HEADER RNA BINDING PROTEIN 29-OCT-25 9YYG TITLE AI-GENERATED RNA-GUIDED NUCLEASE TAM-BOUND STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: AI-DESIGNED RNA-GUIDED NUCLEASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.-.-; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: RNA (116-MER); COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA (5'-D(*GP*GP*TP*TP*GP*AP*TP*C)-3'); COMPND 12 CHAIN: C; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 4; COMPND 15 MOLECULE: DNA (5'-D(*AP*CP*AP*TP*CP*AP*AP*CP*C)-3'); COMPND 16 CHAIN: D; COMPND 17 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: DEINOCOCCUS RADIODURANS; SOURCE 8 ORGANISM_TAXID: 1299; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 MOL_ID: 4; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 18 ORGANISM_TAXID: 32630 KEYWDS CRISPR, NUCLEASE, AI, EVOLUTION SCALE MODELING, INVERSE FOLDING, ESM- KEYWDS 2 IF1, TNPB, TAM, PAM, SPACER, EXONUCLEASE, DNA BINDING PROTEIN-DNA KEYWDS 3 COMPLEX, ENZYME, RIBONUCLEOPROTEIN, RNA, RNA-GUIDED NUCLEASE, CAS12, KEYWDS 4 ISDRA2, ESM, RNA BINDING PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR P.SKOPINTSEV,I.ESAIN-GARCIA,J.DOUDNA REVDAT 1 15-JUL-26 9YYG 0 JRNL AUTH P.SKOPINTSEV,I.ESAIN-GARCIA,J.DOUDNA JRNL TITL AI-GENERATED RNA-GUIDED NUCLEASE TAM-BOUND STATE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, SERIALEM, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC, 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 : REAL REMARK 3 REFINEMENT PROTOCOL : OTHER 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) : 2.800 REMARK 3 NUMBER OF PARTICLES : 389833 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 9YYG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-NOV-25. REMARK 100 THE DEPOSITION ID IS D_1000301627. 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 : AI-DESIGNED RNA-GUIDED NUCLEASE REMARK 245 TAM-BOUND STATE 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 : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 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) : 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, B, C, 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 ASP A 279 REMARK 465 LEU A 280 REMARK 465 ASN A 281 REMARK 465 PRO A 282 REMARK 465 LYS A 283 REMARK 465 ASN A 284 REMARK 465 MET A 285 REMARK 465 MET A 286 REMARK 465 LYS A 287 REMARK 465 ASN A 288 REMARK 465 HIS A 289 REMARK 465 HIS A 290 REMARK 465 LEU A 291 REMARK 465 ALA A 292 REMARK 465 ARG A 293 REMARK 465 ALA A 294 REMARK 465 ILE A 295 REMARK 465 SER A 296 REMARK 465 SER A 322 REMARK 465 ARG A 323 REMARK 465 TRP A 324 REMARK 465 PHE A 325 REMARK 465 PRO A 326 REMARK 465 SER A 327 REMARK 465 SER A 328 REMARK 465 GLN A 329 REMARK 465 LEU A 330 REMARK 465 CYS A 331 REMARK 465 HIS A 332 REMARK 465 VAL A 333 REMARK 465 CYS A 334 REMARK 465 GLY A 335 REMARK 465 HIS A 336 REMARK 465 LYS A 337 REMARK 465 ASN A 338 REMARK 465 PRO A 339 REMARK 465 GLU A 340 REMARK 465 VAL A 341 REMARK 465 LYS A 342 REMARK 465 ASP A 343 REMARK 465 LEU A 344 REMARK 465 SER A 345 REMARK 465 VAL A 346 REMARK 465 ARG A 347 REMARK 465 THR A 348 REMARK 465 TRP A 349 REMARK 465 THR A 350 REMARK 465 CYS A 351 REMARK 465 PRO A 352 REMARK 465 SER A 353 REMARK 465 CYS A 354 REMARK 465 GLY A 355 REMARK 465 THR A 356 REMARK 465 THR A 357 REMARK 465 HIS A 358 REMARK 465 ILE A 378 REMARK 465 SER A 379 REMARK 465 ASP A 380 REMARK 465 THR A 381 REMARK 465 LEU A 382 REMARK 465 ASN A 383 REMARK 465 ALA A 384 REMARK 465 HIS A 385 REMARK 465 GLY A 386 REMARK 465 GLY A 387 REMARK 465 TYR A 388 REMARK 465 VAL A 389 REMARK 465 ARG A 390 REMARK 465 PRO A 391 REMARK 465 ALA A 392 REMARK 465 SER A 393 REMARK 465 ALA A 394 REMARK 465 GLY A 395 REMARK 465 ASN A 396 REMARK 465 GLY A 397 REMARK 465 LEU A 398 REMARK 465 ARG A 399 REMARK 465 SER A 400 REMARK 465 GLU A 401 REMARK 465 ASN A 402 REMARK 465 HIS A 403 REMARK 465 ALA A 404 REMARK 465 THR A 405 REMARK 465 LEU A 406 REMARK 465 VAL A 407 REMARK 465 VAL A 408 REMARK 465 C B -20 REMARK 465 U B -19 REMARK 465 U B -18 REMARK 465 U B -17 REMARK 465 A B -16 REMARK 465 G B -15 REMARK 465 C B 7 REMARK 465 U B 8 REMARK 465 U B 9 REMARK 465 G B 10 REMARK 465 G B 11 REMARK 465 C B 12 REMARK 465 G B 13 REMARK 465 C B 14 REMARK 465 C B 15 REMARK 465 C B 16 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 SER A 46 CB OG REMARK 470 C B 6 C5' C4' O4' C3' O3' C2' O2' REMARK 470 C B 6 C1' N1 C2 O2 N3 C4 N4 REMARK 470 C B 6 C5 C6 REMARK 470 DT C -6 O5' C5' REMARK 470 DG C 1 C8 N7 C5 C6 O6 N1 C2 REMARK 470 DG C 1 N2 N3 C4 REMARK 470 DT D -2 O5' C5' C4' O4' C3' C2' C1' REMARK 470 DT D -2 N1 C2 O2 N3 C4 O4 C5 REMARK 470 DT D -2 C7 C6 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 46 -132.92 57.04 REMARK 500 THR A 68 33.60 -96.88 REMARK 500 ASN A 124 -118.79 58.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-73644 RELATED DB: EMDB REMARK 900 AI-GENERATED RNA-GUIDED NUCLEASE TAM-BOUND STATE DBREF 9YYG A 1 408 PDB 9YYG 9YYG 1 408 DBREF1 9YYG B -115 16 GB OV024757.1 DBREF2 9YYG B 2155018471 2426908 2426777 DBREF 9YYG C -6 1 PDB 9YYG 9YYG -6 1 DBREF 9YYG D -2 6 PDB 9YYG 9YYG -2 6 SEQRES 1 A 408 MET ILE HIS ARG LYS ALA PHE VAL VAL ARG LEU TYR PRO SEQRES 2 A 408 ASN ALA ARG GLN GLU GLU LEU ILE GLU ARG THR LEU GLY SEQRES 3 A 408 SER ALA ARG PHE VAL TYR ASN HIS PHE LEU ALA GLU ARG SEQRES 4 A 408 LYS ALA ALA TYR LYS GLU SER GLY LYS PRO LEU THR TYR SEQRES 5 A 408 GLY GLN MET SER SER LEU LEU THR LYS LEU LYS GLN ALA SEQRES 6 A 408 PRO GLU THR ALA TRP LEU SER GLU VAL ASP LYS PHE ALA SEQRES 7 A 408 LEU GLN ASN SER LEU LYS ASN LEU GLU ARG ALA PHE GLN SEQRES 8 A 408 ASN PHE PHE ARG THR LEU LYS LYS LYS GLY GLU LYS VAL SEQRES 9 A 408 GLY PHE PRO LYS PHE ARG LYS LYS LYS THR GLY GLU SER SEQRES 10 A 408 PHE ARG THR GLN PHE THR ASN ASN ASN ILE GLN ILE GLY SEQRES 11 A 408 LYS GLY LYS LEU LYS LEU PRO LYS LEU GLY TRP VAL LYS SEQRES 12 A 408 THR LYS GLY GLN GLN GLU ILE LYS GLY LYS VAL LEU ASN SEQRES 13 A 408 VAL THR VAL LYS ARG VAL HIS GLU GLY HIS TYR GLU ALA SEQRES 14 A 408 SER VAL LEU VAL GLU VAL GLU ILE PRO GLU LEU PRO GLU SEQRES 15 A 408 ALA PRO LEU LEU ALA ALA GLY VAL ASP LEU GLY ILE LYS SEQRES 16 A 408 ASN PHE ALA VAL VAL THR ASP GLY GLU GLU PHE GLU LYS SEQRES 17 A 408 VAL GLU ASN PRO LYS PHE LEU LYS LYS THR GLU LYS ARG SEQRES 18 A 408 LEU ALA ARG ALA GLN ARG ARG LEU SER ARG ARG LYS LYS SEQRES 19 A 408 GLY SER ALA ARG TRP GLU LYS ALA ARG THR ARG LEU ALA SEQRES 20 A 408 ARG ILE HIS LYS ARG ILE VAL ASN GLN ARG GLN ASP PHE SEQRES 21 A 408 LEU HIS LYS LEU THR THR GLY LEU VAL LYS THR TYR GLN SEQRES 22 A 408 ILE ILE ALA VAL GLU ASP LEU ASN PRO LYS ASN MET MET SEQRES 23 A 408 LYS ASN HIS HIS LEU ALA ARG ALA ILE SER ASP ALA ALA SEQRES 24 A 408 TRP GLY GLU PHE ARG ARG GLN LEU GLU TYR LYS ALA GLU SEQRES 25 A 408 TRP TYR GLY ARG THR VAL ALA LYS VAL SER ARG TRP PHE SEQRES 26 A 408 PRO SER SER GLN LEU CYS HIS VAL CYS GLY HIS LYS ASN SEQRES 27 A 408 PRO GLU VAL LYS ASP LEU SER VAL ARG THR TRP THR CYS SEQRES 28 A 408 PRO SER CYS GLY THR THR HIS ASP ARG ASP GLU ASN ALA SEQRES 29 A 408 ALA LEU ASN ILE ARG ARG GLU ALA LEU VAL ALA ALA GLY SEQRES 30 A 408 ILE SER ASP THR LEU ASN ALA HIS GLY GLY TYR VAL ARG SEQRES 31 A 408 PRO ALA SER ALA GLY ASN GLY LEU ARG SER GLU ASN HIS SEQRES 32 A 408 ALA THR LEU VAL VAL SEQRES 1 B 132 G G U G G C U G C G G G A SEQRES 2 B 132 A U C U C A G A C A C C U SEQRES 3 B 132 U A A A C G C U C A U G G SEQRES 4 B 132 A G G C U A U G U C A G A SEQRES 5 B 132 C C U G C U U C G G C G G SEQRES 6 B 132 G C A A U G G U C U G C G SEQRES 7 B 132 A A G U G A G A A U C A C SEQRES 8 B 132 G C G A C U U U A G U C G SEQRES 9 B 132 U G U G A G G U U C A A G SEQRES 10 B 132 A G U C C C U U G G C G C SEQRES 11 B 132 C C SEQRES 1 C 8 DT DA DT DT DG DA DT DG SEQRES 1 D 9 DT DC DA DT DC DA DA DT DA HELIX 1 AA1 ASN A 14 GLU A 45 1 32 HELIX 2 AA2 THR A 51 ALA A 65 1 15 HELIX 3 AA3 THR A 68 VAL A 74 5 7 HELIX 4 AA4 ASP A 75 LYS A 100 1 26 HELIX 5 AA5 LYS A 213 ARG A 232 1 20 HELIX 6 AA6 SER A 236 THR A 271 1 36 HELIX 7 AA7 ALA A 299 GLY A 315 1 17 HELIX 8 AA8 ASP A 361 GLY A 377 1 17 SHEET 1 AA1 7 GLU A 116 GLN A 121 0 SHEET 2 AA1 7 LYS A 153 HIS A 163 -1 O VAL A 157 N THR A 120 SHEET 3 AA1 7 HIS A 166 GLU A 176 -1 O GLU A 168 N LYS A 160 SHEET 4 AA1 7 ILE A 2 TYR A 12 -1 N VAL A 9 O ALA A 169 SHEET 5 AA1 7 GLY A 140 LYS A 145 -1 O LYS A 143 N TYR A 12 SHEET 6 AA1 7 LYS A 133 LEU A 136 -1 N LEU A 134 O VAL A 142 SHEET 7 AA1 7 ILE A 129 GLY A 130 -1 N GLY A 130 O LYS A 133 SHEET 1 AA2 5 GLU A 207 VAL A 209 0 SHEET 2 AA2 5 ALA A 198 THR A 201 -1 N ALA A 198 O VAL A 209 SHEET 3 AA2 5 LEU A 185 ASP A 191 -1 N GLY A 189 O THR A 201 SHEET 4 AA2 5 TYR A 272 VAL A 277 1 O ILE A 274 N ALA A 188 SHEET 5 AA2 5 THR A 317 LYS A 320 1 O THR A 317 N ILE A 275 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 245 0 0 8 12 0 0 6 5410 4 0 45 END