HEADER RNA BINDING PROTEIN 18-OCT-24 9K31 TITLE CRYO-EM STRUCTURE OF THE YNPSCAS9-GUIDE RNA-TARGET DNA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: YNPSCAS9; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: GUIDE RNA; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: TARGET DNA STRAND; COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 4; COMPND 14 MOLECULE: NON-TARGET DNA STRAND; COMPND 15 CHAIN: D; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METAGENOME; SOURCE 3 ORGANISM_TAXID: 256318; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: METAGENOME; SOURCE 8 ORGANISM_TAXID: 256318; SOURCE 9 EXPRESSION_SYSTEM: EXPRESSION VECTOR PET-MOD; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 1685505; 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 RNA-GUIDED DNA NUCLEASE, RNA BINDING PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR N.NAGAHATA,S.YAMADA,K.YAMASHITA,H.NISHIMASU REVDAT 1 04-FEB-26 9K31 0 JRNL AUTH N.NAGAHATA JRNL TITL CRYO-EM STRUCTURE OF THE YLCAS9-GUIDE RNA-TARGET DNA COMPLEX JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.38 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, CRYOSPARC, SERVALCAT, REMARK 3 CRYOSPARC, CRYOSPARC, CRYOSPARC, REMARK 3 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) : 2.380 REMARK 3 NUMBER OF PARTICLES : 514345 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 9K31 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-OCT-24. REMARK 100 THE DEPOSITION ID IS D_1300052745. 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 : CRYO-EM STRUCTURE OF THE YLCAS9 REMARK 245 -GUIDE RNA-TARGET DNA COMPLEX 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 : 6.00 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 BIOQUANTUM (6K X REMARK 245 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 : 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, 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 -108 REMARK 465 GLY A -107 REMARK 465 HIS A -106 REMARK 465 HIS A -105 REMARK 465 HIS A -104 REMARK 465 HIS A -103 REMARK 465 HIS A -102 REMARK 465 HIS A -101 REMARK 465 GLY A -100 REMARK 465 SER A -99 REMARK 465 LEU A -98 REMARK 465 GLN A -97 REMARK 465 ASP A -96 REMARK 465 SER A -95 REMARK 465 GLU A -94 REMARK 465 VAL A -93 REMARK 465 ASN A -92 REMARK 465 GLN A -91 REMARK 465 GLU A -90 REMARK 465 ALA A -89 REMARK 465 LYS A -88 REMARK 465 PRO A -87 REMARK 465 GLU A -86 REMARK 465 VAL A -85 REMARK 465 LYS A -84 REMARK 465 PRO A -83 REMARK 465 GLU A -82 REMARK 465 VAL A -81 REMARK 465 LYS A -80 REMARK 465 PRO A -79 REMARK 465 GLU A -78 REMARK 465 THR A -77 REMARK 465 HIS A -76 REMARK 465 ILE A -75 REMARK 465 ASN A -74 REMARK 465 LEU A -73 REMARK 465 LYS A -72 REMARK 465 VAL A -71 REMARK 465 SER A -70 REMARK 465 ASP A -69 REMARK 465 GLY A -68 REMARK 465 SER A -67 REMARK 465 SER A -66 REMARK 465 GLU A -65 REMARK 465 ILE A -64 REMARK 465 PHE A -63 REMARK 465 PHE A -62 REMARK 465 LYS A -61 REMARK 465 ILE A -60 REMARK 465 LYS A -59 REMARK 465 LYS A -58 REMARK 465 THR A -57 REMARK 465 THR A -56 REMARK 465 PRO A -55 REMARK 465 LEU A -54 REMARK 465 ARG A -53 REMARK 465 ARG A -52 REMARK 465 LEU A -51 REMARK 465 MET A -50 REMARK 465 GLU A -49 REMARK 465 ALA A -48 REMARK 465 PHE A -47 REMARK 465 ALA A -46 REMARK 465 LYS A -45 REMARK 465 ARG A -44 REMARK 465 GLN A -43 REMARK 465 GLY A -42 REMARK 465 LYS A -41 REMARK 465 GLU A -40 REMARK 465 MET A -39 REMARK 465 ASP A -38 REMARK 465 SER A -37 REMARK 465 LEU A -36 REMARK 465 ARG A -35 REMARK 465 PHE A -34 REMARK 465 LEU A -33 REMARK 465 TYR A -32 REMARK 465 ASP A -31 REMARK 465 GLY A -30 REMARK 465 ILE A -29 REMARK 465 ARG A -28 REMARK 465 ILE A -27 REMARK 465 GLN A -26 REMARK 465 ALA A -25 REMARK 465 ASP A -24 REMARK 465 GLN A -23 REMARK 465 ALA A -22 REMARK 465 PRO A -21 REMARK 465 GLU A -20 REMARK 465 ASP A -19 REMARK 465 LEU A -18 REMARK 465 ASP A -17 REMARK 465 MET A -16 REMARK 465 GLU A -15 REMARK 465 ASP A -14 REMARK 465 ASN A -13 REMARK 465 ASP A -12 REMARK 465 ILE A -11 REMARK 465 ILE A -10 REMARK 465 GLU A -9 REMARK 465 ALA A -8 REMARK 465 HIS A -7 REMARK 465 ARG A -6 REMARK 465 GLU A -5 REMARK 465 GLN A -4 REMARK 465 ILE A -3 REMARK 465 GLY A -2 REMARK 465 GLY A -1 REMARK 465 GLY A 0 REMARK 465 SER A 1 REMARK 465 ASN A 2 REMARK 465 THR A 3 REMARK 465 GLU A 4 REMARK 465 ARG A 670 REMARK 465 HIS A 671 REMARK 465 GLY A 672 REMARK 465 G B -21 REMARK 465 G B 17 REMARK 465 G B 18 REMARK 465 U B 19 REMARK 465 G B 20 REMARK 465 G B 21 REMARK 465 A B 22 REMARK 465 C B 23 REMARK 465 A B 24 REMARK 465 G B 25 REMARK 465 C B 26 REMARK 465 A B 27 REMARK 465 C B 28 REMARK 465 G B 29 REMARK 465 G B 30 REMARK 465 G B 31 REMARK 465 U B 32 REMARK 465 U B 33 REMARK 465 C B 34 REMARK 465 U B 35 REMARK 465 G B 36 REMARK 465 G B 37 REMARK 465 G B 38 REMARK 465 G B 39 REMARK 465 C B 40 REMARK 465 G B 41 REMARK 465 A B 42 REMARK 465 U B 43 REMARK 465 C B 44 REMARK 465 A B 45 REMARK 465 G B 46 REMARK 465 C B 47 REMARK 465 G B 48 REMARK 465 A B 49 REMARK 465 G B 50 REMARK 465 G B 51 REMARK 465 G B 52 REMARK 465 G B 53 REMARK 465 A B 54 REMARK 465 G B 55 REMARK 465 C B 56 REMARK 465 G B 57 REMARK 465 A B 58 REMARK 465 G B 59 REMARK 465 G B 60 REMARK 465 G B 61 REMARK 465 C B 62 REMARK 465 G B 63 REMARK 465 C B 64 REMARK 465 G B 65 REMARK 465 C B 66 REMARK 465 G B 67 REMARK 465 A B 68 REMARK 465 G B 69 REMARK 465 G B 70 REMARK 465 A B 71 REMARK 465 A B 72 REMARK 465 U B 73 REMARK 465 G B 74 REMARK 465 A B 75 REMARK 465 G B 76 REMARK 465 U B 77 REMARK 465 U B 78 REMARK 465 G B 79 REMARK 465 G B 80 REMARK 465 G B 81 REMARK 465 G B 82 REMARK 465 A B 83 REMARK 465 C B 84 REMARK 465 G B 85 REMARK 465 C B 86 REMARK 465 A B 87 REMARK 465 G B 88 REMARK 465 U B 89 REMARK 465 A B 90 REMARK 465 G B 91 REMARK 465 G B 92 REMARK 465 U B 93 REMARK 465 A B 94 REMARK 465 U B 95 REMARK 465 G B 96 REMARK 465 U B 97 REMARK 465 A B 98 REMARK 465 U B 99 REMARK 465 A B 100 REMARK 465 G B 101 REMARK 465 G B 102 REMARK 465 U B 103 REMARK 465 U B 104 REMARK 465 U B 105 REMARK 465 C B 106 REMARK 465 C B 107 REMARK 465 A B 108 REMARK 465 C B 109 REMARK 465 C B 110 REMARK 465 C B 145 REMARK 465 C B 146 REMARK 465 G B 147 REMARK 465 C B 148 REMARK 465 C B 149 REMARK 465 C B 150 REMARK 465 A B 151 REMARK 465 U B 152 REMARK 465 G B 153 REMARK 465 G B 154 REMARK 465 C B 155 REMARK 465 G B 156 REMARK 465 G B 306 REMARK 465 C B 307 REMARK 465 C B 308 REMARK 465 U B 309 REMARK 465 C B 310 REMARK 465 U B 311 REMARK 465 G B 312 REMARK 465 G B 313 REMARK 465 C B 314 REMARK 465 G B 393 REMARK 465 A B 394 REMARK 465 A B 395 REMARK 465 C B 396 REMARK 465 A B 397 REMARK 465 A B 398 REMARK 465 DA C 25 REMARK 465 DT C 26 REMARK 465 DC C 27 REMARK 465 DC C 28 REMARK 465 DT C 29 REMARK 465 DC C 30 REMARK 465 DT C 31 REMARK 465 DA D -31 REMARK 465 DG D -30 REMARK 465 DA D -29 REMARK 465 DG D -28 REMARK 465 DG D -27 REMARK 465 DA D -26 REMARK 465 DT D -25 REMARK 465 DG D -20 REMARK 465 DG D -19 REMARK 465 DG D -18 REMARK 465 DT D -17 REMARK 465 DT D -16 REMARK 465 DT D -15 REMARK 465 DA D -14 REMARK 465 DA D -13 REMARK 465 DT D -12 REMARK 465 DC D -11 REMARK 465 DC D -10 REMARK 465 DA D -3 REMARK 465 DC D -2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DA C -11 P DA C -11 OP3 -0.087 REMARK 500 REMARK 500 REMARK: NULL 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 G B -8 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 DG D 2 O4' - C1' - N9 ANGL. DEV. = 2.6 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 ALA A 13 77.51 -105.08 REMARK 500 LYS A 17 -48.97 -130.72 REMARK 500 ALA A 28 -120.28 52.35 REMARK 500 ASP A 43 34.75 -147.89 REMARK 500 VAL A 266 -58.20 -121.73 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 ZN A 703 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 107 SG REMARK 620 2 CYS A 118 SG 103.6 REMARK 620 3 CYS A 227 SG 113.8 118.4 REMARK 620 4 HIS A 230 ND1 117.9 110.6 93.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 702 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 323 SG REMARK 620 2 CYS A 326 SG 100.0 REMARK 620 3 CYS A 358 SG 114.7 116.6 REMARK 620 4 CYS A 361 SG 114.7 115.1 96.7 REMARK 620 N 1 2 3 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 GLU A 341 OE2 REMARK 620 2 ASN A 362 OD1 87.3 REMARK 620 3 DC C 2 O3' 151.4 78.5 REMARK 620 4 DA C 3 OP1 93.7 87.9 61.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A B 127 OP1 REMARK 620 2 U B 380 OP1 91.5 REMARK 620 3 HOH B 509 O 89.8 90.1 REMARK 620 4 HOH B 514 O 179.1 89.3 90.5 REMARK 620 5 HOH B 516 O 90.0 89.7 179.7 89.7 REMARK 620 6 HOH B 517 O 89.5 179.0 89.9 89.7 90.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A B 127 OP2 REMARK 620 2 HOH B 502 O 179.2 REMARK 620 3 HOH B 512 O 89.2 90.1 REMARK 620 4 HOH B 513 O 89.3 90.4 91.1 REMARK 620 5 HOH B 518 O 90.6 90.2 179.3 89.5 REMARK 620 6 HOH B 519 O 90.8 89.5 89.5 179.4 89.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C B 129 OP1 REMARK 620 2 HOH B 501 O 88.9 REMARK 620 3 HOH B 503 O 91.6 178.7 REMARK 620 4 HOH B 508 O 90.6 89.7 89.1 REMARK 620 5 HOH B 515 O 89.1 91.2 90.1 179.1 REMARK 620 6 HOH B 521 O 178.1 89.4 90.0 90.4 90.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 404 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 504 O REMARK 620 2 HOH B 505 O 90.0 REMARK 620 3 HOH B 506 O 89.4 179.3 REMARK 620 4 HOH B 507 O 90.0 89.7 90.7 REMARK 620 5 HOH B 510 O 90.3 90.1 89.5 179.6 REMARK 620 6 HOH B 520 O 179.3 90.5 90.1 89.5 90.2 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-62003 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF THE YLCAS9-GUIDE RNA-TARGET DNA COMPLEX DBREF 9K31 A -108 672 PDB 9K31 9K31 -108 672 DBREF 9K31 B -21 398 PDB 9K31 9K31 -21 398 DBREF 9K31 C -11 31 PDB 9K31 9K31 -11 31 DBREF 9K31 D -31 11 PDB 9K31 9K31 -31 11 SEQRES 1 A 781 MET GLY HIS HIS HIS HIS HIS HIS GLY SER LEU GLN ASP SEQRES 2 A 781 SER GLU VAL ASN GLN GLU ALA LYS PRO GLU VAL LYS PRO SEQRES 3 A 781 GLU VAL LYS PRO GLU THR HIS ILE ASN LEU LYS VAL SER SEQRES 4 A 781 ASP GLY SER SER GLU ILE PHE PHE LYS ILE LYS LYS THR SEQRES 5 A 781 THR PRO LEU ARG ARG LEU MET GLU ALA PHE ALA LYS ARG SEQRES 6 A 781 GLN GLY LYS GLU MET ASP SER LEU ARG PHE LEU TYR ASP SEQRES 7 A 781 GLY ILE ARG ILE GLN ALA ASP GLN ALA PRO GLU ASP LEU SEQRES 8 A 781 ASP MET GLU ASP ASN ASP ILE ILE GLU ALA HIS ARG GLU SEQRES 9 A 781 GLN ILE GLY GLY GLY SER ASN THR GLU THR ARG GLU GLN SEQRES 10 A 781 VAL LEU GLY ILE ALA PHE GLY PRO LYS HIS VAL GLY ILE SEQRES 11 A 781 ALA LEU VAL ALA ARG GLY ALA SER SER GLU GLU VAL LEU SEQRES 12 A 781 PHE VAL ALA GLU VAL ARG LEU ARG ASP ARG LYS SER LEU SEQRES 13 A 781 LEU ALA ASP ARG ARG ALA LEU ARG ARG GLY ARG ARG GLY SEQRES 14 A 781 ARG LYS ARG TYR ARG GLN PRO LYS ILE PRO GLN ARG GLY SEQRES 15 A 781 GLY GLY ALA THR SER GLN SER GLY GLU GLU SER GLU ARG SEQRES 16 A 781 GLY ARG ALA ALA ALA PRO GLU TYR ARG ARG ALA THR GLY SEQRES 17 A 781 LEU ASN THR GLY ARG ARG ARG CYS LYS PHE VAL ASP PRO SEQRES 18 A 781 GLN THR GLY GLU ILE CYS GLY TRP ASN THR PRO ARG LYS SEQRES 19 A 781 ALA ASN VAL ARG ASP LEU LEU LEU TRP ASN ILE CYS ARG SEQRES 20 A 781 HIS LEU PRO VAL SER VAL SER GLU GLN ALA GLY PHE LEU SEQRES 21 A 781 ALA TYR VAL ASN GLN THR ASN LEU HIS ARG ALA GLU ILE SEQRES 22 A 781 LEU GLY ALA LEU PRO ALA GLU GLU GLN ALA PRO LEU GLU SEQRES 23 A 781 ALA VAL PHE SER GLN GLN ARG ARG PRO LYS ASP GLU ARG SEQRES 24 A 781 LEU LYS ASP ARG LEU ARG ARG LEU GLY VAL ASP ARG HIS SEQRES 25 A 781 LEU ARG SER GLN VAL THR ASP ILE VAL GLY ILE THR SER SEQRES 26 A 781 ARG ARG PRO LEU SER GLY ARG LEU SER PHE CYS ARG GLU SEQRES 27 A 781 HIS PHE LEU ARG HIS HIS GLU GLN SER ARG VAL PRO ARG SEQRES 28 A 781 PRO SER VAL TRP LEU PRO ASN THR VAL GLU MET LYS GLN SEQRES 29 A 781 ALA ASP VAL LEU LYS VAL CYS ARG GLN GLU VAL ALA PRO SEQRES 30 A 781 ARG TRP ARG VAL ASP CYS ILE VAL LEU GLU ARG ALA ASN SEQRES 31 A 781 PHE ASP LEU GLN LEU LEU ARG GLN GLN THR ALA ILE GLU SEQRES 32 A 781 TRP SER VAL GLU ASP TRP GLN ARG GLY PRO ARG TRP GLY SEQRES 33 A 781 TYR ARG ASN THR PHE GLU ALA LYS LYS GLN GLU GLN GLY SEQRES 34 A 781 ASN ARG CYS ALA TYR CYS GLY SER LYS PRO THR ALA LYS SEQRES 35 A 781 ASN ARG LEU ARG LEU GLU LEU GLU ALA VAL ILE PRO GLY SEQRES 36 A 781 GLY GLY ASP THR TRP GLU ASN LEU VAL LEU SER CYS ARG SEQRES 37 A 781 LYS CYS ASN GLU GLY LYS GLY ASN ARG SER PRO ALA GLN SEQRES 38 A 781 ALA GLY MET ARG PHE TRP THR ASP THR GLU THR GLY GLU SEQRES 39 A 781 THR LEU SER PRO ALA PRO LEU GLY ALA ALA HIS VAL SER SEQRES 40 A 781 ARG TYR MET THR GLN THR ASP GLN GLY TRP ARG ARG LEU SEQRES 41 A 781 GLN ALA ALA LEU GLN GLN VAL PHE PRO GLN ALA ALA VAL SEQRES 42 A 781 GLU HIS THR TRP GLY TYR VAL THR SER PHE TYR ARG ASN SEQRES 43 A 781 ARG TRP ASN LEU PRO LYS LYS HIS PHE VAL ASP ALA ALA SEQRES 44 A 781 VAL ILE ALA SER SER HIS GLU LEU GLU ARG PRO VAL SER SEQRES 45 A 781 VAL PRO GLU GLN PRO GLN ARG PHE ALA PRO THR SER GLY SEQRES 46 A 781 GLY LYS GLN LEU PHE ASP THR ASN PRO LEU SER LYS ARG SEQRES 47 A 781 PRO GLU GLY ARG PHE ALA GLN SER LYS ALA ILE VAL CYS SEQRES 48 A 781 GLU GLN GLY THR LEU ALA PHE LYS ASP VAL ALA LYS VAL SEQRES 49 A 781 GLU ASN PRO ARG LYS ARG ALA THR LEU GLN ARG VAL ALA SEQRES 50 A 781 ASP GLU ALA THR ALA ALA ALA LYS ALA ARG GLY GLU THR SEQRES 51 A 781 PRO PRO THR ALA PHE THR ALA GLU MET LEU PRO LYS ILE SEQRES 52 A 781 PRO PHE LYS SER VAL ARG LEU ALA LYS GLN ASP ALA SER SEQRES 53 A 781 ASP THR ASN THR ARG ARG LEU GLY ARG HIS TRP PHE LYS SEQRES 54 A 781 VAL ALA SER ALA VAL ASN ILE ALA THR ILE VAL TYR GLN SEQRES 55 A 781 LEU ASP GLY LYS VAL CYS MET GLN LEU GLN ARG ASN PRO SEQRES 56 A 781 ALA VAL PHE ARG HIS ASP PRO GLY LEU PRO GLN GLY ALA SEQRES 57 A 781 ARG VAL VAL ALA THR PHE ARG LYS GLY ASP LEU VAL GLU SEQRES 58 A 781 CYS ASP ALA GLY ARG GLY ARG VAL THR LYS ASN HIS SER SEQRES 59 A 781 ASN CYS THR LEU THR VAL GLU LEU LEU ASP SER GLY LYS SEQRES 60 A 781 GLU VAL THR ARG LEU ALA LYS SER PHE ARG PRO ARG HIS SEQRES 61 A 781 GLY SEQRES 1 B 420 G G G G A A A U U A G G U SEQRES 2 B 420 G C G C U U G G C A U U U SEQRES 3 B 420 C G C C C U C G C A U U G SEQRES 4 B 420 G U G G A C A G C A C G G SEQRES 5 B 420 G U U C U G G G G C G A U SEQRES 6 B 420 C A G C G A G G G G A G C SEQRES 7 B 420 G A G G G C G C G C G A G SEQRES 8 B 420 G A A U G A G U U G G G G SEQRES 9 B 420 A C G C A G U A G G U A U SEQRES 10 B 420 G U A U A G G U U U C C A SEQRES 11 B 420 C C A G U G U U G A A G G SEQRES 12 B 420 G C G A A A G C A G C C C SEQRES 13 B 420 A G C C A A G U C U C C G SEQRES 14 B 420 C C C A U G G C G G A G C SEQRES 15 B 420 A C G G G A A A C C G G U SEQRES 16 B 420 G G G G A A A C C C G G C SEQRES 17 B 420 C G G C C A C C G U A A G SEQRES 18 B 420 G A G G C A C G U U U G G SEQRES 19 B 420 G G A A C A G G U A G G G SEQRES 20 B 420 G U A A C C C U G A G U G SEQRES 21 B 420 C A A C C U G G G G U G C SEQRES 22 B 420 A C C U U C A G C U C C A SEQRES 23 B 420 G G C U C U G C A A G G C SEQRES 24 B 420 U C G G C C C A G A G G A SEQRES 25 B 420 U U A A C G C C C U A A U SEQRES 26 B 420 C C G C C U C U G G C G G SEQRES 27 B 420 A A G G G A G A G A A A G SEQRES 28 B 420 G C G G U C G U G A G G C SEQRES 29 B 420 C G C A A G G C A A G C C SEQRES 30 B 420 G A G C C A U A C U C C U SEQRES 31 B 420 G U A C C C A A A C C U G SEQRES 32 B 420 A G C G G G A A G G A G A SEQRES 33 B 420 A C A A SEQRES 1 C 43 DA DC DC DC DG DT DT DC DC DC DC DG DC SEQRES 2 C 43 DC DA DA DG DC DG DC DA DC DC DT DA DA SEQRES 3 C 43 DT DT DT DC DC DC DC DG DG DG DA DT DC SEQRES 4 C 43 DC DT DC DT SEQRES 1 D 43 DA DG DA DG DG DA DT DC DC DC DG DG DG SEQRES 2 D 43 DG DT DT DT DA DA DT DC DC DA DC DG DC SEQRES 3 D 43 DG DA DA DC DC DG DG DG DG DG DA DA DC SEQRES 4 D 43 DG DG DG DT HET MG A 701 1 HET ZN A 702 1 HET ZN A 703 1 HET MG B 401 1 HET MG B 402 1 HET MG B 403 1 HET MG B 404 1 HETNAM MG MAGNESIUM ION HETNAM ZN ZINC ION FORMUL 5 MG 5(MG 2+) FORMUL 6 ZN 2(ZN 2+) FORMUL 12 HOH *22(H2 O) HELIX 1 AA1 SER A 46 GLY A 60 1 15 HELIX 2 AA2 GLY A 73 THR A 77 5 5 HELIX 3 AA3 ARG A 124 ASN A 127 5 4 HELIX 4 AA4 VAL A 128 ARG A 138 1 11 HELIX 5 AA5 SER A 143 PHE A 150 1 8 HELIX 6 AA6 LEU A 151 VAL A 154 5 4 HELIX 7 AA7 ARG A 161 ALA A 167 1 7 HELIX 8 AA8 PRO A 169 PHE A 180 1 12 HELIX 9 AA9 ARG A 190 LEU A 198 1 9 HELIX 10 AB1 ASP A 201 GLY A 213 1 13 HELIX 11 AB2 HIS A 230 GLN A 237 5 8 HELIX 12 AB3 PRO A 248 VAL A 266 1 19 HELIX 13 AB4 GLN A 285 ALA A 292 1 8 HELIX 14 AB5 GLU A 298 ARG A 302 5 5 HELIX 15 AB6 ASN A 310 GLY A 320 1 11 HELIX 16 AB7 THR A 350 GLU A 352 5 3 HELIX 17 AB8 CYS A 358 GLY A 366 1 9 HELIX 18 AB9 VAL A 397 GLN A 406 1 10 HELIX 19 AC1 GLY A 407 PHE A 419 1 13 HELIX 20 AC2 TRP A 428 ASN A 440 1 13 HELIX 21 AC3 LYS A 444 ALA A 453 1 10 HELIX 22 AC4 PHE A 509 VAL A 515 5 7 HELIX 23 AC5 ASN A 517 GLY A 539 1 23 HELIX 24 AC6 THR A 547 ILE A 554 5 8 SHEET 1 AA1 6 ALA A 423 GLU A 425 0 SHEET 2 AA1 6 CYS A 274 LEU A 277 1 N ILE A 275 O ALA A 423 SHEET 3 AA1 6 GLU A 7 ALA A 13 1 N LEU A 10 O VAL A 276 SHEET 4 AA1 6 HIS A 18 GLY A 27 -1 O GLY A 20 N ALA A 13 SHEET 5 AA1 6 SER A 30 ARG A 40 -1 O PHE A 35 N LEU A 23 SHEET 6 AA1 6 GLN A 469 PHE A 471 1 O PHE A 471 N ARG A 40 SHEET 1 AA2 2 GLU A 339 ALA A 342 0 SHEET 2 AA2 2 LEU A 354 SER A 357 -1 O VAL A 355 N GLU A 341 SHEET 1 AA3 3 SER A 487 LYS A 488 0 SHEET 2 AA3 3 PHE A 494 ALA A 499 -1 O ALA A 495 N SER A 487 SHEET 3 AA3 3 SER A 558 ALA A 562 -1 O VAL A 559 N LYS A 498 SHEET 1 AA4 2 THR A 571 LEU A 574 0 SHEET 2 AA4 2 HIS A 577 LYS A 580 -1 O HIS A 577 N LEU A 574 SHEET 1 AA5 3 LYS A 597 ARG A 604 0 SHEET 2 AA5 3 ASN A 586 LEU A 594 -1 N ALA A 588 O GLN A 603 SHEET 3 AA5 3 ARG A 620 PHE A 625 -1 O ARG A 620 N GLN A 593 SHEET 1 AA6 4 LEU A 630 GLU A 632 0 SHEET 2 AA6 4 ARG A 637 ASN A 643 -1 O GLY A 638 N VAL A 631 SHEET 3 AA6 4 THR A 648 LEU A 653 -1 O THR A 650 N THR A 641 SHEET 4 AA6 4 GLU A 659 LEU A 663 -1 O ARG A 662 N LEU A 649 LINK SG CYS A 107 ZN ZN A 703 1555 1555 2.32 LINK SG CYS A 118 ZN ZN A 703 1555 1555 2.33 LINK SG CYS A 227 ZN ZN A 703 1555 1555 2.31 LINK ND1 HIS A 230 ZN ZN A 703 1555 1555 2.11 LINK SG CYS A 323 ZN ZN A 702 1555 1555 2.34 LINK SG CYS A 326 ZN ZN A 702 1555 1555 2.33 LINK OE2 GLU A 341 MG MG A 701 1555 1555 2.23 LINK SG CYS A 358 ZN ZN A 702 1555 1555 2.34 LINK SG CYS A 361 ZN ZN A 702 1555 1555 2.35 LINK OD1 ASN A 362 MG MG A 701 1555 1555 2.10 LINK MG MG A 701 O3' DC C 2 1555 1555 2.63 LINK MG MG A 701 OP1 DA C 3 1555 1555 2.29 LINK OP1 A B 127 MG MG B 401 1555 1555 2.09 LINK OP2 A B 127 MG MG B 402 1555 1555 2.05 LINK OP1 C B 129 MG MG B 403 1555 1555 2.07 LINK OP1 U B 380 MG MG B 401 1555 1555 2.07 LINK MG MG B 401 O HOH B 509 1555 1555 2.07 LINK MG MG B 401 O HOH B 514 1555 1555 2.07 LINK MG MG B 401 O HOH B 516 1555 1555 2.06 LINK MG MG B 401 O HOH B 517 1555 1555 2.06 LINK MG MG B 402 O HOH B 502 1555 1555 2.07 LINK MG MG B 402 O HOH B 512 1555 1555 2.05 LINK MG MG B 402 O HOH B 513 1555 1555 2.08 LINK MG MG B 402 O HOH B 518 1555 1555 2.07 LINK MG MG B 402 O HOH B 519 1555 1555 2.07 LINK MG MG B 403 O HOH B 501 1555 1555 2.04 LINK MG MG B 403 O HOH B 503 1555 1555 2.06 LINK MG MG B 403 O HOH B 508 1555 1555 2.07 LINK MG MG B 403 O HOH B 515 1555 1555 2.08 LINK MG MG B 403 O HOH B 521 1555 1555 2.07 LINK MG MG B 404 O HOH B 504 1555 1555 2.08 LINK MG MG B 404 O HOH B 505 1555 1555 2.07 LINK MG MG B 404 O HOH B 506 1555 1555 2.06 LINK MG MG B 404 O HOH B 507 1555 1555 2.05 LINK MG MG B 404 O HOH B 510 1555 1555 2.06 LINK MG MG B 404 O HOH B 520 1555 1555 2.06 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 80612906 CONECT 89112906 CONECT 177012906 CONECT 179712906 CONECT 259212905 CONECT 261512905 CONECT 273412904 CONECT 285412905 CONECT 288012905 CONECT 288712904 CONECT 642312907 CONECT 642412908 CONECT 646812909 CONECT1141012907 CONECT1196512904 CONECT1197712904 CONECT12904 2734 28871196511977 CONECT12905 2592 2615 2854 2880 CONECT12906 806 891 1770 1797 CONECT12907 6423114101291912924 CONECT129071292612927 CONECT12908 6424129121292212923 CONECT129081292812929 CONECT12909 6468129111291312918 CONECT129091292512931 CONECT1291012914129151291612917 CONECT129101292012930 CONECT1291112909 CONECT1291212908 CONECT1291312909 CONECT1291412910 CONECT1291512910 CONECT1291612910 CONECT1291712910 CONECT1291812909 CONECT1291912907 CONECT1292012910 CONECT1292212908 CONECT1292312908 CONECT1292412907 CONECT1292512909 CONECT1292612907 CONECT1292712907 CONECT1292812908 CONECT1292912908 CONECT1293012910 CONECT1293112909 MASTER 511 0 7 24 20 0 0 612928 4 47 102 END