HEADER DNA BINDING PROTEIN/DNA/RNA 22-FEB-24 9AR4 TITLE CRYOEM STRUCTURE OF THERMOCAS9 IN POST-CLEAVAGE STATE BOUND WITH THE TITLE 2 DNA CONTAINING NNNNCCA PAM COMPND MOL_ID: 1; COMPND 2 MOLECULE: SINGLE GUIDE RNA; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: CLEAVED 3' TARGET DNA STRAND; COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: CLEAVED 3' NON-TARGET DNA STRAND; COMPND 11 CHAIN: D; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 4; COMPND 14 MOLECULE: CLEAVED 5' TARGET DNA STRAND; COMPND 15 CHAIN: P; COMPND 16 ENGINEERED: YES; COMPND 17 MOL_ID: 5; COMPND 18 MOLECULE: CLEAVED 5' NON-TARGET DNA STRAND; COMPND 19 CHAIN: X; COMPND 20 ENGINEERED: YES; COMPND 21 MOL_ID: 6; COMPND 22 MOLECULE: CRISPR-ASSOCIATED ENDONUCLEASE CAS9; COMPND 23 CHAIN: A; COMPND 24 EC: 3.1.-.-; COMPND 25 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS THERMODENITRIFICANS; SOURCE 3 ORGANISM_TAXID: 33940; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 9 ORGANISM_TAXID: 32630; SOURCE 10 MOL_ID: 3; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630; SOURCE 14 MOL_ID: 4; SOURCE 15 SYNTHETIC: YES; SOURCE 16 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 17 ORGANISM_TAXID: 32630; SOURCE 18 MOL_ID: 5; SOURCE 19 SYNTHETIC: YES; SOURCE 20 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 21 ORGANISM_TAXID: 32630; SOURCE 22 MOL_ID: 6; SOURCE 23 ORGANISM_SCIENTIFIC: GEOBACILLUS THERMODENITRIFICANS; SOURCE 24 ORGANISM_TAXID: 33940; SOURCE 25 GENE: CAS9-2, CAS9, GTHT12_03401; SOURCE 26 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 27 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CRISPR-CAS9; CAS9; EPIGENETICS; ENDONUCLEASE; HNH; RUVC; METAL KEYWDS 2 BINDING; RNA, DNA BINDING PROTEIN-DNA-RNA COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR Y.SHU,Y.ZHAO,H.LI REVDAT 1 26-FEB-25 9AR4 0 JRNL AUTH M.ROTH,Y.SHU,D.TRASANIDIS,Y.ZHAO,R.HOFFMAN,J.VAN DER OOST, JRNL AUTH 2 H.LI JRNL TITL MOLECULAR BASIS FOR EPIGENETIC-SENSITIVE EDITING BY CAS9 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : 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 : 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) : 2.200 REMARK 3 NUMBER OF PARTICLES : 353229 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 9AR4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-FEB-24. REMARK 100 THE DEPOSITION ID IS D_1000281283. 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 : THERMOCAS9 POST-CLEAVAGE REMARK 245 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 : 7.50 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 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 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) : 6000.00 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: HEXAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, D, P, X, A 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 G B 1 REMARK 465 U B 72 REMARK 465 A B 73 REMARK 465 C B 110 REMARK 465 G B 111 REMARK 465 C B 112 REMARK 465 C B 113 REMARK 465 C B 114 REMARK 465 G B 115 REMARK 465 C B 116 REMARK 465 U B 117 REMARK 465 U B 118 REMARK 465 U B 119 REMARK 465 C B 120 REMARK 465 U B 121 REMARK 465 U B 122 REMARK 465 C B 123 REMARK 465 G B 124 REMARK 465 G B 125 REMARK 465 G B 126 REMARK 465 C B 127 REMARK 465 A B 128 REMARK 465 U B 129 REMARK 465 U B 147 REMARK 465 U B 148 REMARK 465 U B 149 REMARK 465 DA C 40 REMARK 465 GLU A 134 REMARK 465 ARG A 135 REMARK 465 THR A 136 REMARK 465 ASN A 137 REMARK 465 LYS A 138 REMARK 465 GLU A 139 REMARK 465 ASN A 140 REMARK 465 SER A 141 REMARK 465 THR A 142 REMARK 465 MET A 143 REMARK 465 LEU A 144 REMARK 465 LYS A 145 REMARK 465 HIS A 146 REMARK 465 ILE A 147 REMARK 465 GLU A 148 REMARK 465 GLU A 149 REMARK 465 ASN A 150 REMARK 465 GLN A 151 REMARK 465 SER A 152 REMARK 465 ILE A 153 REMARK 465 LEU A 154 REMARK 465 SER A 155 REMARK 465 SER A 156 REMARK 465 TYR A 157 REMARK 465 ARG A 158 REMARK 465 THR A 159 REMARK 465 VAL A 160 REMARK 465 ALA A 161 REMARK 465 GLU A 162 REMARK 465 MET A 163 REMARK 465 VAL A 164 REMARK 465 VAL A 165 REMARK 465 LYS A 166 REMARK 465 ASP A 167 REMARK 465 PRO A 168 REMARK 465 LYS A 169 REMARK 465 PHE A 170 REMARK 465 SER A 171 REMARK 465 LEU A 172 REMARK 465 HIS A 173 REMARK 465 LYS A 174 REMARK 465 ARG A 175 REMARK 465 ASN A 176 REMARK 465 LYS A 177 REMARK 465 GLU A 178 REMARK 465 ASP A 179 REMARK 465 ASN A 180 REMARK 465 TYR A 181 REMARK 465 THR A 182 REMARK 465 ASN A 183 REMARK 465 THR A 184 REMARK 465 SER A 1071 REMARK 465 HIS A 1072 REMARK 465 SER A 1073 REMARK 465 LYS A 1074 REMARK 465 ALA A 1075 REMARK 465 GLY A 1076 REMARK 465 GLU A 1077 REMARK 465 THR A 1078 REMARK 465 ILE A 1079 REMARK 465 ARG A 1080 REMARK 465 PRO A 1081 REMARK 465 LEU A 1082 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 N3 DC C 34 N1 GTP C 101 1.39 REMARK 500 REMARK 500 REMARK: NULL 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 DC C 15 P DC C 15 OP3 -0.131 REMARK 500 DC C 34 C2 DC C 34 N3 0.084 REMARK 500 DC C 34 N3 DC C 34 C4 0.088 REMARK 500 DG D 27 P DG D 27 OP3 -0.130 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 A B 75 C3' - O3' - P ANGL. DEV. = 8.4 DEGREES REMARK 500 C B 136 C6 - N1 - C2 ANGL. DEV. = -3.5 DEGREES REMARK 500 C B 136 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 U B 137 N1 - C2 - O2 ANGL. DEV. = 5.1 DEGREES REMARK 500 U B 137 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 C B 144 N1 - C2 - O2 ANGL. DEV. = 5.1 DEGREES REMARK 500 C B 144 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 C B 144 C2 - N1 - C1' ANGL. DEV. = 7.8 DEGREES REMARK 500 DA C 16 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG C 17 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DG C 18 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC C 21 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC C 34 C2 - N3 - C4 ANGL. DEV. = -7.3 DEGREES REMARK 500 DC C 34 N1 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 DC C 34 C5 - C4 - N4 ANGL. DEV. = -5.1 DEGREES REMARK 500 DA D 33 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC D 39 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DG P 2 O3' - P - OP1 ANGL. DEV. = 7.0 DEGREES REMARK 500 DG P 2 O5' - P - OP1 ANGL. DEV. = -7.9 DEGREES REMARK 500 DA P 13 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 LEU A 286 CA - CB - CG ANGL. DEV. = 13.9 DEGREES REMARK 500 LEU A 305 CA - CB - CG ANGL. DEV. = 20.4 DEGREES REMARK 500 ASP A 546 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 LEU A 751 CA - CB - CG ANGL. DEV. = 15.6 DEGREES REMARK 500 PRO A 878 CA - N - CD ANGL. DEV. = -25.9 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 35 30.85 -93.94 REMARK 500 SER A 229 -60.39 -123.61 REMARK 500 ASN A 322 57.25 -96.42 REMARK 500 LYS A 330 49.59 -89.27 REMARK 500 LEU A 336 61.62 -100.52 REMARK 500 GLU A 404 -4.55 69.12 REMARK 500 LYS A 417 144.93 70.99 REMARK 500 TYR A 536 -169.95 -79.12 REMARK 500 ASN A 541 84.25 -152.88 REMARK 500 GLN A 636 57.80 -96.25 REMARK 500 PHE A 637 -84.81 -110.69 REMARK 500 SER A 638 156.82 174.69 REMARK 500 GLU A 746 45.80 -146.36 REMARK 500 SER A 830 -4.18 68.14 REMARK 500 ASP A 860 76.40 -159.75 REMARK 500 ASN A 875 48.56 38.99 REMARK 500 SER A 924 -61.51 -95.84 REMARK 500 ASP A 935 -118.40 56.86 REMARK 500 THR A 971 -166.11 -125.14 REMARK 500 ARG A 977 -98.42 55.05 REMARK 500 SER A1018 -3.29 75.64 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LEU A 619 GLY A 620 104.28 REMARK 500 ASP A 935 GLY A 936 149.23 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 A1104 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C B 93 OP1 REMARK 620 2 HOH B 305 O 94.6 REMARK 620 3 THR A 478 OG1 111.9 102.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A B 101 OP2 REMARK 620 2 HOH B 304 O 67.0 REMARK 620 3 HOH B 306 O 89.1 90.7 REMARK 620 4 HOH B 309 O 82.4 146.3 74.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U B 102 OP1 REMARK 620 2 HOH B 308 O 127.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1103 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC C 15 OP2 REMARK 620 2 HOH C 202 O 74.3 REMARK 620 3 DC P 14 O3' 93.2 101.9 REMARK 620 4 ASP A 581 OD1 85.3 90.4 166.8 REMARK 620 5 ASN A 605 OD1 101.3 172.8 83.9 83.6 REMARK 620 6 HOH A1205 O 172.5 108.3 79.4 101.7 76.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG D 27 OP3 REMARK 620 2 DG D 27 OP2 64.0 REMARK 620 3 ASP A 8 OD2 160.3 98.2 REMARK 620 4 HOH A1201 O 76.8 113.3 104.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG D 27 OP2 REMARK 620 2 ASP A 8 OD1 111.9 REMARK 620 3 GLU A 500 OE1 125.0 92.8 REMARK 620 4 HOH A1207 O 70.8 66.8 76.0 REMARK 620 5 HOH A1208 O 104.5 118.1 105.3 174.6 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-43769 RELATED DB: EMDB REMARK 900 CRYOEM STRUCTURE OF THERMOCAS9 IN POST-CLEAVAGE STATE BOUND WITH REMARK 900 THE DNA CONTAINING NNNNCCA PAM DBREF 9AR4 B 1 149 PDB 9AR4 9AR4 1 149 DBREF 9AR4 C 15 40 PDB 9AR4 9AR4 15 40 DBREF 9AR4 D 27 40 PDB 9AR4 9AR4 27 40 DBREF 9AR4 P 1 14 PDB 9AR4 9AR4 1 14 DBREF 9AR4 X 2 6 PDB 9AR4 9AR4 2 6 DBREF1 9AR4 A 1 1082 UNP A0A1W6VMQ3_GEOTD DBREF2 9AR4 A A0A1W6VMQ3 1 1082 SEQRES 1 B 149 G G U A G G A U G G C A A SEQRES 2 B 149 G A U C C U G G U A G U C SEQRES 3 B 149 A U A G U U C C C C U G G SEQRES 4 B 149 A A A C A G G G U U A C U SEQRES 5 B 149 A U G A U A A G G G C U U SEQRES 6 B 149 U C U G C C U A U A G G C SEQRES 7 B 149 A G A C U G A C C C G U G SEQRES 8 B 149 G C G U U G G G G A U C G SEQRES 9 B 149 C C U A U C G C C C G C U SEQRES 10 B 149 U U C U U C G G G C A U U SEQRES 11 B 149 C C C C A C U C U U A G G SEQRES 12 B 149 C G U U U U SEQRES 1 C 26 DC DA DG DG DA DT DC DT DT DG DC DC DA SEQRES 2 C 26 DT DC DC DT DA DC DC DT DC DT DA DG DA SEQRES 1 D 14 DG DT DA DT DA DC DA DC DC DA DA DG DC SEQRES 2 D 14 DT SEQRES 1 P 14 DA DG DC DT DT DG DG DT DG DT DA DT DA SEQRES 2 P 14 DC SEQRES 1 X 5 DC DT DA DG DA SEQRES 1 A 1082 MET LYS TYR LYS ILE GLY LEU ASP ILE GLY ILE THR SER SEQRES 2 A 1082 ILE GLY TRP ALA VAL ILE ASN LEU ASP ILE PRO ARG ILE SEQRES 3 A 1082 GLU ASP LEU GLY VAL ARG ILE PHE ASP ARG ALA GLU ASN SEQRES 4 A 1082 PRO LYS THR GLY GLU SER LEU ALA LEU PRO ARG ARG LEU SEQRES 5 A 1082 ALA ARG SER ALA ARG ARG ARG LEU ARG ARG ARG LYS HIS SEQRES 6 A 1082 ARG LEU GLU ARG ILE ARG ARG LEU PHE VAL ARG GLU GLY SEQRES 7 A 1082 ILE LEU THR LYS GLU GLU LEU ASN LYS LEU PHE GLU LYS SEQRES 8 A 1082 LYS HIS GLU ILE ASP VAL TRP GLN LEU ARG VAL GLU ALA SEQRES 9 A 1082 LEU ASP ARG LYS LEU ASN ASN ASP GLU LEU ALA ARG ILE SEQRES 10 A 1082 LEU LEU HIS LEU ALA LYS ARG ARG GLY PHE ARG SER ASN SEQRES 11 A 1082 ARG LYS SER GLU ARG THR ASN LYS GLU ASN SER THR MET SEQRES 12 A 1082 LEU LYS HIS ILE GLU GLU ASN GLN SER ILE LEU SER SER SEQRES 13 A 1082 TYR ARG THR VAL ALA GLU MET VAL VAL LYS ASP PRO LYS SEQRES 14 A 1082 PHE SER LEU HIS LYS ARG ASN LYS GLU ASP ASN TYR THR SEQRES 15 A 1082 ASN THR VAL ALA ARG ASP ASP LEU GLU ARG GLU ILE LYS SEQRES 16 A 1082 LEU ILE PHE ALA LYS GLN ARG GLU TYR GLY ASN ILE VAL SEQRES 17 A 1082 CYS THR GLU ALA PHE GLU HIS GLU TYR ILE SER ILE TRP SEQRES 18 A 1082 ALA SER GLN ARG PRO PHE ALA SER LYS ASP ASP ILE GLU SEQRES 19 A 1082 LYS LYS VAL GLY PHE CYS THR PHE GLU PRO LYS GLU LYS SEQRES 20 A 1082 ARG ALA PRO LYS ALA THR TYR THR PHE GLN SER PHE THR SEQRES 21 A 1082 VAL TRP GLU HIS ILE ASN LYS LEU ARG LEU VAL SER PRO SEQRES 22 A 1082 GLY GLY ILE ARG ALA LEU THR ASP ASP GLU ARG ARG LEU SEQRES 23 A 1082 ILE TYR LYS GLN ALA PHE HIS LYS ASN LYS ILE THR PHE SEQRES 24 A 1082 HIS ASP VAL ARG THR LEU LEU ASN LEU PRO ASP ASP THR SEQRES 25 A 1082 ARG PHE LYS GLY LEU LEU TYR ASP ARG ASN THR THR LEU SEQRES 26 A 1082 LYS GLU ASN GLU LYS VAL ARG PHE LEU GLU LEU GLY ALA SEQRES 27 A 1082 TYR HIS LYS ILE ARG LYS ALA ILE ASP SER VAL TYR GLY SEQRES 28 A 1082 LYS GLY ALA ALA LYS SER PHE ARG PRO ILE ASP PHE ASP SEQRES 29 A 1082 THR PHE GLY TYR ALA LEU THR MET PHE LYS ASP ASP THR SEQRES 30 A 1082 ASP ILE ARG SER TYR LEU ARG ASN GLU TYR GLU GLN ASN SEQRES 31 A 1082 GLY LYS ARG MET GLU ASN LEU ALA ASP LYS VAL TYR ASP SEQRES 32 A 1082 GLU GLU LEU ILE GLU GLU LEU LEU ASN LEU SER PHE SER SEQRES 33 A 1082 LYS PHE GLY HIS LEU SER LEU LYS ALA LEU ARG ASN ILE SEQRES 34 A 1082 LEU PRO TYR MET GLU GLN GLY GLU VAL TYR SER THR ALA SEQRES 35 A 1082 CYS GLU ARG ALA GLY TYR THR PHE THR GLY PRO LYS LYS SEQRES 36 A 1082 LYS GLN LYS THR VAL LEU LEU PRO ASN ILE PRO PRO ILE SEQRES 37 A 1082 ALA ASN PRO VAL VAL MET ARG ALA LEU THR GLN ALA ARG SEQRES 38 A 1082 LYS VAL VAL ASN ALA ILE ILE LYS LYS TYR GLY SER PRO SEQRES 39 A 1082 VAL SER ILE HIS ILE GLU LEU ALA ARG GLU LEU SER GLN SEQRES 40 A 1082 SER PHE ASP GLU ARG ARG LYS MET GLN LYS GLU GLN GLU SEQRES 41 A 1082 GLY ASN ARG LYS LYS ASN GLU THR ALA ILE ARG GLN LEU SEQRES 42 A 1082 VAL GLU TYR GLY LEU THR LEU ASN PRO THR GLY LEU ASP SEQRES 43 A 1082 ILE VAL LYS PHE LYS LEU TRP SER GLU GLN ASN GLY LYS SEQRES 44 A 1082 CYS ALA TYR SER LEU GLN PRO ILE GLU ILE GLU ARG LEU SEQRES 45 A 1082 LEU GLU PRO GLY TYR THR GLU VAL ASP HIS VAL ILE PRO SEQRES 46 A 1082 TYR SER ARG SER LEU ASP ASP SER TYR THR ASN LYS VAL SEQRES 47 A 1082 LEU VAL LEU THR LYS GLU ASN ARG GLU LYS GLY ASN ARG SEQRES 48 A 1082 THR PRO ALA GLU TYR LEU GLY LEU GLY SER GLU ARG TRP SEQRES 49 A 1082 GLN GLN PHE GLU THR PHE VAL LEU THR ASN LYS GLN PHE SEQRES 50 A 1082 SER LYS LYS LYS ARG ASP ARG LEU LEU ARG LEU HIS TYR SEQRES 51 A 1082 ASP GLU ASN GLU GLU ASN GLU PHE LYS ASN ARG ASN LEU SEQRES 52 A 1082 ASN ASP THR ARG TYR ILE SER ARG PHE LEU ALA ASN PHE SEQRES 53 A 1082 ILE ARG GLU HIS LEU LYS PHE ALA ASP SER ASP ASP LYS SEQRES 54 A 1082 GLN LYS VAL TYR THR VAL ASN GLY ARG ILE THR ALA HIS SEQRES 55 A 1082 LEU ARG SER ARG TRP ASN PHE ASN LYS ASN ARG GLU GLU SEQRES 56 A 1082 SER ASN LEU HIS HIS ALA VAL ASP ALA ALA ILE VAL ALA SEQRES 57 A 1082 CYS THR THR PRO SER ASP ILE ALA ARG VAL THR ALA PHE SEQRES 58 A 1082 TYR GLN ARG ARG GLU GLN ASN LYS GLU LEU SER LYS LYS SEQRES 59 A 1082 THR ASP PRO GLN PHE PRO GLN PRO TRP PRO HIS PHE ALA SEQRES 60 A 1082 ASP GLU LEU GLN ALA ARG LEU SER LYS ASN PRO LYS GLU SEQRES 61 A 1082 SER ILE LYS ALA LEU ASN LEU GLY ASN TYR ASP ASN GLU SEQRES 62 A 1082 LYS LEU GLU SER LEU GLN PRO VAL PHE VAL SER ARG MET SEQRES 63 A 1082 PRO LYS ARG SER ILE THR GLY ALA ALA HIS GLN GLU THR SEQRES 64 A 1082 LEU ARG ARG TYR ILE GLY ILE ASP GLU ARG SER GLY LYS SEQRES 65 A 1082 ILE GLN THR VAL VAL LYS LYS LYS LEU SER GLU ILE GLN SEQRES 66 A 1082 LEU ASP LYS THR GLY HIS PHE PRO MET TYR GLY LYS GLU SEQRES 67 A 1082 SER ASP PRO ARG THR TYR GLU ALA ILE ARG GLN ARG LEU SEQRES 68 A 1082 LEU GLU HIS ASN ASN ASP PRO LYS LYS ALA PHE GLN GLU SEQRES 69 A 1082 PRO LEU TYR LYS PRO LYS LYS ASN GLY GLU LEU GLY PRO SEQRES 70 A 1082 ILE ILE ARG THR ILE LYS ILE ILE ASP THR THR ASN GLN SEQRES 71 A 1082 VAL ILE PRO LEU ASN ASP GLY LYS THR VAL ALA TYR ASN SEQRES 72 A 1082 SER ASN ILE VAL ARG VAL ASP VAL PHE GLU LYS ASP GLY SEQRES 73 A 1082 LYS TYR TYR CYS VAL PRO ILE TYR THR ILE ASP MET MET SEQRES 74 A 1082 LYS GLY ILE LEU PRO ASN LYS ALA ILE GLU PRO ASN LYS SEQRES 75 A 1082 PRO TYR SER GLU TRP LYS GLU MET THR GLU ASP TYR THR SEQRES 76 A 1082 PHE ARG PHE SER LEU TYR PRO ASN ASP LEU ILE ARG ILE SEQRES 77 A 1082 GLU PHE PRO ARG GLU LYS THR ILE LYS THR ALA VAL GLY SEQRES 78 A 1082 GLU GLU ILE LYS ILE LYS ASP LEU PHE ALA TYR TYR GLN SEQRES 79 A 1082 THR ILE ASP SER SER ASN GLY GLY LEU SER LEU VAL SER SEQRES 80 A 1082 HIS ASP ASN ASN PHE SER LEU ARG SER ILE GLY SER ARG SEQRES 81 A 1082 THR LEU LYS ARG PHE GLU LYS TYR GLN VAL ASP VAL LEU SEQRES 82 A 1082 GLY ASN ILE TYR LYS VAL ARG GLY GLU LYS ARG VAL GLY SEQRES 83 A 1082 VAL ALA SER SER SER HIS SER LYS ALA GLY GLU THR ILE SEQRES 84 A 1082 ARG PRO LEU HET MG B 201 1 HET MG B 202 1 HET GTP C 101 32 HET MG A1101 1 HET MG A1102 1 HET MG A1103 1 HET MG A1104 1 HETNAM MG MAGNESIUM ION HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE FORMUL 7 MG 6(MG 2+) FORMUL 9 GTP C10 H16 N5 O14 P3 FORMUL 14 HOH *21(H2 O) HELIX 1 AA1 ALA A 47 GLU A 77 1 31 HELIX 2 AA2 THR A 81 LYS A 87 1 7 HELIX 3 AA3 LEU A 88 LYS A 91 5 4 HELIX 4 AA4 ASP A 96 ALA A 104 1 9 HELIX 5 AA5 ASN A 110 ARG A 124 1 15 HELIX 6 AA6 ALA A 186 TYR A 204 1 19 HELIX 7 AA7 THR A 210 ALA A 222 1 13 HELIX 8 AA8 ILE A 233 VAL A 237 5 5 HELIX 9 AA9 THR A 253 LEU A 268 1 16 HELIX 10 AB1 THR A 280 PHE A 292 1 13 HELIX 11 AB2 PHE A 299 LEU A 306 1 8 HELIX 12 AB3 THR A 324 GLU A 329 1 6 HELIX 13 AB4 LEU A 336 GLY A 351 1 16 HELIX 14 AB5 PRO A 360 PHE A 373 1 14 HELIX 15 AB6 ASP A 375 ARG A 384 1 10 HELIX 16 AB7 GLU A 405 LEU A 411 1 7 HELIX 17 AB8 SER A 422 GLN A 435 1 14 HELIX 18 AB9 VAL A 438 GLY A 447 1 10 HELIX 19 AC1 ASN A 470 GLY A 492 1 23 HELIX 20 AC2 SER A 508 TYR A 536 1 29 HELIX 21 AC3 THR A 543 GLN A 556 1 14 HELIX 22 AC4 PRO A 585 LEU A 590 1 6 HELIX 23 AC5 SER A 593 THR A 595 5 3 HELIX 24 AC6 THR A 602 GLY A 609 1 8 HELIX 25 AC7 PRO A 613 GLY A 618 1 6 HELIX 26 AC8 SER A 621 ASN A 634 1 14 HELIX 27 AC9 SER A 638 LEU A 646 1 9 HELIX 28 AD1 LYS A 659 LEU A 681 1 23 HELIX 29 AD2 GLY A 697 TRP A 707 1 11 HELIX 30 AD3 LEU A 718 CYS A 729 1 12 HELIX 31 AD4 THR A 731 ARG A 745 1 15 HELIX 32 AD5 HIS A 765 LEU A 774 1 10 HELIX 33 AD6 ASN A 777 LEU A 785 1 9 HELIX 34 AD7 ASP A 791 SER A 797 1 7 HELIX 35 AD8 SER A 842 ILE A 844 5 3 HELIX 36 AD9 ASP A 860 GLU A 873 1 14 HELIX 37 AE1 THR A 945 GLY A 951 1 7 HELIX 38 AE2 PRO A 963 TRP A 967 5 5 SHEET 1 AA1 6 VAL A 692 ASN A 696 0 SHEET 2 AA1 6 SER A 496 LEU A 501 1 N ILE A 497 O TYR A 693 SHEET 3 AA1 6 TYR A 3 ILE A 9 1 N ILE A 5 O HIS A 498 SHEET 4 AA1 6 SER A 13 ASN A 20 -1 O GLY A 15 N ASP A 8 SHEET 5 AA1 6 ARG A 25 ILE A 33 -1 O GLY A 30 N TRP A 16 SHEET 6 AA1 6 SER A 804 ARG A 805 1 O SER A 804 N ILE A 33 SHEET 1 AA2 3 ILE A 276 ALA A 278 0 SHEET 2 AA2 3 ARG A 269 VAL A 271 -1 N LEU A 270 O ARG A 277 SHEET 3 AA2 3 ARG A 313 PHE A 314 -1 O ARG A 313 N VAL A 271 SHEET 1 AA3 2 LYS A 296 THR A 298 0 SHEET 2 AA3 2 ARG A 332 GLU A 335 -1 O PHE A 333 N ILE A 297 SHEET 1 AA4 2 GLU A 388 GLN A 389 0 SHEET 2 AA4 2 LYS A 392 ARG A 393 -1 O LYS A 392 N GLN A 389 SHEET 1 AA5 2 THR A 578 HIS A 582 0 SHEET 2 AA5 2 LYS A 597 LEU A 601 -1 O VAL A 598 N ASP A 581 SHEET 1 AA6 5 THR A 901 THR A 908 0 SHEET 2 AA6 5 ILE A 833 LYS A 840 -1 N VAL A 837 O ILE A 904 SHEET 3 AA6 5 LEU A 820 ILE A 826 -1 N GLY A 825 O GLN A 834 SHEET 4 AA6 5 THR A 919 ALA A 921 -1 O VAL A 920 N ARG A 821 SHEET 5 AA6 5 ILE A 912 LEU A 914 -1 N LEU A 914 O THR A 919 SHEET 1 AA7 2 TYR A 887 PRO A 889 0 SHEET 2 AA7 2 LEU A 895 ILE A 898 -1 O PRO A 897 N LYS A 888 SHEET 1 AA8 3 LYS A 937 TYR A 944 0 SHEET 2 AA8 3 ILE A 926 LYS A 934 -1 N PHE A 932 O TYR A 939 SHEET 3 AA8 3 THR A 975 LEU A 980 -1 O LEU A 980 N VAL A 929 SHEET 1 AA9 6 SER A1033 ILE A1037 0 SHEET 2 AA9 6 LEU A1023 VAL A1026 -1 N LEU A1025 O LEU A1034 SHEET 3 AA9 6 GLU A1003 ILE A1016 -1 N THR A1015 O SER A1024 SHEET 4 AA9 6 LEU A 985 LYS A 997 -1 N ILE A 986 O ALA A1011 SHEET 5 AA9 6 ARG A1044 VAL A1050 -1 O TYR A1048 N LEU A 985 SHEET 6 AA9 6 ILE A1056 LYS A1058 -1 O TYR A1057 N GLN A1049 LINK P G B 2 O3' GTP C 101 1555 1555 1.60 LINK OP1 C B 93 MG MG A1104 1555 1555 2.07 LINK OP2 A B 101 MG MG B 201 1555 1555 2.11 LINK OP1 U B 102 MG MG B 202 1555 1555 2.65 LINK MG MG B 201 O HOH B 304 1555 1555 2.17 LINK MG MG B 201 O HOH B 306 1555 1555 2.32 LINK MG MG B 201 O HOH B 309 1555 1555 2.84 LINK MG MG B 202 O HOH B 308 1555 1555 2.92 LINK O HOH B 305 MG MG A1104 1555 1555 2.73 LINK OP2 DC C 15 MG MG A1103 1555 1555 2.10 LINK O HOH C 202 MG MG A1103 1555 1555 2.59 LINK OP3 DG D 27 MG MG A1101 1555 1555 2.21 LINK OP2 DG D 27 MG MG A1101 1555 1555 2.29 LINK OP2 DG D 27 MG MG A1102 1555 1555 2.08 LINK O3' DC P 14 MG MG A1103 1555 1555 2.23 LINK OD2 ASP A 8 MG MG A1101 1555 1555 2.08 LINK OD1 ASP A 8 MG MG A1102 1555 1555 2.09 LINK OG1 THR A 478 MG MG A1104 1555 1555 2.50 LINK OE1 GLU A 500 MG MG A1102 1555 1555 2.36 LINK OD1 ASP A 581 MG MG A1103 1555 1555 2.13 LINK OD1 ASN A 605 MG MG A1103 1555 1555 2.25 LINK MG MG A1101 O HOH A1201 1555 1555 2.05 LINK MG MG A1102 O HOH A1207 1555 1555 2.52 LINK MG MG A1102 O HOH A1208 1555 1555 2.09 LINK MG MG A1103 O HOH A1205 1555 1555 2.19 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