HEADER RNA BINDING PROTEIN/RNA 25-FEB-26 11HX TITLE ISCB-TID TRUNCATED AND WRNA BOUND TO TARGET SSRNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISCB; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: WRNA (233-MER); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: TARGET SSRNA; COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630 KEYWDS ISCB, CAS9, HNH, CRISPR-CAS, RNA BINDING PROTEIN, RNA BINDING KEYWDS 2 PROTEIN-RNA COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR C.XU,Q.YANG,X.NIU,A.KE REVDAT 1 03-JUN-26 11HX 0 JRNL AUTH C.XU,Q.YANG,X.NIU,A.KE JRNL TITL ENGINEERED ISCB-OMEGA RNA-SSDNA COMPLEX JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.67 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, PHENIX, CRYOSPARC 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) : 2.670 REMARK 3 NUMBER OF PARTICLES : 319480 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 11HX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-MAR-26. REMARK 100 THE DEPOSITION ID IS D_1000305444. 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 : ISCB-TID TRUNCATED AND WRNA REMARK 245 BOUND TO TARGET SSRNA 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 : 7.50 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 : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 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) : 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 ASN A 434 REMARK 465 GLY A 435 REMARK 465 GLY A 436 REMARK 465 LEU A 437 REMARK 465 GLN A 438 REMARK 465 ILE A 439 REMARK 465 TYR A 440 REMARK 465 VAL A 441 REMARK 465 A B 1 REMARK 465 A B 2 REMARK 465 G B 137 REMARK 465 G B 138 REMARK 465 C B 139 REMARK 465 C B 140 REMARK 465 G B 141 REMARK 465 A B 142 REMARK 465 G B 143 REMARK 465 U B 144 REMARK 465 A B 145 REMARK 465 A B 146 REMARK 465 U B 147 REMARK 465 U B 148 REMARK 465 U B 149 REMARK 465 A B 150 REMARK 465 C B 151 REMARK 465 G B 152 REMARK 465 U B 153 REMARK 465 C B 154 REMARK 465 G B 155 REMARK 465 A B 156 REMARK 465 C B 157 REMARK 465 G B 158 REMARK 465 U B 159 REMARK 465 U B 160 REMARK 465 G B 161 REMARK 465 A B 162 REMARK 465 C B 163 REMARK 465 G B 164 REMARK 465 U B 165 REMARK 465 C B 166 REMARK 465 G B 167 REMARK 465 A B 168 REMARK 465 U B 169 REMARK 465 G B 170 REMARK 465 G B 171 REMARK 465 U B 172 REMARK 465 U B 173 REMARK 465 G B 174 REMARK 465 C B 175 REMARK 465 G B 176 REMARK 465 G B 177 REMARK 465 C B 178 REMARK 465 C B 179 REMARK 465 U C -7 REMARK 465 C C -6 REMARK 465 U C -5 REMARK 465 U C -4 REMARK 465 C C -3 REMARK 465 U C -2 REMARK 465 A C -1 REMARK 465 G C 0 REMARK 465 U C 1 REMARK 465 C C 10 REMARK 465 U C 11 REMARK 465 C C 12 REMARK 465 U C 13 REMARK 465 U C 14 REMARK 465 U C 15 REMARK 465 U C 16 REMARK 465 C C 17 REMARK 465 U C 18 REMARK 465 C C 19 REMARK 465 U C 20 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 144 -14.39 74.13 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 503 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 60 OD1 REMARK 620 2 GLU A 192 OE1 80.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 234 SG REMARK 620 2 CYS A 237 SG 108.5 REMARK 620 3 CYS A 265 SG 112.8 111.7 REMARK 620 4 HIS A 268 ND1 176.7 74.6 66.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 245 ND1 REMARK 620 2 HIS A 273 NE2 105.3 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-75706 RELATED DB: EMDB REMARK 900 ISCB-TID TRUNCATED AND WRNA BOUND TO TARGET SSRNA DBREF 11HX A 1 441 PDB 11HX 11HX 1 441 DBREF 11HX B 1 233 PDB 11HX 11HX 1 233 DBREF 11HX C -7 20 PDB 11HX 11HX -7 20 SEQRES 1 A 441 MET ALA VAL VAL TYR VAL ILE SER LYS SER GLY LYS PRO SEQRES 2 A 441 LEU MET PRO THR THR ARG CYS GLY HIS VAL ARG ILE LEU SEQRES 3 A 441 LEU LYS GLU GLY LYS ALA ARG VAL VAL GLU ARG LYS PRO SEQRES 4 A 441 PHE THR ILE GLN LEU THR TYR GLU SER ALA GLU GLU THR SEQRES 5 A 441 GLN PRO LEU VAL LEU GLY ILE ASP PRO GLY ARG THR ASN SEQRES 6 A 441 ILE GLY MET SER VAL VAL THR GLU SER GLY GLU SER VAL SEQRES 7 A 441 PHE ASN ALA GLN ILE GLU THR ARG ASN LYS ASP VAL PRO SEQRES 8 A 441 LYS LEU MET LYS ASP ARG LYS GLN TYR ARG MET ALA HIS SEQRES 9 A 441 ARG ARG LEU LYS ARG ARG CYS LYS ARG ARG ARG ARG ALA SEQRES 10 A 441 LYS ALA ALA GLY THR ALA PHE GLU GLU GLY GLU LYS GLN SEQRES 11 A 441 ARG LEU LEU PRO GLY CYS PHE LYS PRO ILE THR CYS LYS SEQRES 12 A 441 SER ILE ARG ASN LYS GLU ALA ARG PHE ASN ASN ARG LYS SEQRES 13 A 441 ARG PRO VAL GLY TRP LEU THR PRO THR ALA ASN HIS LEU SEQRES 14 A 441 LEU VAL THR HIS LEU ASN VAL VAL LYS LYS VAL GLN LYS SEQRES 15 A 441 ILE LEU PRO VAL ALA LYS VAL VAL LEU GLU LEU ASN ARG SEQRES 16 A 441 PHE SER PHE MET ALA MET ASN ASN PRO LYS VAL GLN ARG SEQRES 17 A 441 TRP GLN TYR GLN ARG GLY PRO LEU TYR GLY LYS GLY SER SEQRES 18 A 441 VAL GLU GLU ALA VAL SER MET GLN GLN ASP GLY HIS CYS SEQRES 19 A 441 LEU PHE CYS LYS HIS GLY ILE ASP GLU TYR HIS HIS VAL SEQRES 20 A 441 VAL PRO ARG ARG LYS ASN GLY SER GLU THR LEU GLU ASN SEQRES 21 A 441 ARG VAL GLY LEU CYS GLU GLU HIS ASN GLN LEU VAL HIS SEQRES 22 A 441 THR ASP LYS GLU TRP GLU ALA ASN LEU ALA SER LYS LYS SEQRES 23 A 441 SER GLY MET ASN LYS LYS TYR HIS ALA LEU SER VAL LEU SEQRES 24 A 441 ASN GLN ILE ILE PRO TYR LEU ALA ASP GLN LEU ALA ASP SEQRES 25 A 441 MET PHE PRO GLY ASN PHE CYS VAL THR SER GLY GLN ASP SEQRES 26 A 441 THR TYR LEU PHE ARG GLU GLU HIS GLY ILE PRO LYS ASP SEQRES 27 A 441 HIS TYR LEU ASP ALA TYR CYS ILE ALA CYS SER ALA LEU SEQRES 28 A 441 THR ASP ALA LYS LYS VAL SER SER PRO LYS GLY ARG PRO SEQRES 29 A 441 TYR MET VAL HIS GLN PHE ARG ARG HIS ASP ARG GLN ALA SEQRES 30 A 441 CYS HIS LYS ALA ASN LEU ASN ARG SER TYR TYR MET GLY SEQRES 31 A 441 GLY LYS LEU VAL ALA THR ASN ARG HIS LYS ALA MET ASP SEQRES 32 A 441 GLN LYS THR ASP SER LEU GLU GLU TYR ARG ALA ALA HIS SEQRES 33 A 441 SER ALA ALA ASP VAL SER LYS LEU THR VAL LYS HIS PRO SEQRES 34 A 441 SER ALA GLN TYR ASN GLY GLY LEU GLN ILE TYR VAL SEQRES 1 B 233 A A A A G A G U G A A C G SEQRES 2 B 233 A G A G G C U C U U U C A SEQRES 3 B 233 A C U U G A A A A G G U U SEQRES 4 B 233 G A A A G A G C A C A G G SEQRES 5 B 233 C U G A G A C A U U C G U SEQRES 6 B 233 A A G G C C G A A A G G C SEQRES 7 B 233 C G G A C G C A C C C U G SEQRES 8 B 233 G G A U U U C C C C A G U SEQRES 9 B 233 C C C C G G A A C U G C A SEQRES 10 B 233 U A G C G G A U G U C A G SEQRES 11 B 233 U U G A U C G G C C G A G SEQRES 12 B 233 U A A U U U A C G U C G A SEQRES 13 B 233 C G U U G A C G U C G A U SEQRES 14 B 233 G G U U G C G G C C G A U SEQRES 15 B 233 C A G A U A A G C C A G G SEQRES 16 B 233 G G G A A C A A U C A C C SEQRES 17 B 233 U C U C U G G A A A C A G SEQRES 18 B 233 A G A G A G U U U U A C SEQRES 1 C 28 U C U U C U A G U C U C G SEQRES 2 C 28 U U C A C U C U U U U C U SEQRES 3 C 28 C U HET ZN A 501 1 HET MG A 502 1 HET MG A 503 1 HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION FORMUL 4 ZN ZN 2+ FORMUL 5 MG 2(MG 2+) HELIX 1 AA1 ARG A 19 GLY A 30 1 12 HELIX 2 AA2 LYS A 88 LEU A 107 1 20 HELIX 3 AA3 ARG A 109 GLY A 121 1 13 HELIX 4 AA4 THR A 163 LYS A 182 1 20 HELIX 5 AA5 ASN A 194 ALA A 200 1 7 HELIX 6 AA6 SER A 221 GLN A 230 1 10 HELIX 7 AA7 PRO A 249 ASN A 253 5 5 HELIX 8 AA8 THR A 257 GLU A 259 5 3 HELIX 9 AA9 CYS A 265 ASP A 275 1 11 HELIX 10 AB1 ASP A 275 HIS A 294 1 20 HELIX 11 AB2 SER A 297 PHE A 314 1 18 HELIX 12 AB3 GLY A 323 GLY A 334 1 12 HELIX 13 AB4 ASP A 338 TYR A 340 5 3 HELIX 14 AB5 LEU A 341 ALA A 350 1 10 HELIX 15 AB6 SER A 408 HIS A 416 1 9 HELIX 16 AB7 SER A 417 LEU A 424 1 8 SHEET 1 AA1 4 PRO A 13 THR A 17 0 SHEET 2 AA1 4 VAL A 4 ILE A 7 -1 N VAL A 6 O LEU A 14 SHEET 3 AA1 4 THR A 41 LEU A 44 1 O ILE A 42 N TYR A 5 SHEET 4 AA1 4 ALA A 32 GLU A 36 -1 N VAL A 35 O THR A 41 SHEET 1 AA2 8 GLY A 214 PRO A 215 0 SHEET 2 AA2 8 GLN A 207 GLN A 210 -1 N GLN A 210 O GLY A 214 SHEET 3 AA2 8 PHE A 318 SER A 322 1 O VAL A 320 N TRP A 209 SHEET 4 AA2 8 LYS A 188 LEU A 193 1 N LEU A 193 O THR A 321 SHEET 5 AA2 8 LEU A 55 ASP A 60 1 N LEU A 57 O VAL A 190 SHEET 6 AA2 8 ASN A 65 THR A 72 -1 O SER A 69 N GLY A 58 SHEET 7 AA2 8 SER A 77 GLU A 84 -1 O ILE A 83 N ILE A 66 SHEET 8 AA2 8 TYR A 365 HIS A 368 1 O VAL A 367 N GLU A 84 SHEET 1 AA3 2 GLU A 128 ARG A 131 0 SHEET 2 AA3 2 ILE A 140 LYS A 143 -1 O ILE A 140 N ARG A 131 SHEET 1 AA4 2 GLU A 243 HIS A 246 0 SHEET 2 AA4 2 ARG A 261 LEU A 264 -1 O LEU A 264 N GLU A 243 SHEET 1 AA5 3 LEU A 393 ALA A 395 0 SHEET 2 AA5 3 TYR A 387 TYR A 388 -1 N TYR A 387 O ALA A 395 SHEET 3 AA5 3 THR A 425 VAL A 426 -1 O THR A 425 N TYR A 388 LINK OD1 ASP A 60 MG MG A 503 1555 1555 2.09 LINK OE1 GLU A 192 MG MG A 503 1555 1555 2.25 LINK SG CYS A 234 ZN ZN A 501 1555 1555 2.32 LINK SG CYS A 237 ZN ZN A 501 1555 1555 2.31 LINK ND1 HIS A 245 MG MG A 502 1555 1555 2.06 LINK SG CYS A 265 ZN ZN A 501 1555 1555 2.31 LINK ND1 HIS A 268 ZN ZN A 501 1555 1555 2.07 LINK NE2 HIS A 273 MG MG A 502 1555 1555 2.03 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 CONECT 467 7676 CONECT 1534 7676 CONECT 1876 7674 CONECT 1901 7674 CONECT 1968 7675 CONECT 2128 7674 CONECT 2153 7674 CONECT 2198 7675 CONECT 7674 1876 1901 2128 2153 CONECT 7675 1968 2198 CONECT 7676 467 1534 MASTER 223 0 3 16 19 0 0 6 7673 3 11 55 END