O3' - P ANGL. DEV. = -9.7 DEGREES REMARK 500 U B 8 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 A B 10 N1 - C6 - N6 ANGL. DEV. = -4.6 DEGREES REMARK 500 C B 11 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 A B 12 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 A B 12 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 A B 12 N1 - C6 - N6 ANGL. DEV. = -5.2 DEGREES REMARK 500 U B 19 C3' - O3' - P ANGL. DEV. = -9.4 DEGREES REMARK 500 U B 20 C3' - O3' - P ANGL. DEV. = -12.6 DEGREES REMARK 500 U B 21 C3' - O3' - P ANGL. DEV. = -13.0 DEGREES REMARK 500 G B 22 C3' - O3' - P ANGL. DEV. = -17.6 DEGREES REMARK 500 C C 4 C3' - O3' - P ANGL. DEV. = -8.8 DEGREES REMARK 500 A C 5 C3' - O3' - P ANGL. DEV. = -8.6 DEGREES REMARK 500 C C 8 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 C C 10 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 C C 11 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 A C 12 C4 - C5 - C6 ANGL. DEV. = -3.6 DEGREES REMARK 500 A C 12 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 A C 12 N1 - C6 - N6 ANGL. DEV. = -5.9 DEGREES REMARK 500 C C 19 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 C C 19 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES REMARK 500 A C 20 O4' - C4' - C3' ANGL. DEV. = 6.0 DEGREES REMARK 500 A C 20 C5' - C4' - O4' ANGL. DEV. = 5.7 DEGREES REMARK 500 A C 20 N1 - C6 - N6 ANGL. DEV. = -4.8 DEGREES REMARK 500 U C 22 C3' - O3' - P ANGL. DEV. = -11.2 DEGREES REMARK 500 C C 23 C3' - O3' - P ANGL. DEV. = -9.0 DEGREES REMARK 500 A C 25 O3' - P - OP2 ANGL. DEV. = 14.8 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 THR A 146 -160.59 -123.23 REMARK 500 ALA A 276 27.69 -79.12 REMARK 500 TYR A 298 -168.56 -114.69 REMARK 500 MET A 372 -177.77 -69.67 REMARK 500 ASP A 374 -48.19 -132.37 REMARK 500 ALA A 410 -16.97 -148.05 REMARK 500 LYS A 489 57.96 -99.72 REMARK 500 LYS A 505 54.41 -103.04 REMARK 500 ARG A 520 30.94 -81.23 REMARK 500 SER A 521 15.97 -147.38 REMARK 500 ALA A 600 -48.74 64.09 REMARK 500 PHE A 685 47.69 -151.94 REMARK 500 LEU A 709 54.89 38.76 REMARK 500 GLU A 754 -52.66 -130.34 REMARK 500 ASP A 804 31.05 -150.88 REMARK 500 ASP A 805 -30.03 -139.12 REMARK 500 SER A 861 47.10 -84.42 REMARK 500 LEU A 892 34.70 -99.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 739 0.10 SIDE CHAIN REMARK 500 G B 7 0.07 SIDE CHAIN 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 A 901 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 670 OD1 REMARK 620 2 ASP A 670 OD2 66.3 REMARK 620 3 ASP A 740 OD2 107.8 104.8 REMARK 620 4 U C 16 OP1 157.6 127.5 86.7 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-49407 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF SIWI-PIRNA-TARGET(25-NT)-GTSF1 COMPLEX DBREF 9NHB A 1 899 UNP A8D8P8 SIWI_BOMMO 1 899 DBREF 9NHB B 1 25 PDB 9NHB 9NHB 1 25 DBREF 9NHB C 1 27 PDB 9NHB 9NHB 1 27 DBREF1 9NHB E 1 149 UNP A0A8R1WGS4_BOMMO DBREF2 9NHB E A0A8R1WGS4 1 149 SEQRES 1 A 899 MET SER GLU PRO ARG GLY ARG GLY ARG ALA ARG GLY ARG SEQRES 2 A 899 ALA GLY ARG GLY GLY ASP GLY GLY GLY PRO ALA PRO ARG SEQRES 3 A 899 ARG PRO GLY GLU GLN ALA GLY PRO SER GLN GLN SER MET SEQRES 4 A 899 PRO PRO GLY PRO ARG PRO GLN PRO PRO SER GLY TRP GLY SEQRES 5 A 899 PRO GLN SER SER VAL PRO PRO VAL ARG ALA GLY VAL PRO SEQRES 6 A 899 THR PRO THR ALA GLN ALA GLY ARG ALA SER HIS ARG VAL SEQRES 7 A 899 THR PRO THR THR HIS GLU HIS PRO GLY ASP ILE ASP VAL SEQRES 8 A 899 GLN GLN ARG MET GLN LYS LEU GLU LEU GLY PRO HIS SER SEQRES 9 A 899 SER GLY GLY GLY ASP ALA SER SER VAL VAL GLY ARG GLY SEQRES 10 A 899 SER ARG ARG GLY GLY GLY ARG VAL LEU PRO GLU THR ILE SEQRES 11 A 899 SER ILE LEU ARG THR ARG PRO GLU ALA VAL THR SER LYS SEQRES 12 A 899 LYS GLY THR SER GLY THR PRO LEU ASP LEU LEU ALA ASN SEQRES 13 A 899 TYR PHE THR VAL GLU THR THR PRO LYS TRP GLY LEU TYR SEQRES 14 A 899 GLN TYR HIS VAL ASP ILE SER PRO GLU GLU ASP SER THR SEQRES 15 A 899 GLY VAL ARG LYS ALA LEU MET ARG VAL HIS SER LYS THR SEQRES 16 A 899 LEU GLY GLY TYR LEU PHE ASP GLY THR VAL LEU TYR THR SEQRES 17 A 899 VAL ASN ARG LEU HIS PRO ASP PRO MET GLU LEU TYR SER SEQRES 18 A 899 ASP ARG LYS THR ASP ASN GLU ARG MET ARG ILE LEU ILE SEQRES 19 A 899 LYS LEU THR CYS GLU VAL SER PRO GLY ASP TYR HIS TYR SEQRES 20 A 899 ILE GLN ILE PHE ASN ILE ILE ILE ARG LYS CYS PHE ASN SEQRES 21 A 899 LEU LEU LYS LEU GLN LEU MET GLY ARG ASP TYR PHE ASP SEQRES 22 A 899 PRO GLU ALA LYS ILE ASP ILE PRO GLU PHE LYS LEU GLN SEQRES 23 A 899 ILE TRP PRO GLY TYR LYS THR THR ILE ASN GLN TYR GLU SEQRES 24 A 899 ASP ARG LEU LEU LEU VAL THR GLU ILE ALA HIS LYS VAL SEQRES 25 A 899 LEU ARG MET ASP THR VAL LEU GLN MET LEU SER GLU TYR SEQRES 26 A 899 ALA ALA THR LYS GLY ASN ASN TYR LYS LYS ILE PHE LEU SEQRES 27 A 899 GLU ASP VAL VAL GLY LYS ILE VAL MET THR ASP TYR ASN SEQRES 28 A 899 LYS ARG THR TYR ARG VAL ASP ASP VAL ALA TRP ASN VAL SEQRES 29 A 899 SER PRO LYS SER THR PHE LYS MET ARG ASP GLU ASN ILE SEQRES 30 A 899 THR TYR ILE GLU TYR TYR TYR LYS LYS TYR ASN LEU ARG SEQRES 31 A 899 ILE GLN ASP PRO GLY GLN PRO LEU LEU ILE SER ARG SER SEQRES 32 A 899 LYS PRO ARG GLU ILE ARG ALA GLY LEU PRO GLU LEU ILE SEQRES 33 A 899 TYR LEU VAL PRO GLU LEU CYS ARG GLN THR GLY LEU SER SEQRES 34 A 899 ASP GLU MET ARG ALA ASN PHE LYS LEU MET ARG SER LEU SEQRES 35 A 899 ASP VAL HIS THR LYS ILE GLY PRO ASP LYS ARG ILE GLU SEQRES 36 A 899 LYS LEU ASN ASN PHE ASN ARG ARG PHE THR SER THR PRO SEQRES 37 A 899 GLU VAL VAL GLU GLU LEU ALA THR TRP SER LEU LYS LEU SEQRES 38 A 899 SER LYS GLU LEU VAL LYS ILE LYS GLY ARG GLN LEU PRO SEQRES 39 A 899 PRO GLU ASN ILE ILE GLN ALA ASN ASN VAL LYS TYR PRO SEQRES 40 A 899 ALA GLY ASP THR THR GLU GLY TRP THR ARG ASP MET ARG SEQRES 41 A 899 SER LYS HIS LEU LEU ALA ILE ALA GLN LEU ASN SER TRP SEQRES 42 A 899 VAL VAL ILE THR PRO GLU ARG GLN ARG ARG ASP THR GLU SEQRES 43 A 899 SER PHE ILE ASP LEU ILE ILE LYS THR GLY GLY GLY VAL SEQRES 44 A 899 GLY PHE ARG MET ARG SER PRO ASP LEU VAL VAL ILE ARG SEQRES 45 A 899 HIS ASP GLY PRO ILE GLU TYR ALA ASN MET CYS GLU GLU SEQRES 46 A 899 VAL ILE ALA ARG LYS ASN PRO ALA LEU ILE LEU CYS VAL SEQRES 47 A 899 LEU ALA ARG ASN TYR ALA ASP ARG TYR GLU ALA ILE LYS SEQRES 48 A 899 LYS LYS CYS THR VAL ASP ARG ALA VAL PRO THR GLN VAL SEQRES 49 A 899 VAL CYS ALA ARG ASN MET SER SER LYS SER ALA MET SER SEQRES 50 A 899 ILE ALA THR LYS VAL ALA ILE GLN ILE ASN CYS LYS LEU SEQRES 51 A 899 GLY GLY SER PRO TRP THR VAL ASP ILE PRO LEU PRO SER SEQRES 52 A 899 LEU MET VAL VAL GLY TYR ASP VAL CYS HIS ASP THR ARG SEQRES 53 A 899 SER LYS GLU LYS SER PHE GLY ALA PHE VAL ALA THR LEU SEQRES 54 A 899 ASP LYS GLN MET THR GLN TYR TYR SER ILE VAL ASN ALA SEQRES 55 A 899 HIS THR SER GLY GLU GLU LEU SER SER HIS MET GLY PHE SEQRES 56 A 899 ASN ILE ALA SER ALA VAL LYS LYS PHE ARG GLU LYS ASN SEQRES 57 A 899 GLY THR TYR PRO ALA ARG ILE PHE ILE TYR ARG ASP GLY SEQRES 58 A 899 VAL GLY ASP GLY GLN ILE PRO TYR VAL HIS SER HIS GLU SEQRES 59 A 899 VAL ALA GLU ILE LYS LYS LYS LEU ALA GLU ILE TYR ALA SEQRES 60 A 899 GLY VAL GLU ILE LYS LEU ALA PHE ILE ILE VAL SER LYS SEQRES 61 A 899 ARG ILE ASN THR ARG ILE PHE VAL GLN ARG GLY ARG SER SEQRES 62 A 899 GLY GLU ASN PRO ARG PRO GLY THR VAL ILE ASP ASP VAL SEQRES 63 A 899 VAL THR LEU PRO GLU ARG TYR ASP PHE TYR LEU VAL SER SEQRES 64 A 899 GLN ASN VAL ARG GLU GLY THR ILE ALA PRO THR SER TYR SEQRES 65 A 899 ASN VAL ILE GLU ASP THR THR GLY LEU ASN PRO ASP ARG SEQRES 66 A 899 ILE GLN ARG LEU THR TYR LYS LEU THR HIS LEU TYR PHE SEQRES 67 A 899 ASN CYS SER SER GLN VAL ARG VAL PRO SER VAL CYS GLN SEQRES 68 A 899 TYR ALA HIS LYS LEU ALA PHE LEU ALA ALA ASN SER LEU SEQRES 69 A 899 HIS ASN GLN PRO HIS TYR SER LEU ASN GLU THR LEU TYR SEQRES 70 A 899 PHE LEU SEQRES 1 B 25 U G G A G U G U G A C A A SEQRES 2 B 25 U G G U G U U U G A U A2M SEQRES 1 C 27 U A U C A A A C A C C A U SEQRES 2 C 27 U G U C A C A C U C C A A SEQRES 3 C 27 A SEQRES 1 E 149 MET GLU VAL THR ILE ALA ASN PRO LYS PRO ASN GLN MET SEQRES 2 E 149 ILE THR CYS PRO TYR GLU LYS ALA HIS ILE VAL GLU HIS SEQRES 3 E 149 TYR ARG MET HIS ILE HIS LEU GLN LYS CYS ARG LYS GLN SEQRES 4 E 149 HIS PRO ALA CYS ASN LYS VAL GLN CYS PRO PHE ASP ALA SEQRES 5 E 149 THR HIS VAL VAL ASN ASP VAL GLU LEU ASP PHE HIS VAL SEQRES 6 E 149 THR VAL CYS PRO LYS ARG HIS MET LEU ASP THR GLN LEU SEQRES 7 E 149 TYR ILE THR ASP ASP GLU TYR ARG PRO THR VAL GLU VAL SEQRES 8 E 149 HIS ALA THR PRO VAL LEU PRO SER ASP GLU ASN TRP ASP SEQRES 9 E 149 ASP GLU THR SER THR SER TYR ILE PRO ASP PRO SER LYS SEQRES 10 E 149 LYS GLY ALA HIS ILE ILE THR LYS ALA LYS GLY LEU THR SEQRES 11 E 149 ARG SER GLU ARG GLN SER LEU ARG LYS GLU LEU ILE LYS SEQRES 12 E 149 THR TYR ARG PRO LEU GLU HET MG A 901 1 HETNAM MG MAGNESIUM ION FORMUL 5 MG MG 2+ HELIX 1 AA1 SER A 181 ARG A 190 1 10 HELIX 2 AA2 VAL A 191 SER A 193 5 3 HELIX 3 AA3 HIS A 246 LEU A 262 1 17 HELIX 4 AA4 THR A 317 GLY A 330 1 14 HELIX 5 AA5 TYR A 333 VAL A 342 1 10 HELIX 6 AA6 TYR A 379 ASN A 388 1 10 HELIX 7 AA7 ASN A 435 LYS A 447 1 13 HELIX 8 AA8 GLY A 449 THR A 467 1 19 HELIX 9 AA9 THR A 467 TRP A 477 1 11 HELIX 10 AB1 GLN A 541 GLY A 558 1 18 HELIX 11 AB2 GLY A 575 ASN A 591 1 17 HELIX 12 AB3 TYR A 603 THR A 615 1 13 HELIX 13 AB4 CYS A 626 MET A 630 5 5 HELIX 14 AB5 SER A 634 LEU A 650 1 17 HELIX 15 AB6 SER A 710 GLY A 729 1 20 HELIX 16 AB7 GLN A 746 GLU A 754 1 9 HELIX 17 AB8 GLU A 754 ALA A 767 1 14 HELIX 18 AB9 ASN A 842 LEU A 853 1 12 HELIX 19 AC1 PRO A 867 SER A 883 1 17 HELIX 20 AC2 HIS A 889 ASN A 893 5 5 SHEET 1 AA1 8 THR A 149 PRO A 150 0 SHEET 2 AA1 8 ARG A 491 GLN A 492 -1 O GLN A 492 N THR A 149 SHEET 3 AA1 8 THR A 801 ILE A 803 -1 O VAL A 802 N ARG A 491 SHEET 4 AA1 8 TYR A 816 VAL A 818 -1 O TYR A 816 N ILE A 803 SHEET 5 AA1 8 THR A 830 ASP A 837 -1 O THR A 830 N LEU A 817 SHEET 6 AA1 8 LEU A 773 SER A 779 -1 N ILE A 777 O ASN A 833 SHEET 7 AA1 8 ARG A 734 ARG A 739 1 N ILE A 737 O ILE A 776 SHEET 8 AA1 8 LEU A 664 TYR A 669 1 N VAL A 667 O TYR A 738 SHEET 1 AA2 4 LYS A 487 ILE A 488 0 SHEET 2 AA2 4 LEU A 153 LEU A 154 -1 N LEU A 153 O ILE A 488 SHEET 3 AA2 4 PHE A 787 ARG A 790 -1 O PHE A 787 N LEU A 154 SHEET 4 AA2 4 SER A 793 GLU A 795 -1 O SER A 793 N ARG A 790 SHEET 1 AA3 5 TYR A 157 THR A 159 0 SHEET 2 AA3 5 LEU A 302 ARG A 314 -1 O LEU A 304 N PHE A 158 SHEET 3 AA3 5 LEU A 285 GLN A 297 -1 N TRP A 288 O LYS A 311 SHEET 4 AA3 5 ASP A 270 PHE A 272 -1 N TYR A 271 O TYR A 291 SHEET 5 AA3 5 GLN A 265 MET A 267 -1 N GLN A 265 O PHE A 272 SHEET 1 AA4 4 TYR A 157 THR A 159 0 SHEET 2 AA4 4 LEU A 302 ARG A 314 -1 O LEU A 304 N PHE A 158 SHEET 3 AA4 4 LEU A 285 GLN A 297 -1 N TRP A 288 O LYS A 311 SHEET 4 AA4 4 ILE A 278 ILE A 280 -1 N ILE A 278 O ILE A 287 SHEET 1 AA5 4 VAL A 205 THR A 208 0 SHEET 2 AA5 4 TYR A 169 ILE A 175 -1 N TYR A 171 O LEU A 206 SHEET 3 AA5 4 ARG A 229 LEU A 236 -1 O LYS A 235 N HIS A 172 SHEET 4 AA5 4 LEU A 219 ASP A 222 -1 N SER A 221 O MET A 230 SHEET 1 AA6 3 THR A 354 ARG A 356 0 SHEET 2 AA6 3 ILE A 345 THR A 348 -1 N VAL A 346 O TYR A 355 SHEET 3 AA6 3 CYS A 423 GLN A 425 -1 O ARG A 424 N MET A 347 SHEET 1 AA7 2 THR A 369 LYS A 371 0 SHEET 2 AA7 2 ASN A 376 THR A 378 -1 O ILE A 377 N PHE A 370 SHEET 1 AA8 2 LEU A 399 SER A 401 0 SHEET 2 AA8 2 ILE A 416 LEU A 418 -1 O LEU A 418 N LEU A 399 SHEET 1 AA9 2 ASN A 497 GLN A 500 0 SHEET 2 AA9 2 VAL A 504 PRO A 507 -1 O TYR A 506 N ILE A 498 SHEET 1 AB1 4 VAL A 569 ILE A 571 0 SHEET 2 AB1 4 VAL A 534 PRO A 538 1 N THR A 537 O ILE A 571 SHEET 3 AB1 4 ILE A 595 VAL A 598 1 O VAL A 598 N ILE A 536 SHEET 4 AB1 4 THR A 622 VAL A 625 1 O GLN A 623 N ILE A 595 SHEET 1 AB2 3 CYS A 672 HIS A 673 0 SHEET 2 AB2 3 SER A 681 PHE A 682 -1 O PHE A 682 N CYS A 672 SHEET 3 AB2 3 ALA A 702 HIS A 703 -1 O HIS A 703 N SER A 681 SHEET 1 AB3 2 ALA A 687 THR A 688 0 SHEET 2 AB3 2 TYR A 696 TYR A 697 -1 O TYR A 697 N ALA A 687 LINK OD1 ASP A 670 MG MG A 901 1555 1555 1.94 LINK OD2 ASP A 670 MG MG A 901 1555 1555 1.91 LINK OD2 ASP A 740 MG MG A 901 1555 1555 2.01 LINK MG MG A 901 OP1 U C 16 1555 1555 2.03 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 6041 LEU A 899 TER 6540 A B 23 TER 7020 A C 25 TER 7060 ASP E 104 HETATM 7061 MG MG A 901 131.778 133.316 128.603 1.00 44.02 MG CONECT 4221 7061 CONECT 4222 7061 CONECT 4764 7061 CONECT 6815 7061 CONECT 7061 4221 4222 4764 6815 MASTER 554 0 1 20 43 0 0 6 7057 4 5 87 END