HEADER IMMUNE SYSTEM/RNA/DNA 21-FEB-24 8W2Z TITLE CAS9D 6BP R-LOOP SEED COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: HNH NUCLEASE DOMAIN-CONTAINING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: SGRNA; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA TARGET STRAND; COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 4; COMPND 14 MOLECULE: DNA NON-TARGET STRAND; COMPND 15 CHAIN: D; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DELTAPROTEOBACTERIA; SOURCE 3 ORGANISM_TAXID: 28221; SOURCE 4 GENE: A2022_01700; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: NICO DE3; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: DELTAPROTEOBACTERIA; SOURCE 10 ORGANISM_TAXID: 28221; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 12 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 13 EXPRESSION_SYSTEM_STRAIN: NICO DE3; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 ORGANISM_SCIENTIFIC: ESCHERICHIA PHAGE LAMBDA; SOURCE 17 ORGANISM_TAXID: 2681611; SOURCE 18 MOL_ID: 4; SOURCE 19 SYNTHETIC: YES; SOURCE 20 ORGANISM_SCIENTIFIC: ESCHERICHIA PHAGE LAMBDA; SOURCE 21 ORGANISM_TAXID: 2681611 KEYWDS CRISPR-CAS9, ENDONUCLEASE, BINARY COMPLEX, EFFECTOR, SGRNA, IMMUNE KEYWDS 2 SYSTEM-RNA-DNA COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR R.FREGOSO OCAMPO,J.P.K.BRAVO,D.W.TAYLOR REVDAT 1 15-JAN-25 8W2Z 0 JRNL AUTH R.F.OCAMPO,J.P.K.BRAVO,T.L.DANGERFIELD,I.NOCEDAL,S.A.JIRDE, JRNL AUTH 2 L.M.ALEXANDER,N.C.THOMAS,A.DAS,S.NIELSON,K.A.JOHNSON, JRNL AUTH 3 C.T.BROWN,C.N.BUTTERFIELD,D.S.A.GOLTSMAN,D.W.TAYLOR JRNL TITL DNA TARGETING BY COMPACT CAS9D AND ITS RESURRECTED ANCESTOR. JRNL REF NAT COMMUN V. 16 457 2025 JRNL REFN ESSN 2041-1723 JRNL PMID 39774105 JRNL DOI 10.1038/S41467-024-55573-4 REMARK 2 REMARK 2 RESOLUTION. 3.37 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) : 3.370 REMARK 3 NUMBER OF PARTICLES : 70093 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 8W2Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-FEB-24. REMARK 100 THE DEPOSITION ID IS D_1000281767. 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 : CAS9D:SGRNA: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 : 7.90 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) : 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) : 8000.00 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, 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 MET A 1 REMARK 465 GLU A 2 REMARK 465 ARG A 3 REMARK 465 GLU A 102 REMARK 465 GLU A 103 REMARK 465 LYS A 104 REMARK 465 THR A 105 REMARK 465 SER A 106 REMARK 465 GLU A 107 REMARK 465 GLU A 108 REMARK 465 ILE A 109 REMARK 465 GLU A 110 REMARK 465 ALA A 111 REMARK 465 MET A 112 REMARK 465 ASP A 113 REMARK 465 VAL A 114 REMARK 465 GLU A 115 REMARK 465 GLU A 116 REMARK 465 ARG A 117 REMARK 465 LYS A 118 REMARK 465 GLN A 119 REMARK 465 TRP A 120 REMARK 465 GLU A 121 REMARK 465 LYS A 122 REMARK 465 GLU A 123 REMARK 465 LYS A 124 REMARK 465 CYS A 187 REMARK 465 GLY A 188 REMARK 465 VAL A 189 REMARK 465 GLU A 315 REMARK 465 SER A 316 REMARK 465 ASN A 317 REMARK 465 ASN A 318 REMARK 465 PHE A 319 REMARK 465 ASP A 320 REMARK 465 ILE A 321 REMARK 465 ALA A 322 REMARK 465 ALA A 323 REMARK 465 LYS A 324 REMARK 465 THR A 325 REMARK 465 GLN A 326 REMARK 465 GLY A 327 REMARK 465 LYS A 328 REMARK 465 LYS A 329 REMARK 465 ARG A 330 REMARK 465 LEU A 331 REMARK 465 ALA A 332 REMARK 465 LYS A 333 REMARK 465 GLU A 334 REMARK 465 GLU A 335 REMARK 465 TYR A 336 REMARK 465 GLY A 337 REMARK 465 LYS A 338 REMARK 465 GLY A 339 REMARK 465 PRO A 340 REMARK 465 ARG A 341 REMARK 465 GLU A 342 REMARK 465 GLY A 343 REMARK 465 LYS A 344 REMARK 465 GLU A 345 REMARK 465 THR A 346 REMARK 465 ARG A 347 REMARK 465 LYS A 348 REMARK 465 GLU A 349 REMARK 465 ALA A 350 REMARK 465 LEU A 351 REMARK 465 LEU A 352 REMARK 465 ARG A 353 REMARK 465 GLU A 354 REMARK 465 THR A 355 REMARK 465 ASP A 356 REMARK 465 GLY A 357 REMARK 465 ARG A 358 REMARK 465 CYS A 359 REMARK 465 ILE A 360 REMARK 465 TYR A 361 REMARK 465 CYS A 362 REMARK 465 GLY A 363 REMARK 465 LYS A 364 REMARK 465 SER A 365 REMARK 465 ILE A 366 REMARK 465 ASP A 367 REMARK 465 ILE A 368 REMARK 465 SER A 369 REMARK 465 ASN A 370 REMARK 465 ALA A 371 REMARK 465 HIS A 372 REMARK 465 ASP A 373 REMARK 465 ASP A 374 REMARK 465 HIS A 375 REMARK 465 ILE A 376 REMARK 465 PHE A 377 REMARK 465 PRO A 378 REMARK 465 ARG A 379 REMARK 465 LYS A 380 REMARK 465 ALA A 381 REMARK 465 GLY A 382 REMARK 465 GLY A 383 REMARK 465 LEU A 384 REMARK 465 ASN A 385 REMARK 465 ILE A 386 REMARK 465 PHE A 387 REMARK 465 ALA A 388 REMARK 465 ASN A 389 REMARK 465 LEU A 390 REMARK 465 VAL A 391 REMARK 465 ALA A 392 REMARK 465 CYS A 393 REMARK 465 CYS A 394 REMARK 465 ALA A 395 REMARK 465 VAL A 396 REMARK 465 CYS A 397 REMARK 465 ASN A 398 REMARK 465 GLU A 399 REMARK 465 ASN A 400 REMARK 465 LYS A 401 REMARK 465 LYS A 402 REMARK 465 GLY A 403 REMARK 465 ARG A 404 REMARK 465 THR A 405 REMARK 465 PRO A 406 REMARK 465 LEU A 407 REMARK 465 GLU A 408 REMARK 465 SER A 409 REMARK 465 GLY A 410 REMARK 465 ILE A 411 REMARK 465 SER A 412 REMARK 465 PRO A 413 REMARK 465 LYS A 414 REMARK 465 PRO A 415 REMARK 465 GLU A 416 REMARK 465 ILE A 417 REMARK 465 ILE A 418 REMARK 465 ALA A 419 REMARK 465 PHE A 420 REMARK 465 MET A 421 REMARK 465 LYS A 422 REMARK 465 ASN A 423 REMARK 465 ASP A 424 REMARK 465 LEU A 425 REMARK 465 LYS A 426 REMARK 465 LYS A 427 REMARK 465 LYS A 428 REMARK 465 ILE A 429 REMARK 465 LEU A 430 REMARK 465 GLU A 431 REMARK 465 ASP A 432 REMARK 465 ALA A 433 REMARK 465 ARG A 434 REMARK 465 ASN A 435 REMARK 465 ILE A 436 REMARK 465 ASN A 437 REMARK 465 THR A 438 REMARK 465 VAL A 439 REMARK 465 ASP A 440 REMARK 465 PHE A 441 REMARK 465 ASN A 442 REMARK 465 LYS A 443 REMARK 465 TYR A 444 REMARK 465 MET A 445 REMARK 465 SER A 446 REMARK 465 HIS A 447 REMARK 465 GLN A 473 REMARK 465 SER A 474 REMARK 465 GLY A 475 REMARK 465 ILE A 476 REMARK 465 TYR A 477 REMARK 465 THR A 478 REMARK 465 ALA A 479 REMARK 465 TYR A 480 REMARK 465 PHE A 481 REMARK 465 ARG A 482 REMARK 465 ARG A 483 REMARK 465 TRP A 484 REMARK 465 TRP A 485 REMARK 465 GLY A 486 REMARK 465 PHE A 487 REMARK 465 LYS A 488 REMARK 465 LYS A 489 REMARK 465 GLU A 490 REMARK 465 ARG A 491 REMARK 465 GLY A 492 REMARK 465 ASN A 493 REMARK 465 SER A 506 REMARK 465 ARG A 507 REMARK 465 LYS A 508 REMARK 465 GLY A 509 REMARK 465 TYR A 510 REMARK 465 SER A 511 REMARK 465 ASP A 512 REMARK 465 ASP A 513 REMARK 465 GLY A 514 REMARK 465 LEU A 515 REMARK 465 VAL A 516 REMARK 465 ASP A 517 REMARK 465 MET A 518 REMARK 465 THR A 519 REMARK 465 LEU A 520 REMARK 465 LYS A 521 REMARK 465 PRO A 522 REMARK 465 LYS A 523 REMARK 465 TYR A 524 REMARK 465 ASN A 525 REMARK 465 LYS A 526 REMARK 465 GLY A 527 REMARK 465 GLY A 528 REMARK 465 GLU A 529 REMARK 465 PHE A 530 REMARK 465 ASP A 531 REMARK 465 PRO A 532 REMARK 465 GLU A 533 REMARK 465 LYS A 534 REMARK 465 HIS A 535 REMARK 465 LEU A 536 REMARK 465 PRO A 537 REMARK 465 GLU A 538 REMARK 465 PRO A 539 REMARK 465 ASN A 744 REMARK 465 SER A 745 REMARK 465 ALA A 746 REMARK 465 GLU A 747 REMARK 465 G B 1 REMARK 465 A B 2 REMARK 465 C B 3 REMARK 465 G B 4 REMARK 465 C B 5 REMARK 465 A B 6 REMARK 465 U B 7 REMARK 465 A B 8 REMARK 465 A B 9 REMARK 465 U B 147 REMARK 465 U B 148 REMARK 465 U B 149 REMARK 465 A B 150 REMARK 465 A B 151 REMARK 465 U B 152 REMARK 465 U B 153 REMARK 465 U B 154 REMARK 465 U B 155 REMARK 465 U B 156 REMARK 465 U B 157 REMARK 465 U B 158 REMARK 465 DA C -19 REMARK 465 DG C -18 REMARK 465 DC C -17 REMARK 465 DT C -16 REMARK 465 DG C -15 REMARK 465 DA C -14 REMARK 465 DC C 6 REMARK 465 DA C 7 REMARK 465 DT C 8 REMARK 465 DC C 9 REMARK 465 DT C 10 REMARK 465 DT C 11 REMARK 465 DT C 12 REMARK 465 DA C 13 REMARK 465 DT C 14 REMARK 465 DG C 15 REMARK 465 DC C 16 REMARK 465 DG C 17 REMARK 465 DT C 18 REMARK 465 DC C 19 REMARK 465 DA C 20 REMARK 465 DG C 21 REMARK 465 DC C 22 REMARK 465 DA C 23 REMARK 465 DG C 24 REMARK 465 DA C 25 REMARK 465 DG C 26 REMARK 465 DA C 27 REMARK 465 DT C 28 REMARK 465 DT C 29 REMARK 465 DT C 30 REMARK 465 DC C 31 REMARK 465 DT C 32 REMARK 465 DG C 33 REMARK 465 DC C 34 REMARK 465 DT C 35 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 4 CG CD OE1 OE2 REMARK 470 VAL A 21 CG1 CG2 REMARK 470 ARG A 24 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 25 CG ND1 CD2 CE1 NE2 REMARK 470 GLN A 27 CG CD OE1 NE2 REMARK 470 LEU A 29 CG CD1 CD2 REMARK 470 ASP A 39 CG OD1 OD2 REMARK 470 ASP A 99 CG OD1 OD2 REMARK 470 MET A 100 CG SD CE REMARK 470 GLN A 125 CG CD OE1 NE2 REMARK 470 GLU A 126 CG CD OE1 OE2 REMARK 470 TRP A 127 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 127 CZ3 CH2 REMARK 470 GLU A 128 CG CD OE1 OE2 REMARK 470 GLU A 129 CG CD OE1 OE2 REMARK 470 LEU A 224 CG CD1 CD2 REMARK 470 ARG A 228 CG CD NE CZ NH1 NH2 REMARK 470 PHE A 236 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG A 237 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 238 CG CD CE NZ REMARK 470 LYS A 240 CG CD CE NZ REMARK 470 THR A 241 OG1 CG2 REMARK 470 ILE A 245 CG1 CG2 CD1 REMARK 470 ASN A 255 CG OD1 ND2 REMARK 470 GLU A 273 CG CD OE1 OE2 REMARK 470 HIS A 274 CG ND1 CD2 CE1 NE2 REMARK 470 SER A 275 OG REMARK 470 LYS A 276 CG CD CE NZ REMARK 470 ARG A 279 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 280 CG CD CE NZ REMARK 470 ARG A 283 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 310 CG OD1 ND2 REMARK 470 LYS A 311 CG CD CE NZ REMARK 470 LYS A 467 CG CD CE NZ REMARK 470 ILE A 470 CG1 CG2 CD1 REMARK 470 LEU A 495 CG CD1 CD2 REMARK 470 HIS A 496 CG ND1 CD2 CE1 NE2 REMARK 470 HIS A 497 CG ND1 CD2 CE1 NE2 REMARK 470 LEU A 499 CG CD1 CD2 REMARK 470 ASP A 500 CG OD1 OD2 REMARK 470 VAL A 502 CG1 CG2 REMARK 470 ILE A 503 CG1 CG2 CD1 REMARK 470 LEU A 504 CG CD1 CD2 REMARK 470 MET A 544 CG SD CE REMARK 470 ASP A 581 CG OD1 OD2 REMARK 470 ASP A 600 CG OD1 OD2 REMARK 470 THR A 601 OG1 CG2 REMARK 470 ASP A 609 CG OD1 OD2 REMARK 470 LYS A 613 CG CD CE NZ REMARK 470 PHE A 617 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LEU A 624 CG CD1 CD2 REMARK 470 GLU A 663 CG CD OE1 OE2 REMARK 470 LYS A 664 CG CD CE NZ REMARK 470 LYS A 666 CG CD CE NZ REMARK 470 ARG A 691 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 708 CG OD1 OD2 REMARK 470 ASP A 729 CG OD1 OD2 REMARK 470 LYS A 731 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 U B 92 C3' - O3' - P ANGL. DEV. = 7.7 DEGREES REMARK 500 G B 142 N9 - C1' - C2' ANGL. DEV. = 10.6 DEGREES REMARK 500 G B 142 O4' - C1' - N9 ANGL. DEV. = 9.4 DEGREES REMARK 500 DT C 5 O3' - P - OP1 ANGL. DEV. = 14.0 DEGREES REMARK 500 DT C 5 OP1 - P - OP2 ANGL. DEV. = -12.4 DEGREES REMARK 500 DG D 3 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 ASP A 38 -146.48 58.20 REMARK 500 SER A 134 -2.84 68.20 REMARK 500 ARG A 135 -136.77 52.58 REMARK 500 PHE A 174 33.76 -140.75 REMARK 500 CYS A 264 -158.39 -150.64 REMARK 500 GLU A 273 33.43 -99.27 REMARK 500 ARG A 283 37.30 -96.75 REMARK 500 ALA A 285 76.36 -161.06 REMARK 500 CYS A 618 71.15 59.09 REMARK 500 ASN A 644 -121.50 53.45 REMARK 500 GLU A 663 -122.60 58.18 REMARK 500 THR A 718 -109.54 50.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-43760 RELATED DB: EMDB REMARK 900 AN INTRICATELY FOLDED GUIDE RNA SCAFFOLD ENABLES DNA TARGETING BY REMARK 900 THE COMPACT CAS9D NUCLEASE DBREF1 8W2Z A 1 747 UNP A0A1F8ZSN4_9DELT DBREF2 8W2Z A A0A1F8ZSN4 1 747 DBREF 8W2Z B 1 158 PDB 8W2Z 8W2Z 1 158 DBREF 8W2Z C -19 35 PDB 8W2Z 8W2Z -19 35 DBREF 8W2Z D 0 13 PDB 8W2Z 8W2Z 0 13 SEQADV 8W2Z A UNP A0A1F8ZSN GLN 213 DELETION SEQADV 8W2Z GLU A 529 UNP A0A1F8ZSN GLY 529 CONFLICT SEQADV 8W2Z PRO A 532 UNP A0A1F8ZSN SER 532 CONFLICT SEQADV 8W2Z MET A 544 UNP A0A1F8ZSN ARG 544 CONFLICT SEQADV 8W2Z ARG A 549 UNP A0A1F8ZSN LYS 549 CONFLICT SEQRES 1 A 746 MET GLU ARG GLU LEU VAL LEU GLY ILE ASP TYR GLY GLY SEQRES 2 A 746 LYS TYR THR GLY LEU ALA VAL VAL ASP ARG ARG HIS ASN SEQRES 3 A 746 GLN VAL LEU TYR ALA ASN ARG LEU LYS MET ARG ASP ASP SEQRES 4 A 746 VAL ALA GLY ILE LEU LYS ASP ARG ARG LYS GLN ARG GLY SEQRES 5 A 746 ILE ARG ARG THR ALA GLN THR LYS LYS LYS ARG LEU ARG SEQRES 6 A 746 GLU LEU LYS ASN TYR LEU LYS SER ILE GLY TYR ASN GLU SEQRES 7 A 746 SER THR ALA THR PHE GLU THR VAL TYR SER LEU ALA HIS SEQRES 8 A 746 LYS ARG GLY TYR ASP TYR ALA ASP MET PRO GLU GLU LYS SEQRES 9 A 746 THR SER GLU GLU ILE GLU ALA MET ASP VAL GLU GLU ARG SEQRES 10 A 746 LYS GLN TRP GLU LYS GLU LYS GLN GLU TRP GLU GLU THR SEQRES 11 A 746 LYS ARG ASN SER ARG HIS ARG LYS GLU VAL VAL LYS ASP SEQRES 12 A 746 VAL HIS LYS ALA MET ILE GLU GLY ARG ALA THR GLU GLU SEQRES 13 A 746 GLN ILE LYS ARG VAL GLU ARG ILE PHE ASN LYS GLN TYR SEQRES 14 A 746 ARG PRO LYS ARG PHE ASN ASN ARG ILE LEU THR LYS CYS SEQRES 15 A 746 LYS VAL GLU ASP CYS GLY VAL ASN THR PRO LEU ARG LYS SEQRES 16 A 746 ASN VAL ARG ASP LEU LEU ILE GLU ASN ILE VAL ARG PHE SEQRES 17 A 746 PHE PRO ILE GLU SER GLU LYS ASP ASN LEU LYS ASP ALA SEQRES 18 A 746 VAL LEU ASP LYS ASN ARG ARG GLU GLU VAL LYS SER PHE SEQRES 19 A 746 PHE ARG LYS HIS LYS THR ASP GLU HIS ILE ARG LYS GLN SEQRES 20 A 746 VAL TYR ASP ILE ALA ASP ASN LYS LEU SER GLY ARG THR SEQRES 21 A 746 VAL PHE CYS LYS GLU HIS ILE LEU GLU HIS THR GLU HIS SEQRES 22 A 746 SER LYS GLU GLU ARG LYS VAL PHE ARG LEU ALA PRO SER SEQRES 23 A 746 LEU LYS THR LYS ILE GLU ASN VAL LEU ALA VAL ILE LYS SEQRES 24 A 746 ASP GLU ILE LEU PRO LYS PHE THR VAL ASN LYS VAL VAL SEQRES 25 A 746 MET GLU SER ASN ASN PHE ASP ILE ALA ALA LYS THR GLN SEQRES 26 A 746 GLY LYS LYS ARG LEU ALA LYS GLU GLU TYR GLY LYS GLY SEQRES 27 A 746 PRO ARG GLU GLY LYS GLU THR ARG LYS GLU ALA LEU LEU SEQRES 28 A 746 ARG GLU THR ASP GLY ARG CYS ILE TYR CYS GLY LYS SER SEQRES 29 A 746 ILE ASP ILE SER ASN ALA HIS ASP ASP HIS ILE PHE PRO SEQRES 30 A 746 ARG LYS ALA GLY GLY LEU ASN ILE PHE ALA ASN LEU VAL SEQRES 31 A 746 ALA CYS CYS ALA VAL CYS ASN GLU ASN LYS LYS GLY ARG SEQRES 32 A 746 THR PRO LEU GLU SER GLY ILE SER PRO LYS PRO GLU ILE SEQRES 33 A 746 ILE ALA PHE MET LYS ASN ASP LEU LYS LYS LYS ILE LEU SEQRES 34 A 746 GLU ASP ALA ARG ASN ILE ASN THR VAL ASP PHE ASN LYS SEQRES 35 A 746 TYR MET SER HIS ALA SER ILE GLY TRP ARG TYR MET ARG SEQRES 36 A 746 ASP ARG LEU ARG GLU SER ALA GLY ASN LYS LYS LEU PRO SEQRES 37 A 746 ILE GLU ARG GLN SER GLY ILE TYR THR ALA TYR PHE ARG SEQRES 38 A 746 ARG TRP TRP GLY PHE LYS LYS GLU ARG GLY ASN THR LEU SEQRES 39 A 746 HIS HIS ALA LEU ASP ALA VAL ILE LEU ALA SER ARG LYS SEQRES 40 A 746 GLY TYR SER ASP ASP GLY LEU VAL ASP MET THR LEU LYS SEQRES 41 A 746 PRO LYS TYR ASN LYS GLY GLY GLU PHE ASP PRO GLU LYS SEQRES 42 A 746 HIS LEU PRO GLU PRO ILE GLU PHE LYS MET ASP LYS GLY SEQRES 43 A 746 SER ARG GLY SER ALA LEU HIS ASP ARG ASN PRO LEU SER SEQRES 44 A 746 TYR LYS LYS GLY ILE ILE THR ARG ARG PHE MET VAL THR SEQRES 45 A 746 GLU ILE GLU CYS GLY LYS GLU ASP ASP VAL ILE SER GLU SEQRES 46 A 746 THR TYR ARG GLU LYS LEU LYS GLU ALA PHE LYS ARG PHE SEQRES 47 A 746 ASP THR LYS LYS GLY LYS CYS LEU THR ASP LYS GLU ALA SEQRES 48 A 746 LYS GLU ALA GLY PHE CYS ILE LYS LYS ASN GLU LEU VAL SEQRES 49 A 746 MET SER LEU LYS CYS SER ILE LYS GLY THR GLY PRO GLY SEQRES 50 A 746 GLN MET ILE ARG ILE ASN ASN ASN VAL PHE LYS THR ASN SEQRES 51 A 746 VAL HIS ASN VAL GLY VAL ASP VAL TYR LEU ASP GLU LYS SEQRES 52 A 746 GLY LYS LYS LYS ALA TYR GLU ARG LYS ASN PRO ARG LEU SEQRES 53 A 746 SER LYS HIS PHE ILE GLU PRO PRO PRO GLN PRO ASN GLY SEQRES 54 A 746 ARG VAL SER PHE THR LEU LYS ARG ARG ASP MET VAL THR SEQRES 55 A 746 VAL GLU GLY GLU ASP ALA ILE TYR ARG ILE LYS LYS LEU SEQRES 56 A 746 GLY THR SER PRO THR ILE GLU ALA VAL VAL GLY SER ASP SEQRES 57 A 746 GLY LYS THR ARG THR VAL SER ALA THR LYS LEU THR LYS SEQRES 58 A 746 ALA ASN SER ALA GLU SEQRES 1 B 158 G A C G C A U A A A G A U SEQRES 2 B 158 G A G A C G C G U U A C A SEQRES 3 B 158 G U U A A G G C U C U G A SEQRES 4 B 158 A A A G A G C C U U A A U SEQRES 5 B 158 U G U A A A A C G C C U A SEQRES 6 B 158 U A C A G U G A A G G G A SEQRES 7 B 158 U A U A C G C U U G G G U SEQRES 8 B 158 U U G U C C A G C C U G A SEQRES 9 B 158 G C C U C U A U G C C A G SEQRES 10 B 158 A A A U G G C G C C U U C SEQRES 11 B 158 A U C G U G G G U U A G G SEQRES 12 B 158 A C A U U U A A U U U U U SEQRES 13 B 158 U U SEQRES 1 C 55 DA DG DC DT DG DA DC DG DT DT DT DG DT SEQRES 2 C 55 DA DC DT DC DC DA DG DC DG DT DC DT DC SEQRES 3 C 55 DA DT DC DT DT DT DA DT DG DC DG DT DC SEQRES 4 C 55 DA DG DC DA DG DA DG DA DT DT DT DC DT SEQRES 5 C 55 DG DC DT SEQRES 1 D 14 DC DT DG DG DA DG DT DA DC DA DA DA DC SEQRES 2 D 14 DG HELIX 1 AA1 GLY A 42 GLY A 75 1 34 HELIX 2 AA2 THR A 80 ALA A 90 1 11 HELIX 3 AA3 HIS A 136 GLU A 150 1 15 HELIX 4 AA4 THR A 154 LYS A 167 1 14 HELIX 5 AA5 VAL A 197 ARG A 207 1 11 HELIX 6 AA6 GLU A 215 ASP A 225 1 11 HELIX 7 AA7 LYS A 226 GLU A 231 5 6 HELIX 8 AA8 VAL A 232 HIS A 239 1 8 HELIX 9 AA9 ASP A 242 ALA A 253 1 12 HELIX 10 AB1 LEU A 288 ILE A 303 1 16 HELIX 11 AB2 SER A 449 ALA A 463 1 15 HELIX 12 AB3 LEU A 495 ALA A 505 1 11 HELIX 13 AB4 SER A 585 PHE A 599 1 15 HELIX 14 AB5 LYS A 610 GLU A 614 5 5 HELIX 15 AB6 GLY A 636 GLY A 638 5 3 HELIX 16 AB7 SER A 736 THR A 738 5 3 SHEET 1 AA1 5 GLN A 27 LEU A 34 0 SHEET 2 AA1 5 THR A 16 ASP A 22 -1 N ASP A 22 O GLN A 27 SHEET 3 AA1 5 LEU A 5 ASP A 10 -1 N GLY A 8 O ALA A 19 SHEET 4 AA1 5 LYS A 311 VAL A 313 1 O VAL A 313 N ILE A 9 SHEET 5 AA1 5 ILE A 470 GLU A 471 1 O GLU A 471 N VAL A 312 SHEET 1 AA2 3 SER A 560 LYS A 562 0 SHEET 2 AA2 3 ILE A 565 MET A 571 -1 O ILE A 565 N LYS A 562 SHEET 3 AA2 3 SER A 627 SER A 631 -1 O LEU A 628 N PHE A 570 SHEET 1 AA3 2 MET A 640 ILE A 643 0 SHEET 2 AA3 2 ASN A 646 LYS A 649 -1 O ASN A 646 N ILE A 643 SHEET 1 AA4 3 LYS A 666 LYS A 673 0 SHEET 2 AA4 3 ASN A 654 ASP A 662 -1 N GLY A 656 O ARG A 672 SHEET 3 AA4 3 ARG A 691 LEU A 696 -1 O LEU A 696 N VAL A 657 SHEET 1 AA5 5 ARG A 733 THR A 734 0 SHEET 2 AA5 5 THR A 721 ALA A 724 -1 N ILE A 722 O ARG A 733 SHEET 3 AA5 5 ILE A 710 LYS A 715 -1 N ARG A 712 O GLU A 723 SHEET 4 AA5 5 MET A 701 VAL A 704 -1 N VAL A 702 O TYR A 711 SHEET 5 AA5 5 LEU A 740 LYS A 742 -1 O THR A 741 N THR A 703 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