HEADER RNA BINDING PROTEIN/RNA/DNA 16-OCT-23 8WS5 TITLE CRYO-EM STRUCTURE OF CAS12-1-N2/CRRNA/TARGET DNA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAS12-1-N2; 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 8WS5 0 JRNL AUTH Z.KUO,Z.XI JRNL TITL CRYO-EM STRUCTURE OF CAS12-1-N2/CRRNA/TARGET DNA COMPLEX JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.29 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) : 3.290 REMARK 3 NUMBER OF PARTICLES : 113093 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 8WS5 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_1300041561. 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 -N2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA 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 PHE A 57 REMARK 465 ASP A 101 REMARK 465 PHE A 102 REMARK 465 GLY A 103 REMARK 465 GLY A 231 REMARK 465 THR A 232 REMARK 465 PRO A 233 REMARK 465 ASN A 234 REMARK 465 ARG A 235 REMARK 465 LEU A 236 REMARK 465 SER A 237 REMARK 465 ILE A 238 REMARK 465 PRO A 239 REMARK 465 LYS A 240 REMARK 465 GLY A 241 REMARK 465 GLN A 242 REMARK 465 PHE A 335 REMARK 465 ALA A 356 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 LEU A 109 46.19 -88.17 REMARK 500 PRO A 208 -179.07 -63.24 REMARK 500 ALA A 226 133.60 -172.26 REMARK 500 VAL A 246 75.58 43.99 REMARK 500 HIS A 253 31.03 -145.17 REMARK 500 LYS A 259 -169.37 -161.33 REMARK 500 LEU A 328 45.77 -79.79 REMARK 500 LYS A 329 -38.21 -131.94 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-37798 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF CAS12-1-N2/CRRNA/TARGET DNA COMPLEX DBREF 8WS5 A 57 356 PDB 8WS5 8WS5 57 356 DBREF 8WS5 C -32 9 PDB 8WS5 8WS5 -32 9 DBREF 8WS5 B -25 20 PDB 8WS5 8WS5 -25 20 DBREF 8WS5 D -9 32 PDB 8WS5 8WS5 -9 32 SEQRES 1 A 300 PHE CYS PRO PRO ALA LYS VAL ASN ILE LEU ALA GLN SER SEQRES 2 A 300 ARG PRO LEU SER GLU TRP PRO ILE ASN LEU VAL SER LYS SEQRES 3 A 300 GLY VAL GLN GLU TYR VAL TYR GLY LEU THR ALA ALA GLU SEQRES 4 A 300 ARG GLU ALA ASN GLY ASP PHE GLY THR SER ARG LYS SER SEQRES 5 A 300 LEU ASP ARG TRP PHE ALA ARG THR GLY VAL PRO THR HIS SEQRES 6 A 300 GLY TYR THR THR VAL GLN GLY LEU ASN LEU ILE LEU ARG SEQRES 7 A 300 HIS THR PHE ASN ARG TYR ASP GLY VAL ILE LYS LYS VAL SEQRES 8 A 300 GLU THR ARG ASN GLU LYS ARG ARG SER LYS ALA THR ARG SEQRES 9 A 300 ILE ASN VAL SER ARG GLU ALA ASP GLY LEU PRO PRO ILE SEQRES 10 A 300 GLU ALA GLU PRO GLU GLU THR ALA PHE GLY PRO ASP GLY SEQRES 11 A 300 LYS LEU LYS GLU ARG PRO GLY ILE ASN PRO SER ILE TYR SEQRES 12 A 300 CYS TYR GLN GLN VAL SER PRO VAL PRO TYR ASN PRO ALA SEQRES 13 A 300 LYS HIS PRO ALA LEU PRO PHE SER GLY VAL ASP PRO GLY SEQRES 14 A 300 ALA PRO LEU PRO LEU GLY THR PRO ASN ARG LEU SER ILE SEQRES 15 A 300 PRO LYS GLY GLN PRO GLY TYR VAL PRO GLU TRP GLN ARG SEQRES 16 A 300 PRO HIS LEU SER THR LYS ASN LYS ARG ILE ARG LYS TRP SEQRES 17 A 300 TYR ALA ARG ALA ASN TRP ARG ARG LYS PRO GLY ARG LYS SEQRES 18 A 300 SER VAL LEU ASP GLU ALA LYS LEU LYS GLU ALA ALA LEU SEQRES 19 A 300 LYS GLU ALA ILE PRO ILE ILE VAL THR ILE GLY LYS ASP SEQRES 20 A 300 TRP ILE VAL MET ASP ALA ARG GLY LEU LEU ARG ALA VAL SEQRES 21 A 300 TYR TRP ARG GLY ILE ALA LYS PRO GLY LEU SER LEU LYS SEQRES 22 A 300 GLU LEU LEU GLY PHE PHE SER GLY ASP PRO VAL LEU ASP SEQRES 23 A 300 PRO LYS ARG GLY ILE ALA THR PHE THR PHE LYS LEU GLY SEQRES 24 A 300 ALA 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 PRO A 71 GLU A 74 5 4 HELIX 2 AA2 TRP A 75 TYR A 89 1 15 HELIX 3 AA3 ALA A 94 GLY A 100 1 7 HELIX 4 AA4 LYS A 107 THR A 116 1 10 HELIX 5 AA5 THR A 125 GLY A 169 1 45 HELIX 6 AA6 PRO A 247 ARG A 251 5 5 HELIX 7 AA7 ALA A 266 TRP A 270 5 5 HELIX 8 AA8 ALA A 283 GLU A 292 1 10 HELIX 9 AA9 ALA A 309 ARG A 319 1 11 SHEET 1 AA1 4 ALA A 61 ASN A 64 0 SHEET 2 AA1 4 ILE A 347 PHE A 350 -1 O ALA A 348 N VAL A 63 SHEET 3 AA1 4 VAL A 340 ASP A 342 -1 N VAL A 340 O THR A 349 SHEET 4 AA1 4 ILE A 198 TYR A 199 -1 N ILE A 198 O LEU A 341 SHEET 1 AA2 3 ALA A 67 GLN A 68 0 SHEET 2 AA2 3 ASP A 303 VAL A 306 -1 O VAL A 306 N ALA A 67 SHEET 3 AA2 3 ILE A 297 ILE A 300 -1 N VAL A 298 O ILE A 305 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 MASTER 214 0 0 9 7 0 0 6 3770 4 0 36 END