HEADER RNA BINDING PROTEIN/RNA/DNA 16-OCT-23 8WRW TITLE CRYO-EM MINI STRUCTURE OF CAS12-1-N1/CRRNA/TARGET DNA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAS12-1-N1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: TS; COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: CRRNA; COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 4; COMPND 14 MOLECULE: NTS; COMPND 15 CHAIN: D; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: UNCLASSIFIED SEQUENCES; SOURCE 3 ORGANISM_TAXID: 12908; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: UNCLASSIFIED SEQUENCES; SOURCE 9 ORGANISM_TAXID: 12908; SOURCE 10 EXPRESSION_SYSTEM: UNCLASSIFIED SEQUENCES; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 12908; SOURCE 12 MOL_ID: 3; SOURCE 13 ORGANISM_SCIENTIFIC: UNCLASSIFIED SEQUENCES; SOURCE 14 ORGANISM_TAXID: 12908; SOURCE 15 EXPRESSION_SYSTEM: UNCLASSIFIED SEQUENCES; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 12908; SOURCE 17 MOL_ID: 4; SOURCE 18 ORGANISM_SCIENTIFIC: UNCLASSIFIED SEQUENCES; SOURCE 19 ORGANISM_TAXID: 12908; SOURCE 20 EXPRESSION_SYSTEM: UNCLASSIFIED SEQUENCES; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 12908 KEYWDS CRISPR-CAS, RNA BINDING PROTEIN-RNA-DNA COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR Z.KUO,Z.XI REVDAT 1 16-APR-25 8WRW 0 JRNL AUTH Z.KUO,Z.XI JRNL TITL CRYO-EM MINI STRUCTURE OF CAS12-1-N1/CRRNA/TARGET DNA JRNL TITL 2 COMPLEX JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.01 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL 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) : 3.010 REMARK 3 NUMBER OF PARTICLES : 94944 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 8WRW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-OCT-23. REMARK 100 THE DEPOSITION ID IS D_1300041564. 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 : THE TERNARY COMPLEX OF CAS12-1 REMARK 245 -N1 WITH CRRNA AND TARGET DNA 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 : 7.40 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 : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 5000.00 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, B, D 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 THR A 2 REMARK 465 PRO A 3 REMARK 465 LYS A 4 REMARK 465 THR A 5 REMARK 465 GLU A 6 REMARK 465 THR A 7 REMARK 465 PRO A 8 REMARK 465 VAL A 9 REMARK 465 GLY A 10 REMARK 465 ALA A 11 REMARK 465 LEU A 12 REMARK 465 ILE A 13 REMARK 465 LYS A 14 REMARK 465 LYS A 15 REMARK 465 PHE A 16 REMARK 465 PHE A 17 REMARK 465 PRO A 18 REMARK 465 GLY A 19 REMARK 465 LYS A 20 REMARK 465 ARG A 21 REMARK 465 PHE A 22 REMARK 465 GLN A 23 REMARK 465 LYS A 24 REMARK 465 ASN A 25 REMARK 465 TYR A 26 REMARK 465 LEU A 27 REMARK 465 LYS A 28 REMARK 465 ASP A 29 REMARK 465 ALA A 30 REMARK 465 GLY A 31 REMARK 465 LYS A 32 REMARK 465 LYS A 33 REMARK 465 LEU A 34 REMARK 465 LYS A 35 REMARK 465 ARG A 36 REMARK 465 GLU A 37 REMARK 465 GLY A 38 REMARK 465 GLU A 39 REMARK 465 ALA A 40 REMARK 465 ALA A 41 REMARK 465 ALA A 42 REMARK 465 VAL A 43 REMARK 465 GLU A 44 REMARK 465 TYR A 45 REMARK 465 LEU A 46 REMARK 465 SER A 47 REMARK 465 GLY A 48 REMARK 465 LYS A 49 REMARK 465 GLN A 50 REMARK 465 GLU A 51 REMARK 465 ASP A 52 REMARK 465 HIS A 53 REMARK 465 PRO A 54 REMARK 465 ALA A 55 REMARK 465 ASN A 56 REMARK 465 PHE A 57 REMARK 465 PRO A 184 REMARK 465 ASP A 185 REMARK 465 ALA A 212 REMARK 465 LYS A 213 REMARK 465 ALA A 216 REMARK 465 LEU A 217 REMARK 465 PRO A 218 REMARK 465 PHE A 219 REMARK 465 ASP A 223 REMARK 465 PRO A 224 REMARK 465 HIS A 253 REMARK 465 LEU A 254 REMARK 465 SER A 255 REMARK 465 THR A 256 REMARK 465 LYS A 257 REMARK 465 ASN A 258 REMARK 465 LYS A 259 REMARK 465 ARG A 260 REMARK 465 LYS A 277 REMARK 465 SER A 278 REMARK 465 VAL A 279 REMARK 465 LEU A 280 REMARK 465 ASP A 281 REMARK 465 GLU A 282 REMARK 465 ALA A 283 REMARK 465 LYS A 284 REMARK 465 LEU A 285 REMARK 465 LYS A 286 REMARK 465 ALA A 356 REMARK 465 VAL A 357 REMARK 465 ALA A 358 REMARK 465 VAL A 359 REMARK 465 DC C -32 REMARK 465 DT C -31 REMARK 465 DG C -30 REMARK 465 DC C -29 REMARK 465 DC C -28 REMARK 465 DC C -27 REMARK 465 DT C -26 REMARK 465 DT C -25 REMARK 465 DG C -24 REMARK 465 DC C -23 REMARK 465 DA C -22 REMARK 465 DA C -21 REMARK 465 DC C 7 REMARK 465 DC C 8 REMARK 465 DA C 9 REMARK 465 U B -25 REMARK 465 C B -24 REMARK 465 A B -23 REMARK 465 A B -22 REMARK 465 C B -21 REMARK 465 G B -20 REMARK 465 DT D -9 REMARK 465 DG D -8 REMARK 465 DG D -7 REMARK 465 DT D 1 REMARK 465 DC D 2 REMARK 465 DC D 3 REMARK 465 DC D 4 REMARK 465 DC D 5 REMARK 465 DT D 6 REMARK 465 DA D 7 REMARK 465 DC D 8 REMARK 465 DG D 9 REMARK 465 DT D 10 REMARK 465 DG D 11 REMARK 465 DC D 12 REMARK 465 DT D 13 REMARK 465 DG D 14 REMARK 465 DC D 15 REMARK 465 DT D 16 REMARK 465 DG D 17 REMARK 465 DA D 18 REMARK 465 DA D 19 REMARK 465 DG D 20 REMARK 465 DT D 21 REMARK 465 DT D 22 REMARK 465 DG D 23 REMARK 465 DC D 24 REMARK 465 DA D 25 REMARK 465 DA D 26 REMARK 465 DG D 27 REMARK 465 DG D 28 REMARK 465 DG D 29 REMARK 465 DC D 30 REMARK 465 DA D 31 REMARK 465 DG D 32 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 179 CG CD OE1 OE2 REMARK 470 PRO A 324 CB CG CD 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 205 152.80 -49.20 REMARK 500 THR A 232 71.07 49.85 REMARK 500 LYS A 302 49.18 -84.22 REMARK 500 LYS A 323 -168.30 -120.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-37792 RELATED DB: EMDB REMARK 900 CRYO-EM MINI STRUCTURE OF CAS12-1-N1/CRRNA/TARGET DNA COMPLEX DBREF 8WRW A 1 359 PDB 8WRW 8WRW 1 359 DBREF 8WRW C -32 9 PDB 8WRW 8WRW -32 9 DBREF 8WRW B -25 20 PDB 8WRW 8WRW -25 20 DBREF 8WRW D -9 32 PDB 8WRW 8WRW -9 32 SEQRES 1 A 359 MET THR PRO LYS THR GLU THR PRO VAL GLY ALA LEU ILE SEQRES 2 A 359 LYS LYS PHE PHE PRO GLY LYS ARG PHE GLN LYS ASN TYR SEQRES 3 A 359 LEU LYS ASP ALA GLY LYS LYS LEU LYS ARG GLU GLY GLU SEQRES 4 A 359 ALA ALA ALA VAL GLU TYR LEU SER GLY LYS GLN GLU ASP SEQRES 5 A 359 HIS PRO ALA ASN PHE CYS PRO PRO ALA LYS VAL ASN ILE SEQRES 6 A 359 LEU ALA GLN SER ARG PRO LEU SER GLU TRP PRO ILE ASN SEQRES 7 A 359 LEU VAL SER LYS GLY VAL GLN GLU TYR VAL TYR GLY LEU SEQRES 8 A 359 THR ALA ALA GLU ARG GLU ALA ASN GLY ASP PHE GLY THR SEQRES 9 A 359 SER ARG LYS SER LEU ASP ARG TRP PHE ALA ARG THR GLY SEQRES 10 A 359 VAL PRO THR HIS GLY TYR THR THR VAL GLN GLY LEU ASN SEQRES 11 A 359 LEU ILE LEU ARG HIS THR PHE ASN ARG TYR ASP GLY VAL SEQRES 12 A 359 ILE LYS LYS VAL GLU THR ARG ASN GLU LYS ARG ARG SER SEQRES 13 A 359 LYS ALA THR ARG ILE ASN VAL SER ARG GLU ALA ASP GLY SEQRES 14 A 359 LEU PRO PRO ILE GLU ALA GLU PRO GLU GLU THR ALA PHE SEQRES 15 A 359 GLY PRO ASP GLY LYS LEU LYS GLU ARG PRO GLY ILE ASN SEQRES 16 A 359 PRO SER ILE TYR CYS TYR GLN GLN VAL SER PRO VAL PRO SEQRES 17 A 359 TYR ASN PRO ALA LYS HIS PRO ALA LEU PRO PHE SER GLY SEQRES 18 A 359 VAL ASP PRO GLY ALA PRO LEU PRO LEU GLY THR PRO ASN SEQRES 19 A 359 ARG LEU SER ILE PRO LYS GLY GLN PRO GLY TYR VAL PRO SEQRES 20 A 359 GLU TRP GLN ARG PRO HIS LEU SER THR LYS ASN LYS ARG SEQRES 21 A 359 ILE ARG LYS TRP TYR ALA ARG ALA ASN TRP ARG ARG LYS SEQRES 22 A 359 PRO GLY ARG LYS SER VAL LEU ASP GLU ALA LYS LEU LYS SEQRES 23 A 359 GLU ALA ALA LEU LYS GLU ALA ILE PRO ILE ILE VAL THR SEQRES 24 A 359 ILE GLY LYS ASP TRP ILE VAL MET ASP ALA ARG GLY LEU SEQRES 25 A 359 LEU ARG ALA VAL TYR TRP ARG GLY ILE ALA LYS PRO GLY SEQRES 26 A 359 LEU SER LEU LYS GLU LEU LEU GLY PHE PHE SER GLY ASP SEQRES 27 A 359 PRO VAL LEU ASP PRO LYS ARG GLY ILE ALA THR PHE THR SEQRES 28 A 359 PHE LYS LEU GLY ALA VAL ALA VAL SEQRES 1 C 42 DC DT DG DC DC DC DT DT DG DC DA DA DC SEQRES 2 C 42 DT DT DC DA DG DC DA DG DC DA DC DG DT SEQRES 3 C 42 DA DG DG DG DG DA DG DA DA DT DT DG DG SEQRES 4 C 42 DC DC DA SEQRES 1 B 46 U C A A C G C U U G C U C SEQRES 2 B 46 G G U U C G C C G A G A C SEQRES 3 B 46 U C C C C U A C G U G C U SEQRES 4 B 46 G C U G A A G SEQRES 1 D 42 DT DG DG DC DC DA DA DT DT DC DT DC DC SEQRES 2 D 42 DC DC DT DA DC DG DT DG DC DT DG DC DT SEQRES 3 D 42 DG DA DA DG DT DT DG DC DA DA DG DG DG SEQRES 4 D 42 DC DA DG HELIX 1 AA1 TRP A 75 GLY A 90 1 16 HELIX 2 AA2 THR A 92 GLY A 100 1 9 HELIX 3 AA3 SER A 105 THR A 116 1 12 HELIX 4 AA4 THR A 125 ASN A 130 1 6 HELIX 5 AA5 LEU A 131 GLY A 169 1 39 HELIX 6 AA6 TYR A 201 SER A 205 5 5 HELIX 7 AA7 ALA A 288 GLU A 292 1 5 HELIX 8 AA8 ASP A 308 TRP A 318 1 11 HELIX 9 AA9 SER A 327 PHE A 335 1 9 SHEET 1 AA1 7 ILE A 198 TYR A 199 0 SHEET 2 AA1 7 VAL A 340 ASP A 342 -1 O LEU A 341 N ILE A 198 SHEET 3 AA1 7 ILE A 347 THR A 351 -1 O THR A 349 N VAL A 340 SHEET 4 AA1 7 PRO A 60 GLN A 68 -1 N VAL A 63 O ALA A 348 SHEET 5 AA1 7 TRP A 304 MET A 307 -1 O VAL A 306 N LEU A 66 SHEET 6 AA1 7 ILE A 296 THR A 299 -1 N VAL A 298 O ILE A 305 SHEET 7 AA1 7 VAL A 207 PRO A 208 -1 N VAL A 207 O ILE A 297 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 2128 GLY A 355 TER 2691 DG C 6 TER 3535 G B 20 TER 3675 DC D 0 MASTER 279 0 0 9 7 0 0 6 3671 4 0 40 END