HEADER DNA BINDING PROTEIN/RNA/DNA 29-SEP-25 9WZR TITLE PMCAS12M-CRRNA-TARGET DNA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSPOSASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: RNA; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA(TS); COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 4; COMPND 14 MOLECULE: DNA(NTS); COMPND 15 CHAIN: D; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PELOMICROBIUM METHYLOTROPHICUM; SOURCE 3 ORGANISM_TAXID: 2602750; SOURCE 4 GENE: FR698_00030; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: PELOMICROBIUM METHYLOTROPHICUM; SOURCE 10 ORGANISM_TAXID: 2602750; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: PELOMICROBIUM METHYLOTROPHICUM; SOURCE 14 ORGANISM_TAXID: 2602750; SOURCE 15 MOL_ID: 4; SOURCE 16 ORGANISM_SCIENTIFIC: PELOMICROBIUM METHYLOTROPHICUM; SOURCE 17 ORGANISM_TAXID: 2602750; SOURCE 18 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 19 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS CRISPR, DNA, RNA, CYRO-EM, COMPLEX, DNA BINDING PROTEIN/RNA/DNA, DNA KEYWDS 2 BINDING PROTEIN-RNA-DNA COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR J.MENG,Y.TAO REVDAT 1 23-SEP-26 9WZR 0 JRNL AUTH J.MENG,Y.TAO JRNL TITL STRUCTURE-GUIDED DISCOVERY AND ENGINEERING OF MINIATURE JRNL TITL 2 CRISPR-CAS12M FOR EPIGENOME EDITING JRNL REF NAT.STRUCT.MOL.BIOL. 2026 JRNL REFN ESSN 1545-9985 JRNL DOI 10.1038/S41594-026-01890-9 REMARK 2 REMARK 2 RESOLUTION. 3.21 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) : 3.210 REMARK 3 NUMBER OF PARTICLES : 155865 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 9WZR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 20-DEC-25. REMARK 100 THE DEPOSITION ID IS D_1300055642. 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 : PMCAS12M 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 : PROTEIN 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 GLACIOS REMARK 245 DETECTOR TYPE : TFS FALCON 4I (4K 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 : OTHER REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 4000.00 REMARK 245 ILLUMINATION MODE : OTHER REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : OTHER REMARK 245 ACCELERATION VOLTAGE (KV) : 200 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 LYS A 2 REMARK 465 ASN A 3 REMARK 465 ILE A 4 REMARK 465 ALA A 5 REMARK 465 VAL A 6 REMARK 465 GLN A 7 REMARK 465 THR A 8 REMARK 465 ASN A 9 REMARK 465 LYS A 10 REMARK 465 ALA A 11 REMARK 465 ALA A 12 REMARK 465 THR A 13 REMARK 465 GLY A 595 REMARK 465 PRO A 596 REMARK 465 ALA A 597 REMARK 465 ARG A 598 REMARK 465 ALA A 599 REMARK 465 VAL A 600 REMARK 465 GLU A 601 REMARK 465 A B -36 REMARK 465 U B -35 REMARK 465 C B -34 REMARK 465 A B -33 REMARK 465 C B -32 REMARK 465 A B -31 REMARK 465 A B 18 REMARK 465 G B 19 REMARK 465 A B 20 REMARK 465 DA C -8 REMARK 465 DT C -7 REMARK 465 DA C -6 REMARK 465 DC C -5 REMARK 465 DG C -4 REMARK 465 DT C -3 REMARK 465 DT C -2 REMARK 465 DC C -1 REMARK 465 DT C 0 REMARK 465 DA D 20 REMARK 465 DA D 21 REMARK 465 DC D 22 REMARK 465 DG D 23 REMARK 465 DT D 24 REMARK 465 DA D 25 REMARK 465 DT D 26 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 ARG A 98 -4.35 69.38 REMARK 500 LYS A 100 -4.71 68.23 REMARK 500 GLN A 137 41.42 -107.53 REMARK 500 SER A 281 72.19 52.34 REMARK 500 ASP A 396 26.99 48.12 REMARK 500 ALA A 420 109.59 -48.15 REMARK 500 PRO A 436 45.71 -79.43 REMARK 500 ALA A 526 70.69 53.07 REMARK 500 ALA A 557 -60.69 -91.65 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 701 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 327 ND2 REMARK 620 2 ASP A 581 OD1 100.6 REMARK 620 3 DA D 14 OP2 100.1 115.9 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-66405 RELATED DB: EMDB REMARK 900 STRUCTURE FOR PMCAS12M DBREF1 9WZR A 1 601 UNP A0A5C7EM61_9PROT DBREF2 9WZR A A0A5C7EM61 1 601 DBREF 9WZR B -36 20 PDB 9WZR 9WZR -36 20 DBREF 9WZR C -8 27 PDB 9WZR 9WZR -8 27 DBREF 9WZR D -10 26 PDB 9WZR 9WZR -10 26 SEQRES 1 A 601 MET LYS ASN ILE ALA VAL GLN THR ASN LYS ALA ALA THR SEQRES 2 A 601 GLU SER ALA VAL THR VAL PHE ARG TYR GLY LEU LEU ALA SEQRES 3 A 601 PRO ILE ASN TRP GLY ARG ASP VAL GLU ASP GLU LEU TYR SEQRES 4 A 601 ARG MET ASN ALA LEU TRP ASN LYS LEU VAL GLU ILE GLU SEQRES 5 A 601 ARG ALA ASN ARG GLU ARG TYR ARG GLU ILE ILE SER THR SEQRES 6 A 601 SER PRO ALA LEU SER GLU VAL SER GLU ARG ILE GLU ALA SEQRES 7 A 601 LEU HIS ARG GLU ARG GLU ASP LEU ILE ALA GLU ARG LYS SEQRES 8 A 601 ARG ARG ARG ALA SER ALA ARG SER LYS SER LYS ALA ASP SEQRES 9 A 601 THR ALA ASP LEU ASP GLU ARG ILE LYS ALA ILE LYS ALA SEQRES 10 A 601 GLU LEU ALA PRO LEU TYR GLU GLN ARG LYS SER LEU ALA SEQRES 11 A 601 ALA GLU ALA ARG GLU GLN GLN LYS PRO LEU LEU ASP ALA SEQRES 12 A 601 LEU GLU ALA GLU ARG ARG GLU ALA VAL LYS ALA ALA ARG SEQRES 13 A 601 GLN SER SER GLY CYS PHE TRP PRO ASN TYR ASN ALA VAL SEQRES 14 A 601 ILE ALA SER TYR GLU ILE ALA ARG LYS ARG ALA MET LYS SEQRES 15 A 601 THR GLY ALA ASP LEU ARG PHE ARG ARG PHE SER ARG GLU SEQRES 16 A 601 GLY ARG LEU VAL ASN GLN ILE GLN GLY GLY MET SER VAL SEQRES 17 A 601 GLU ASP LEU PHE SER CYS ARG HIS SER GLN VAL GLY ILE SEQRES 18 A 601 ARG LEU GLY GLY GLN SER ARG GLY ARG GLN THR GLY THR SEQRES 19 A 601 LEU TYR VAL THR ALA TYR THR GLY ARG ASP GLU SER GLY SEQRES 20 A 601 ARG ARG ILE ARG ARG ASN VAL GLU PHE PRO ILE ILE LEU SEQRES 21 A 601 HIS ARG PRO PHE PRO LYS ASP ALA VAL ILE LYS GLU VAL SEQRES 22 A 601 ALA VAL ASN ILE ARG ARG ARG SER PRO SER VAL VAL SER SEQRES 23 A 601 GLY GLN THR GLU THR ASP ASP GLY ARG ILE ILE GLU TYR SEQRES 24 A 601 GLY GLU ALA GLU TYR SER VAL ALA PHE THR CYS GLN THR SEQRES 25 A 601 PRO ALA PRO GLU LYS SER ALA GLY SER SER ALA ALA GLY SEQRES 26 A 601 ILE ASN ILE GLY TRP LYS ARG VAL SER GLY GLY LEU ARG SEQRES 27 A 601 VAL ALA THR ALA ALA PHE HIS ASP GLY THR PHE GLU HIS SEQRES 28 A 601 LEU ILE LEU PRO ASP GLU TRP VAL LYS LYS TYR GLU ARG SEQRES 29 A 601 VAL GLN ALA LEU ARG SER GLY ILE ASP ASP ALA ASP ASN SEQRES 30 A 601 GLU MET HIS ALA ALA LEU ARG GLN ALA LEU GLN GLY MET SEQRES 31 A 601 PRO LEU TRP GLU ARG ASP GLY PRO MET VAL GLU GLY LEU SEQRES 32 A 601 SER ASP SER ASP HIS ARG LEU LEU SER ALA ILE LYS ARG SEQRES 33 A 601 ALA PRO ARG ALA PRO GLY ARG ALA MET ASP ALA LEU ALA SEQRES 34 A 601 TRP ARG LEU LYS GLU THR PRO ASN MET PRO PHE VAL ALA SEQRES 35 A 601 ASP LEU GLY ALA THR ILE GLU ALA TRP ARG LYS ALA ARG SEQRES 36 A 601 LYS ARG MET ILE LEU GLU MET ASP ASN LEU ARG GLY LYS SEQRES 37 A 601 LEU LEU ALA ARG ARG LYS ASP LEU TYR ARG THR PHE ALA SEQRES 38 A 601 ALA ARG ILE ALA ALA TYR ALA GLY ALA ILE ALA ILE ASP SEQRES 39 A 601 ASP THR ASP TYR ARG GLN ALA ALA LEU VAL GLU ARG THR SEQRES 40 A 601 ASP GLY GLU ASP LEU GLU LEU HIS GLU GLN ALA ARG ARG SEQRES 41 A 601 GLN ARG VAL MET ALA ALA PRO TYR GLU LEU ARG LEU ALA SEQRES 42 A 601 ILE GLU GLN ALA ALA ALA LYS ARG GLY GLY TYR VAL GLU SEQRES 43 A 601 ARG HIS ARG GLY SER VAL ASN HIS CYS ARG ALA CYS ARG SEQRES 44 A 601 SER ARG ASN VAL SER GLY ASP ILE ALA ARG HIS CYS HIS SEQRES 45 A 601 ALA CYS GLY ALA VAL PHE ASP VAL ASP GLU ASN ALA ALA SEQRES 46 A 601 LEU ASN LEU LEU HIS THR LEU ILE ALA GLY PRO ALA ARG SEQRES 47 A 601 ALA VAL GLU SEQRES 1 B 56 A U C A C A A A G C C U G SEQRES 2 B 56 C U C C G C G G C U U G G SEQRES 3 B 56 U A G U G G A G A C C U C SEQRES 4 B 56 C C U A U C A G U G A U A SEQRES 5 B 56 G A G A SEQRES 1 C 36 DA DT DA DC DG DT DT DC DT DC DT DA DT SEQRES 2 C 36 DC DA DC DT DG DA DT DA DG DG DG DA DG SEQRES 3 C 36 DT DA DA DA DG DT DC DT DG DC SEQRES 1 D 36 DG DC DA DG DA DC DT DT DT DA DC DT DC SEQRES 2 D 36 DC DC DT DA DT DC DA DG DT DG DA DT DA SEQRES 3 D 36 DG DA DG DA DA DC DG DT DA DT HET MG A 701 1 HETNAM MG MAGNESIUM ION FORMUL 5 MG MG 2+ HELIX 1 AA1 GLY A 31 SER A 64 1 34 HELIX 2 AA2 SER A 66 ARG A 98 1 33 HELIX 3 AA3 THR A 105 GLN A 137 1 33 HELIX 4 AA4 GLN A 137 SER A 158 1 22 HELIX 5 AA5 PHE A 162 GLY A 184 1 23 HELIX 6 AA6 VAL A 208 SER A 213 1 6 HELIX 7 AA7 PRO A 355 LEU A 387 1 33 HELIX 8 AA8 SER A 404 ALA A 417 1 14 HELIX 9 AA9 PRO A 421 LYS A 433 1 13 HELIX 10 AB1 LEU A 444 ALA A 488 1 45 HELIX 11 AB2 ASP A 497 LEU A 503 1 7 HELIX 12 AB3 HIS A 515 ALA A 526 1 12 HELIX 13 AB4 ALA A 526 ARG A 541 1 16 HELIX 14 AB5 VAL A 580 ALA A 594 1 15 SHEET 1 AA1 7 GLY A 196 SER A 207 0 SHEET 2 AA1 7 VAL A 269 GLU A 290 -1 O ILE A 270 N MET A 206 SHEET 3 AA1 7 ARG A 295 PRO A 313 -1 O GLU A 301 N ARG A 280 SHEET 4 AA1 7 SER A 15 LEU A 24 -1 N THR A 18 O CYS A 310 SHEET 5 AA1 7 ARG A 252 LEU A 260 -1 O ILE A 259 N GLY A 23 SHEET 6 AA1 7 ARG A 230 TYR A 240 -1 N LEU A 235 O PHE A 256 SHEET 7 AA1 7 GLY A 220 SER A 227 -1 N SER A 227 O ARG A 230 SHEET 1 AA2 5 PHE A 349 LEU A 354 0 SHEET 2 AA2 5 GLY A 336 PHE A 344 -1 N LEU A 337 O LEU A 354 SHEET 3 AA2 5 ALA A 323 VAL A 333 -1 N ASN A 327 O THR A 341 SHEET 4 AA2 5 ALA A 490 ASP A 494 1 O ALA A 492 N ILE A 326 SHEET 5 AA2 5 TYR A 544 HIS A 548 1 O GLU A 546 N ILE A 491 SHEET 1 AA3 3 VAL A 563 SER A 564 0 SHEET 2 AA3 3 ALA A 568 CYS A 571 -1 O HIS A 570 N SER A 564 SHEET 3 AA3 3 VAL A 577 ASP A 579 -1 O PHE A 578 N ARG A 569 LINK ND2 ASN A 327 MG MG A 701 1555 1555 2.05 LINK OD1 ASP A 581 MG MG A 701 1555 1555 2.18 LINK MG MG A 701 OP2 DA D 14 1555 1555 2.70 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 2502 6761 CONECT 4508 6761 CONECT 6635 6761 CONECT 6761 2502 4508 6635 MASTER 187 0 1 14 15 0 0 6 6757 4 4 58 END