HEADER RNA BINDING PROTEIN/RNA 11-FEB-25 9LV7 TITLE THE CRYO-EM STRUCTURE OF DRT2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (281-MER); COMPND 3 CHAIN: R; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: ANTIVIRAL REVERSE TRANSCRIPTASE DRT2; COMPND 7 CHAIN: A; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KLEBSIELLA PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 573; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: KLEBSIELLA PNEUMONIAE; SOURCE 8 ORGANISM_TAXID: 573; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS DRT2, NCRNA, REVERSE TRANSCRIPTASE, RNA BINDING PROTEIN/RNA, RNA KEYWDS 2 BINDING PROTEIN-RNA COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR X.GAO,H.ZHU,S.CUI,K.ZHU REVDAT 1 19-AUG-26 9LV7 0 JRNL AUTH X.GAO,H.ZHU,S.CUI,K.ZHU,M.LI JRNL TITL CRYO-EM STRUCTURES OF TYPE 2 DEFENSE-ASSOCIATED REVERSE JRNL TITL 2 TRANSCRIPTASE (DRT2) SYSTEMS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.72 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) : 3.720 REMARK 3 NUMBER OF PARTICLES : 52514 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING ONLY REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 9LV7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 14-FEB-25. REMARK 100 THE DEPOSITION ID IS D_1300056484. 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 : CRYO-EM STRUCTURE OF THE REMARK 245 DRT2(YCAA) RT-NCRNA 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 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) : 6000.00 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: R, A 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 G R 1 REMARK 465 C R 2 REMARK 465 C R 3 REMARK 465 C R 4 REMARK 465 U R 5 REMARK 465 A R 6 REMARK 465 A R 7 REMARK 465 A R 8 REMARK 465 C R 9 REMARK 465 A R 10 REMARK 465 A R 11 REMARK 465 A R 12 REMARK 465 G R 13 REMARK 465 G R 14 REMARK 465 U R 15 REMARK 465 U R 16 REMARK 465 U R 17 REMARK 465 A R 18 REMARK 465 G R 19 REMARK 465 G R 20 REMARK 465 G R 21 REMARK 465 G R 22 REMARK 465 U R 23 REMARK 465 A R 24 REMARK 465 U R 25 REMARK 465 U R 26 REMARK 465 G R 27 REMARK 465 U R 28 REMARK 465 A R 29 REMARK 465 C R 30 REMARK 465 A R 31 REMARK 465 G R 32 REMARK 465 G R 33 REMARK 465 U R 34 REMARK 465 U R 35 REMARK 465 G R 36 REMARK 465 U R 37 REMARK 465 C R 38 REMARK 465 A R 39 REMARK 465 A R 40 REMARK 465 G R 41 REMARK 465 C R 42 REMARK 465 C R 43 REMARK 465 U R 44 REMARK 465 C R 45 REMARK 465 C R 46 REMARK 465 C R 47 REMARK 465 A R 48 REMARK 465 C R 49 REMARK 465 A R 50 REMARK 465 G R 51 REMARK 465 G R 52 REMARK 465 U R 53 REMARK 465 C R 54 REMARK 465 U R 55 REMARK 465 U R 56 REMARK 465 G R 57 REMARK 465 G R 58 REMARK 465 U R 59 REMARK 465 G R 60 REMARK 465 A R 61 REMARK 465 A R 62 REMARK 465 A R 63 REMARK 465 C R 64 REMARK 465 C R 65 REMARK 465 A R 66 REMARK 465 A R 67 REMARK 465 U R 68 REMARK 465 C R 69 REMARK 465 A R 70 REMARK 465 C R 71 REMARK 465 U R 72 REMARK 465 G R 73 REMARK 465 U R 74 REMARK 465 G R 75 REMARK 465 A R 76 REMARK 465 C R 77 REMARK 465 G R 78 REMARK 465 A R 79 REMARK 465 C R 80 REMARK 465 G R 81 REMARK 465 G R 82 REMARK 465 U R 83 REMARK 465 A R 84 REMARK 465 A R 85 REMARK 465 G R 86 REMARK 465 C R 87 REMARK 465 A R 88 REMARK 465 A R 89 REMARK 465 C R 90 REMARK 465 A R 91 REMARK 465 C R 92 REMARK 465 U R 93 REMARK 465 U R 94 REMARK 465 G R 95 REMARK 465 G R 96 REMARK 465 A R 97 REMARK 465 U R 98 REMARK 465 G R 99 REMARK 465 A R 100 REMARK 465 U R 101 REMARK 465 A R 102 REMARK 465 U R 103 REMARK 465 U R 104 REMARK 465 C R 105 REMARK 465 A R 106 REMARK 465 U R 107 REMARK 465 A R 108 REMARK 465 A R 109 REMARK 465 U R 110 REMARK 465 U R 111 REMARK 465 G R 112 REMARK 465 A R 113 REMARK 465 C R 114 REMARK 465 U R 115 REMARK 465 C R 116 REMARK 465 C R 117 REMARK 465 A R 118 REMARK 465 C R 119 REMARK 465 G R 120 REMARK 465 C R 121 REMARK 465 U R 122 REMARK 465 A R 123 REMARK 465 C R 124 REMARK 465 U R 125 REMARK 465 G R 126 REMARK 465 A R 127 REMARK 465 U R 128 REMARK 465 U R 129 REMARK 465 A R 130 REMARK 465 C R 131 REMARK 465 A R 132 REMARK 465 U R 133 REMARK 465 U R 134 REMARK 465 A R 135 REMARK 465 U R 136 REMARK 465 A R 137 REMARK 465 C R 138 REMARK 465 A R 139 REMARK 465 G R 140 REMARK 465 C R 141 REMARK 465 A R 142 REMARK 465 U R 143 REMARK 465 A R 144 REMARK 465 U R 145 REMARK 465 C R 146 REMARK 465 U R 147 REMARK 465 A R 148 REMARK 465 A R 149 REMARK 465 C R 150 REMARK 465 A R 151 REMARK 465 U R 152 REMARK 465 U R 153 REMARK 465 U R 178 REMARK 465 U R 179 REMARK 465 A R 180 REMARK 465 G R 181 REMARK 465 G R 221 REMARK 465 G R 222 REMARK 465 U R 223 REMARK 465 U R 240 REMARK 465 C R 241 REMARK 465 C R 242 REMARK 465 U R 274 REMARK 465 U R 275 REMARK 465 U R 276 REMARK 465 G R 277 REMARK 465 C R 278 REMARK 465 U R 279 REMARK 465 A R 280 REMARK 465 A R 281 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 LYS A 56 CG CD CE NZ REMARK 470 ASP A 57 CG OD1 OD2 REMARK 470 LYS A 58 CG CD CE NZ REMARK 470 SER A 59 OG REMARK 470 THR A 60 OG1 CG2 REMARK 470 LYS A 61 CG CD CE NZ REMARK 470 GLN A 62 CG CD OE1 NE2 REMARK 470 LEU A 63 CG CD1 CD2 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 SER A 116 -167.77 -126.47 REMARK 500 ARG A 179 57.38 -95.89 REMARK 500 TYR A 267 112.66 175.31 REMARK 500 CYS A 268 -110.95 52.40 REMARK 500 MET A 271 -163.90 -122.66 REMARK 500 LEU A 272 108.05 179.78 REMARK 500 ASP A 312 -116.31 55.98 REMARK 500 TYR A 323 109.71 -160.60 REMARK 500 ARG A 390 45.66 -142.26 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-63415 RELATED DB: EMDB REMARK 900 THE CRYO-EM STRUCTURE OF DRT2 DBREF1 9LV7 R 1 281 GB CP063277.1 DBREF2 9LV7 R 1920786575 4973021 4973301 DBREF 9LV7 A 1 425 PDB 9LV7 9LV7 1 425 SEQRES 1 R 281 G C C C U A A A C A A A G SEQRES 2 R 281 G U U U A G G G G U A U U SEQRES 3 R 281 G U A C A G G U U G U C A SEQRES 4 R 281 A G C C U C C C A C A G G SEQRES 5 R 281 U C U U G G U G A A A C C SEQRES 6 R 281 A A U C A C U G U G A C G SEQRES 7 R 281 A C G G U A A G C A A C A SEQRES 8 R 281 C U U G G A U G A U A U U SEQRES 9 R 281 C A U A A U U G A C U C C SEQRES 10 R 281 A C G C U A C U G A U U A SEQRES 11 R 281 C A U U A U A C A G C A U SEQRES 12 R 281 A U C U A A C A U U U G C SEQRES 13 R 281 G G C G A G G U U C A C A SEQRES 14 R 281 A U U U G U A U U U A G G SEQRES 15 R 281 U A C U G A U U G U G G A SEQRES 16 R 281 U G A G A A G G U U G G A SEQRES 17 R 281 G A A A G A C C A C U U G SEQRES 18 R 281 G U U A A G C C G G A G G SEQRES 19 R 281 A U G U G U C C U A G A A SEQRES 20 R 281 U U G U C G C U A U U C U SEQRES 21 R 281 G U C A U C C U C C G G U SEQRES 22 R 281 U U U G C U A A SEQRES 1 A 425 MET ASN ASN ASP ASP TYR PRO TRP PHE ARG LYS ARG GLY SEQRES 2 A 425 TYR LEU HIS PHE ASP GLU PRO VAL SER LEU LYS LYS ALA SEQRES 3 A 425 VAL LYS TYR VAL SER SER PRO GLU LYS ILE ILE LYS HIS SEQRES 4 A 425 SER PHE LEU PRO PHE LEU SER PHE GLU VAL LYS SER PHE SEQRES 5 A 425 LYS ILE LYS LYS ASP LYS SER THR LYS GLN LEU SER LYS SEQRES 6 A 425 THR GLU LYS LEU ARG PRO ILE ALA TYR SER SER HIS LEU SEQRES 7 A 425 ASP SER HIS ILE TYR ALA PHE TYR ALA GLU TYR LEU THR SEQRES 8 A 425 GLY HIS TYR GLU LEU LEU ILE GLN GLU ASN ASN LEU HIS SEQRES 9 A 425 GLU ASN ILE LEU ALA PHE ARG SER LEU ASN LYS SER ASN SEQRES 10 A 425 ILE GLU PHE ALA LYS ARG ALA PHE ASP THR ILE THR GLU SEQRES 11 A 425 MET GLY GLU CYS SER ALA VAL ALA LEU ASP LEU SER GLY SEQRES 12 A 425 PHE PHE ASP ASN LEU ASP HIS GLN ILE LEU LYS HIS GLN SEQRES 13 A 425 TRP CYS LYS VAL ILE GLY THR GLU ALA LEU PRO GLN ASP SEQRES 14 A 425 HIS PHE ALA ILE TYR LYS SER ILE THR ARG TYR SER LYS SEQRES 15 A 425 VAL ASP LYS ASN ARG ALA TYR GLU ILE LEU GLY ILE SER SEQRES 16 A 425 LYS ASN ASN PRO LYS TYR ASN ARG ARG LYS ILE CYS THR SEQRES 17 A 425 PRO VAL ASP PHE ARG ASN LYS ILE ARG LYS ASN GLY LEU SEQRES 18 A 425 ILE ILE VAL ASN ASN SER GLN LYS GLY ILE PRO GLN GLY SEQRES 19 A 425 SER PRO ILE SER ALA LEU LEU SER ASN ILE TYR MET LEU SEQRES 20 A 425 ASP PHE ASP ILE GLU MET ARG ASP TYR ALA GLN GLU ARG SEQRES 21 A 425 GLY GLY HIS TYR TYR ARG TYR CYS ALA ALA MET LEU PHE SEQRES 22 A 425 ILE VAL PRO THR LYS TYR ASN LYS THR LEU ALA GLY ASP SEQRES 23 A 425 VAL ALA GLN ARG ILE LYS HIS LEU LYS VAL GLU LEU ASN SEQRES 24 A 425 THR LYS LYS THR GLU ILE ARG ASP PHE ILE TYR LYS ASP SEQRES 25 A 425 SER THR LEU VAL ALA ASN MET PRO LEU GLN TYR LEU GLY SEQRES 26 A 425 PHE ILE PHE ASP GLY SER ASN ILE LEU LEU ARG SER SER SEQRES 27 A 425 SER LEU ALA ARG TYR SER GLU ARG MET LYS ARG GLY VAL SEQRES 28 A 425 ARG LEU ALA LYS ALA THR MET ASP SER LYS ASN ARG ILE SEQRES 29 A 425 ARG GLU ASN LYS GLY GLU ALA LEU LYS ALA LEU PHE LYS SEQRES 30 A 425 LYS LYS LEU TYR ALA ARG TYR SER HIS ILE GLY ARG ARG SEQRES 31 A 425 ASN PHE LEU THR TYR GLY TYR ARG ALA ALA LYS ILE MET SEQRES 32 A 425 ASN SER LYS ALA ILE LYS ARG GLN LEU LYS PRO LEU GLN SEQRES 33 A 425 LYS ARG LEU GLU ASN GLU ILE LEU LYS HELIX 1 AA1 SER A 22 SER A 31 1 10 HELIX 2 AA2 SER A 32 HIS A 39 1 8 HELIX 3 AA3 SER A 76 ASN A 102 1 27 HELIX 4 AA4 SER A 116 GLY A 132 1 17 HELIX 5 AA5 PHE A 144 LEU A 148 5 5 HELIX 6 AA6 ASP A 149 GLY A 162 1 14 HELIX 7 AA7 PRO A 167 ARG A 179 1 13 HELIX 8 AA8 LYS A 185 GLY A 193 1 9 HELIX 9 AA9 THR A 208 ILE A 216 1 9 HELIX 10 AB1 ILE A 237 MET A 246 1 10 HELIX 11 AB2 MET A 246 GLU A 259 1 14 HELIX 12 AB3 PRO A 276 ASN A 280 5 5 HELIX 13 AB4 THR A 282 ILE A 291 1 10 HELIX 14 AB5 ARG A 336 LYS A 368 1 33 HELIX 15 AB6 LYS A 377 SER A 385 1 9 HELIX 16 AB7 ASN A 391 ASN A 404 1 14 HELIX 17 AB8 SER A 405 LYS A 413 1 9 HELIX 18 AB9 PRO A 414 LYS A 425 1 12 SHEET 1 AA1 4 LYS A 65 TYR A 74 0 SHEET 2 AA1 4 PHE A 44 ILE A 54 -1 N VAL A 49 O ARG A 70 SHEET 3 AA1 4 SER A 181 ASP A 184 1 O SER A 181 N PHE A 44 SHEET 4 AA1 4 ILE A 223 VAL A 224 -1 O ILE A 223 N LYS A 182 SHEET 1 AA2 5 HIS A 263 TYR A 264 0 SHEET 2 AA2 5 PHE A 273 VAL A 275 -1 O ILE A 274 N HIS A 263 SHEET 3 AA2 5 SER A 135 ALA A 138 -1 N VAL A 137 O PHE A 273 SHEET 4 AA2 5 GLU A 304 LYS A 311 -1 O GLU A 304 N ALA A 138 SHEET 5 AA2 5 THR A 314 ALA A 317 -1 O THR A 314 N LYS A 311 SHEET 1 AA3 2 LEU A 141 SER A 142 0 SHEET 2 AA3 2 GLU A 297 LEU A 298 -1 O GLU A 297 N SER A 142 SHEET 1 AA4 3 LEU A 321 GLN A 322 0 SHEET 2 AA4 3 PHE A 326 PHE A 328 -1 O PHE A 328 N LEU A 321 SHEET 3 AA4 3 ILE A 333 LEU A 335 -1 O LEU A 334 N ILE A 327 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 317 0 0 18 14 0 0 6 5826 2 0 55 END