HEADER HYDROLASE/RNA/DNA 27-JUL-17 5Y36 TITLE CRYO-EM STRUCTURE OF SPCAS9-SGRNA-DNA TERNARY COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SPCAS9,SPYCAS9; COMPND 5 EC: 3.1.-.-; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: SINGLE-GUIDE RNA; COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: COMPLEMENTARY DNA STRAND; COMPND 14 CHAIN: C; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: NON-COMPLEMENTARY DNA STRAND; COMPND 18 CHAIN: D; COMPND 19 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PYOGENES SEROTYPE M1; SOURCE 3 ORGANISM_TAXID: 301447; SOURCE 4 GENE: CAS9, CSN1, SPY_1046; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET28A; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 11 ORGANISM_TAXID: 10090; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 15 ORGANISM_TAXID: 10090; SOURCE 16 MOL_ID: 4; SOURCE 17 SYNTHETIC: YES; SOURCE 18 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 19 ORGANISM_TAXID: 10090 KEYWDS GENOME EDITTING, CRIPSR-CAS9, DNA CLEAVAGE MECHANISM, HYDROLASE-DNA- KEYWDS 2 RNA COMPLEX, HYDROLASE-RNA-DNA COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR Q.HUANG,G.LI,C.HUAI REVDAT 2 27-MAR-24 5Y36 1 REMARK LINK REVDAT 1 06-DEC-17 5Y36 0 JRNL AUTH C.HUAI,G.LI,R.YAO,Y.ZHANG,M.CAO,L.KONG,C.JIA,H.YUAN,H.CHEN, JRNL AUTH 2 D.LU,Q.HUANG JRNL TITL STRUCTURAL INSIGHTS INTO DNA CLEAVAGE ACTIVATION OF JRNL TITL 2 CRISPR-CAS9 SYSTEM JRNL REF NAT COMMUN V. 8 1375 2017 JRNL REFN ESSN 2041-1723 JRNL PMID 29123204 JRNL DOI 10.1038/S41467-017-01496-2 REMARK 2 REMARK 2 RESOLUTION. 5.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, RELION, CTFFIND3, NAMD, REMARK 3 ROSETTA, RELION, RELION, RELION, RELION REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 4OO8 REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE FIT REMARK 3 REFINEMENT TARGET : CORRELATION COEFFICIENT REMARK 3 OVERALL ANISOTROPIC B VALUE : 80.000 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) : 5.200 REMARK 3 NUMBER OF PARTICLES : 57484 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING ONLY REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 5Y36 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-JUL-17. REMARK 100 THE DEPOSITION ID IS D_1300004542. 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 : SPCAS9-SGRNA-TARGET DNA REMARK 245 COMPLEX; SPCAS9; SINGLE-GUIDE REMARK 245 RNA; TARGET DNA REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.45 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : BLOT FOR 4 SECONDS BEFORE REMARK 245 PLUGING REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : CAS9 PROTEIN FROM STREPTOCOCCUS REMARK 245 PYOGENES; 99 MER RNA THAT GUIDE CAS9 PROTEIN TO RECOGNIZE AND REMARK 245 BIND TO TARGET DNA; TARGET DNA FOR CAS9-SGRNA BINDING REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 592 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1300.00 REMARK 245 MAXIMUM DEFOCUS (NM) : NULL 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) : 1000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : 18000 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 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 CB MET A 1021 O4 DT D 23 1.77 REMARK 500 CA PHE A 164 OP1 U B 19 1.85 REMARK 500 O LYS A 163 OP1 U B 19 1.95 REMARK 500 ND1 HIS A 1311 N2 DG D 36 1.97 REMARK 500 OH TYR A 325 OP1 U B 45 2.10 REMARK 500 O LYS A 163 OP2 U B 19 2.10 REMARK 500 O ARG A 919 C7 DT D 32 2.12 REMARK 500 OH TYR A 72 OP2 U B 50 2.16 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 D 19 C5' DC D 19 C4' 0.044 REMARK 500 DT D 23 C5' DT D 23 C4' 0.044 REMARK 500 DG D 38 C5' DG D 38 C4' 0.043 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 ARG A 40 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG A 221 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 TYR A 517 CB - CG - CD2 ANGL. DEV. = -4.2 DEGREES REMARK 500 TYR A 517 CB - CG - CD1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 967 NE - CZ - NH1 ANGL. DEV. = 7.2 DEGREES REMARK 500 ARG A 967 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 U B 1 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 C B 3 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 C B 4 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 C B 6 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 C B 8 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 C B 9 O4' - C1' - N1 ANGL. DEV. = 5.6 DEGREES REMARK 500 U B 12 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 U B 12 C3' - O3' - P ANGL. DEV. = 9.2 DEGREES REMARK 500 C B 13 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES REMARK 500 C B 17 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 G B 20 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 G B 27 O4' - C1' - N9 ANGL. DEV. = 6.2 DEGREES REMARK 500 G B 29 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 C B 30 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 U B 37 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 C B 40 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 U B 45 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 A B 51 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 C B 55 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 U B 59 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 C B 60 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 C B 61 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES REMARK 500 A B 65 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 C B 67 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 C B 70 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 G B 82 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 C B 83 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 C B 85 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 C B 86 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 C B 91 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 G B 95 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 C B 96 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 DT C 6 O4' - C4' - C3' ANGL. DEV. = -4.1 DEGREES REMARK 500 DA C 12 C3' - O3' - P ANGL. DEV. = 13.6 DEGREES REMARK 500 DT C 13 O4' - C4' - C3' ANGL. DEV. = -4.6 DEGREES REMARK 500 DT C 13 C1' - O4' - C4' ANGL. DEV. = -6.3 DEGREES REMARK 500 DG C 27 O4' - C4' - C3' ANGL. DEV. = -2.9 DEGREES REMARK 500 DG C 27 C1' - O4' - C4' ANGL. DEV. = -6.1 DEGREES REMARK 500 DG C 27 O4' - C1' - C2' ANGL. DEV. = -5.0 DEGREES REMARK 500 DA C 28 O4' - C4' - C3' ANGL. DEV. = -3.8 DEGREES REMARK 500 DC C 29 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DC C 29 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES REMARK 500 DT C 30 C3' - O3' - P ANGL. DEV. = 14.4 DEGREES REMARK 500 DG C 31 O4' - C4' - C3' ANGL. DEV. = -3.9 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 63 ANGLE DEVIATIONS. 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 59 -80.31 3.41 REMARK 500 LEU A 106 155.40 71.90 REMARK 500 HIS A 116 64.83 35.63 REMARK 500 PHE A 164 53.23 -91.80 REMARK 500 ASN A 178 20.57 -142.55 REMARK 500 ASP A 180 75.95 -150.30 REMARK 500 ASN A 199 72.40 -158.92 REMARK 500 GLU A 311 -33.02 83.35 REMARK 500 ALA A 315 67.61 -118.19 REMARK 500 ASP A 353 105.74 145.86 REMARK 500 GLU A 471 -95.42 -125.04 REMARK 500 LEU A 551 -72.34 -88.96 REMARK 500 GLU A 584 -148.10 -85.91 REMARK 500 LEU A 607 -91.72 -93.50 REMARK 500 ASP A 628 106.76 -48.29 REMARK 500 LYS A 652 68.51 -67.76 REMARK 500 ARG A 653 -72.70 -124.86 REMARK 500 ASN A 668 28.39 -144.64 REMARK 500 ASP A 686 -155.44 -159.11 REMARK 500 ALA A 689 177.25 64.92 REMARK 500 ASP A 699 118.88 -39.25 REMARK 500 ALA A 711 -81.11 -95.96 REMARK 500 LEU A 727 114.64 74.56 REMARK 500 ALA A 728 139.48 79.95 REMARK 500 ASN A 776 -72.59 -137.68 REMARK 500 ASN A 818 179.10 63.95 REMARK 500 SER A 851 -129.39 65.77 REMARK 500 SER A 860 139.68 -171.10 REMARK 500 ARG A 905 -8.53 -142.83 REMARK 500 LEU A 908 115.33 72.02 REMARK 500 ASP A 912 54.35 -94.15 REMARK 500 LYS A 918 123.38 136.11 REMARK 500 LEU A 921 105.53 -163.17 REMARK 500 ASN A 979 101.37 -169.82 REMARK 500 VAL A1009 -64.69 64.22 REMARK 500 ARG A1078 -55.34 -132.32 REMARK 500 GLU A1099 -175.89 -171.11 REMARK 500 ASN A1115 12.37 -144.60 REMARK 500 SER A1136 65.19 62.73 REMARK 500 LYS A1158 73.75 -67.38 REMARK 500 ALA A1215 -79.79 -75.15 REMARK 500 SER A1216 -74.82 -148.36 REMARK 500 ASN A1224 111.35 69.57 REMARK 500 SER A1248 -61.19 -161.21 REMARK 500 HIS A1262 78.04 -115.02 REMARK 500 VAL A1280 -72.06 -121.78 REMARK 500 LEU A1282 -72.84 81.22 REMARK 500 ALA A1285 -99.59 47.54 REMARK 500 TYR A1326 -77.96 -85.79 REMARK 500 PHE A1327 -82.79 -125.73 REMARK 500 REMARK 500 THIS ENTRY HAS 51 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 40 0.12 SIDE CHAIN REMARK 500 ARG A 976 0.12 SIDE CHAIN 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 A1402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 839 OD1 REMARK 620 2 ASP A 861 OD2 116.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 986 OD2 REMARK 620 2 DA D 34 OP2 120.1 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 1401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 1402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG D 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-8236 RELATED DB: EMDB DBREF 5Y36 A 1 1368 UNP Q99ZW2 CAS9_STRP1 1 1368 DBREF 5Y36 B -2 97 PDB 5Y36 5Y36 -2 97 DBREF 5Y36 C 1 41 PDB 5Y36 5Y36 1 41 DBREF 5Y36 D 15 55 PDB 5Y36 5Y36 15 55 SEQADV 5Y36 ALA A 10 UNP Q99ZW2 ASP 10 ENGINEERED MUTATION SEQADV 5Y36 ALA A 840 UNP Q99ZW2 HIS 840 ENGINEERED MUTATION SEQRES 1 A 1368 MET ASP LYS LYS TYR SER ILE GLY LEU ALA ILE GLY THR SEQRES 2 A 1368 ASN SER VAL GLY TRP ALA VAL ILE THR ASP GLU TYR LYS SEQRES 3 A 1368 VAL PRO SER LYS LYS PHE LYS VAL LEU GLY ASN THR ASP SEQRES 4 A 1368 ARG HIS SER ILE LYS LYS ASN LEU ILE GLY ALA LEU LEU SEQRES 5 A 1368 PHE ASP SER GLY GLU THR ALA GLU ALA THR ARG LEU LYS SEQRES 6 A 1368 ARG THR ALA ARG ARG ARG TYR THR ARG ARG LYS ASN ARG SEQRES 7 A 1368 ILE CYS TYR LEU GLN GLU ILE PHE SER ASN GLU MET ALA SEQRES 8 A 1368 LYS VAL ASP ASP SER PHE PHE HIS ARG LEU GLU GLU SER SEQRES 9 A 1368 PHE LEU VAL GLU GLU ASP LYS LYS HIS GLU ARG HIS PRO SEQRES 10 A 1368 ILE PHE GLY ASN ILE VAL ASP GLU VAL ALA TYR HIS GLU SEQRES 11 A 1368 LYS TYR PRO THR ILE TYR HIS LEU ARG LYS LYS LEU VAL SEQRES 12 A 1368 ASP SER THR ASP LYS ALA ASP LEU ARG LEU ILE TYR LEU SEQRES 13 A 1368 ALA LEU ALA HIS MET ILE LYS PHE ARG GLY HIS PHE LEU SEQRES 14 A 1368 ILE GLU GLY ASP LEU ASN PRO ASP ASN SER ASP VAL ASP SEQRES 15 A 1368 LYS LEU PHE ILE GLN LEU VAL GLN THR TYR ASN GLN LEU SEQRES 16 A 1368 PHE GLU GLU ASN PRO ILE ASN ALA SER GLY VAL ASP ALA SEQRES 17 A 1368 LYS ALA ILE LEU SER ALA ARG LEU SER LYS SER ARG ARG SEQRES 18 A 1368 LEU GLU ASN LEU ILE ALA GLN LEU PRO GLY GLU LYS LYS SEQRES 19 A 1368 ASN GLY LEU PHE GLY ASN LEU ILE ALA LEU SER LEU GLY SEQRES 20 A 1368 LEU THR PRO ASN PHE LYS SER ASN PHE ASP LEU ALA GLU SEQRES 21 A 1368 ASP ALA LYS LEU GLN LEU SER LYS ASP THR TYR ASP ASP SEQRES 22 A 1368 ASP LEU ASP ASN LEU LEU ALA GLN ILE GLY ASP GLN TYR SEQRES 23 A 1368 ALA ASP LEU PHE LEU ALA ALA LYS ASN LEU SER ASP ALA SEQRES 24 A 1368 ILE LEU LEU SER ASP ILE LEU ARG VAL ASN THR GLU ILE SEQRES 25 A 1368 THR LYS ALA PRO LEU SER ALA SER MET ILE LYS ARG TYR SEQRES 26 A 1368 ASP GLU HIS HIS GLN ASP LEU THR LEU LEU LYS ALA LEU SEQRES 27 A 1368 VAL ARG GLN GLN LEU PRO GLU LYS TYR LYS GLU ILE PHE SEQRES 28 A 1368 PHE ASP GLN SER LYS ASN GLY TYR ALA GLY TYR ILE ASP SEQRES 29 A 1368 GLY GLY ALA SER GLN GLU GLU PHE TYR LYS PHE ILE LYS SEQRES 30 A 1368 PRO ILE LEU GLU LYS MET ASP GLY THR GLU GLU LEU LEU SEQRES 31 A 1368 VAL LYS LEU ASN ARG GLU ASP LEU LEU ARG LYS GLN ARG SEQRES 32 A 1368 THR PHE ASP ASN GLY SER ILE PRO HIS GLN ILE HIS LEU SEQRES 33 A 1368 GLY GLU LEU HIS ALA ILE LEU ARG ARG GLN GLU ASP PHE SEQRES 34 A 1368 TYR PRO PHE LEU LYS ASP ASN ARG GLU LYS ILE GLU LYS SEQRES 35 A 1368 ILE LEU THR PHE ARG ILE PRO TYR TYR VAL GLY PRO LEU SEQRES 36 A 1368 ALA ARG GLY ASN SER ARG PHE ALA TRP MET THR ARG LYS SEQRES 37 A 1368 SER GLU GLU THR ILE THR PRO TRP ASN PHE GLU GLU VAL SEQRES 38 A 1368 VAL ASP LYS GLY ALA SER ALA GLN SER PHE ILE GLU ARG SEQRES 39 A 1368 MET THR ASN PHE ASP LYS ASN LEU PRO ASN GLU LYS VAL SEQRES 40 A 1368 LEU PRO LYS HIS SER LEU LEU TYR GLU TYR PHE THR VAL SEQRES 41 A 1368 TYR ASN GLU LEU THR LYS VAL LYS TYR VAL THR GLU GLY SEQRES 42 A 1368 MET ARG LYS PRO ALA PHE LEU SER GLY GLU GLN LYS LYS SEQRES 43 A 1368 ALA ILE VAL ASP LEU LEU PHE LYS THR ASN ARG LYS VAL SEQRES 44 A 1368 THR VAL LYS GLN LEU LYS GLU ASP TYR PHE LYS LYS ILE SEQRES 45 A 1368 GLU CYS PHE ASP SER VAL GLU ILE SER GLY VAL GLU ASP SEQRES 46 A 1368 ARG PHE ASN ALA SER LEU GLY THR TYR HIS ASP LEU LEU SEQRES 47 A 1368 LYS ILE ILE LYS ASP LYS ASP PHE LEU ASP ASN GLU GLU SEQRES 48 A 1368 ASN GLU ASP ILE LEU GLU ASP ILE VAL LEU THR LEU THR SEQRES 49 A 1368 LEU PHE GLU ASP ARG GLU MET ILE GLU GLU ARG LEU LYS SEQRES 50 A 1368 THR TYR ALA HIS LEU PHE ASP ASP LYS VAL MET LYS GLN SEQRES 51 A 1368 LEU LYS ARG ARG ARG TYR THR GLY TRP GLY ARG LEU SER SEQRES 52 A 1368 ARG LYS LEU ILE ASN GLY ILE ARG ASP LYS GLN SER GLY SEQRES 53 A 1368 LYS THR ILE LEU ASP PHE LEU LYS SER ASP GLY PHE ALA SEQRES 54 A 1368 ASN ARG ASN PHE MET GLN LEU ILE HIS ASP ASP SER LEU SEQRES 55 A 1368 THR PHE LYS GLU ASP ILE GLN LYS ALA GLN VAL SER GLY SEQRES 56 A 1368 GLN GLY ASP SER LEU HIS GLU HIS ILE ALA ASN LEU ALA SEQRES 57 A 1368 GLY SER PRO ALA ILE LYS LYS GLY ILE LEU GLN THR VAL SEQRES 58 A 1368 LYS VAL VAL ASP GLU LEU VAL LYS VAL MET GLY ARG HIS SEQRES 59 A 1368 LYS PRO GLU ASN ILE VAL ILE GLU MET ALA ARG GLU ASN SEQRES 60 A 1368 GLN THR THR GLN LYS GLY GLN LYS ASN SER ARG GLU ARG SEQRES 61 A 1368 MET LYS ARG ILE GLU GLU GLY ILE LYS GLU LEU GLY SER SEQRES 62 A 1368 GLN ILE LEU LYS GLU HIS PRO VAL GLU ASN THR GLN LEU SEQRES 63 A 1368 GLN ASN GLU LYS LEU TYR LEU TYR TYR LEU GLN ASN GLY SEQRES 64 A 1368 ARG ASP MET TYR VAL ASP GLN GLU LEU ASP ILE ASN ARG SEQRES 65 A 1368 LEU SER ASP TYR ASP VAL ASP ALA ILE VAL PRO GLN SER SEQRES 66 A 1368 PHE LEU LYS ASP ASP SER ILE ASP ASN LYS VAL LEU THR SEQRES 67 A 1368 ARG SER ASP LYS ASN ARG GLY LYS SER ASP ASN VAL PRO SEQRES 68 A 1368 SER GLU GLU VAL VAL LYS LYS MET LYS ASN TYR TRP ARG SEQRES 69 A 1368 GLN LEU LEU ASN ALA LYS LEU ILE THR GLN ARG LYS PHE SEQRES 70 A 1368 ASP ASN LEU THR LYS ALA GLU ARG GLY GLY LEU SER GLU SEQRES 71 A 1368 LEU ASP LYS ALA GLY PHE ILE LYS ARG GLN LEU VAL GLU SEQRES 72 A 1368 THR ARG GLN ILE THR LYS HIS VAL ALA GLN ILE LEU ASP SEQRES 73 A 1368 SER ARG MET ASN THR LYS TYR ASP GLU ASN ASP LYS LEU SEQRES 74 A 1368 ILE ARG GLU VAL LYS VAL ILE THR LEU LYS SER LYS LEU SEQRES 75 A 1368 VAL SER ASP PHE ARG LYS ASP PHE GLN PHE TYR LYS VAL SEQRES 76 A 1368 ARG GLU ILE ASN ASN TYR HIS HIS ALA HIS ASP ALA TYR SEQRES 77 A 1368 LEU ASN ALA VAL VAL GLY THR ALA LEU ILE LYS LYS TYR SEQRES 78 A 1368 PRO LYS LEU GLU SER GLU PHE VAL TYR GLY ASP TYR LYS SEQRES 79 A 1368 VAL TYR ASP VAL ARG LYS MET ILE ALA LYS SER GLU GLN SEQRES 80 A 1368 GLU ILE GLY LYS ALA THR ALA LYS TYR PHE PHE TYR SER SEQRES 81 A 1368 ASN ILE MET ASN PHE PHE LYS THR GLU ILE THR LEU ALA SEQRES 82 A 1368 ASN GLY GLU ILE ARG LYS ARG PRO LEU ILE GLU THR ASN SEQRES 83 A 1368 GLY GLU THR GLY GLU ILE VAL TRP ASP LYS GLY ARG ASP SEQRES 84 A 1368 PHE ALA THR VAL ARG LYS VAL LEU SER MET PRO GLN VAL SEQRES 85 A 1368 ASN ILE VAL LYS LYS THR GLU VAL GLN THR GLY GLY PHE SEQRES 86 A 1368 SER LYS GLU SER ILE LEU PRO LYS ARG ASN SER ASP LYS SEQRES 87 A 1368 LEU ILE ALA ARG LYS LYS ASP TRP ASP PRO LYS LYS TYR SEQRES 88 A 1368 GLY GLY PHE ASP SER PRO THR VAL ALA TYR SER VAL LEU SEQRES 89 A 1368 VAL VAL ALA LYS VAL GLU LYS GLY LYS SER LYS LYS LEU SEQRES 90 A 1368 LYS SER VAL LYS GLU LEU LEU GLY ILE THR ILE MET GLU SEQRES 91 A 1368 ARG SER SER PHE GLU LYS ASN PRO ILE ASP PHE LEU GLU SEQRES 92 A 1368 ALA LYS GLY TYR LYS GLU VAL LYS LYS ASP LEU ILE ILE SEQRES 93 A 1368 LYS LEU PRO LYS TYR SER LEU PHE GLU LEU GLU ASN GLY SEQRES 94 A 1368 ARG LYS ARG MET LEU ALA SER ALA GLY GLU LEU GLN LYS SEQRES 95 A 1368 GLY ASN GLU LEU ALA LEU PRO SER LYS TYR VAL ASN PHE SEQRES 96 A 1368 LEU TYR LEU ALA SER HIS TYR GLU LYS LEU LYS GLY SER SEQRES 97 A 1368 PRO GLU ASP ASN GLU GLN LYS GLN LEU PHE VAL GLU GLN SEQRES 98 A 1368 HIS LYS HIS TYR LEU ASP GLU ILE ILE GLU GLN ILE SER SEQRES 99 A 1368 GLU PHE SER LYS ARG VAL ILE LEU ALA ASP ALA ASN LEU SEQRES 100 A 1368 ASP LYS VAL LEU SER ALA TYR ASN LYS HIS ARG ASP LYS SEQRES 101 A 1368 PRO ILE ARG GLU GLN ALA GLU ASN ILE ILE HIS LEU PHE SEQRES 102 A 1368 THR LEU THR ASN LEU GLY ALA PRO ALA ALA PHE LYS TYR SEQRES 103 A 1368 PHE ASP THR THR ILE ASP ARG LYS ARG TYR THR SER THR SEQRES 104 A 1368 LYS GLU VAL LEU ASP ALA THR LEU ILE HIS GLN SER ILE SEQRES 105 A 1368 THR GLY LEU TYR GLU THR ARG ILE ASP LEU SER GLN LEU SEQRES 106 A 1368 GLY GLY ASP SEQRES 1 B 99 G G U A C C G C U C C A G SEQRES 2 B 99 U C G U U C A U G G U U U SEQRES 3 B 99 U A G A G C U A G A A A U SEQRES 4 B 99 A G C A A G U U A A A A U SEQRES 5 B 99 A A G G C U A G U C C G U SEQRES 6 B 99 U A U C A A C U U G A A A SEQRES 7 B 99 A A G U G G C A C C G A G SEQRES 8 B 99 U C G G U G C U SEQRES 1 C 41 DA DC DA DT DT DT DT DC DG DG DG DA DT SEQRES 2 C 41 DG DG DT DC DC DT DC DA DT DG DA DA DC SEQRES 3 C 41 DG DA DC DT DG DG DA DG DC DG DG DT DA SEQRES 4 C 41 DA DT SEQRES 1 D 41 DA DT DT DA DC DC DG DC DT DC DC DA DG SEQRES 2 D 41 DT DC DG DT DT DC DA DT DG DA DG DG DA SEQRES 3 D 41 DC DC DA DT DC DC DC DG DA DA DA DA DT SEQRES 4 D 41 DG DT HET MG A1401 1 HET MG A1402 1 HET MG D 101 1 HETNAM MG MAGNESIUM ION FORMUL 5 MG 3(MG 2+) HELIX 1 AA1 THR A 58 ASP A 94 1 37 HELIX 2 AA2 SER A 96 GLU A 103 1 8 HELIX 3 AA3 VAL A 107 LYS A 111 5 5 HELIX 4 AA4 ASN A 121 VAL A 126 1 6 HELIX 5 AA5 THR A 134 ASP A 144 1 11 HELIX 6 AA6 ASP A 150 PHE A 164 1 15 HELIX 7 AA7 VAL A 181 PHE A 196 1 16 HELIX 8 AA8 ASP A 207 ALA A 214 1 8 HELIX 9 AA9 SER A 217 LEU A 229 1 13 HELIX 10 AB1 GLY A 236 LEU A 246 1 11 HELIX 11 AB2 THR A 270 GLY A 283 1 14 HELIX 12 AB3 TYR A 286 LEU A 306 1 21 HELIX 13 AB4 ALA A 315 LEU A 343 1 29 HELIX 14 AB5 LYS A 346 PHE A 352 1 7 HELIX 15 AB6 ASP A 353 ASN A 357 5 5 HELIX 16 AB7 GLY A 358 GLY A 365 1 8 HELIX 17 AB8 SER A 368 MET A 383 1 16 HELIX 18 AB9 THR A 386 GLU A 396 1 11 HELIX 19 AC1 THR A 404 GLY A 408 5 5 HELIX 20 AC2 PRO A 411 GLN A 426 1 16 HELIX 21 AC3 PRO A 431 PHE A 446 1 16 HELIX 22 AC4 ASN A 477 VAL A 482 1 6 HELIX 23 AC5 ASP A 483 MET A 495 1 13 HELIX 24 AC6 SER A 512 LYS A 526 1 15 HELIX 25 AC7 SER A 541 LEU A 552 1 12 HELIX 26 AC8 THR A 560 ASP A 567 1 8 HELIX 27 AC9 ASP A 567 ILE A 572 1 6 HELIX 28 AD1 GLY A 592 LYS A 602 1 11 HELIX 29 AD2 GLU A 611 PHE A 626 1 16 HELIX 30 AD3 ASP A 628 TYR A 639 1 12 HELIX 31 AD4 ASP A 644 LYS A 652 1 9 HELIX 32 AD5 SER A 663 GLY A 669 1 7 HELIX 33 AD6 THR A 678 SER A 685 1 8 HELIX 34 AD7 ASN A 692 ASP A 699 1 8 HELIX 35 AD8 PHE A 704 ALA A 711 1 8 HELIX 36 AD9 SER A 719 ILE A 724 1 6 HELIX 37 AE1 SER A 730 MET A 751 1 22 HELIX 38 AE2 ASN A 776 GLY A 792 1 17 HELIX 39 AE3 GLN A 794 HIS A 799 1 6 HELIX 40 AE4 ASN A 808 ASN A 818 1 11 HELIX 41 AE5 ASP A 829 LEU A 833 5 5 HELIX 42 AE6 SER A 851 ASP A 853 5 3 HELIX 43 AE7 ASP A 861 GLY A 865 5 5 HELIX 44 AE8 SER A 872 ALA A 889 1 18 HELIX 45 AE9 THR A 893 ASN A 899 1 7 HELIX 46 AF1 THR A 901 GLY A 906 1 6 HELIX 47 AF2 GLU A 910 ILE A 917 5 8 HELIX 48 AF3 ILE A 927 ASN A 940 1 14 HELIX 49 AF4 LYS A 959 LEU A 962 5 4 HELIX 50 AF5 VAL A 963 PHE A 970 1 8 HELIX 51 AF6 VAL A 975 ASN A 979 5 5 HELIX 52 AF7 TYR A 981 LYS A 1000 1 20 HELIX 53 AF8 ARG A 1019 ILE A 1022 5 4 HELIX 54 AF9 ALA A 1023 ILE A 1029 1 7 HELIX 55 AG1 PHE A 1037 LYS A 1047 1 11 HELIX 56 AG2 ARG A 1078 SER A 1088 1 11 HELIX 57 AG3 ILE A 1168 GLU A 1175 1 8 HELIX 58 AG4 ASN A 1177 GLY A 1186 1 10 HELIX 59 AG5 LYS A 1191 ILE A 1195 5 5 HELIX 60 AG6 SER A 1230 TYR A 1242 1 13 HELIX 61 AG7 PRO A 1249 HIS A 1262 1 14 HELIX 62 AG8 HIS A 1264 ILE A 1281 1 18 HELIX 63 AG9 ASN A 1286 HIS A 1297 1 12 HELIX 64 AH1 PRO A 1301 ILE A 1310 1 10 HELIX 65 AH2 HIS A 1311 ASN A 1317 5 7 HELIX 66 AH3 GLU A 1341 LEU A 1343 5 3 SHEET 1 AA1 6 VAL A 955 THR A 957 0 SHEET 2 AA1 6 PRO A 756 MET A 763 1 N ILE A 759 O ILE A 956 SHEET 3 AA1 6 TYR A 5 ILE A 11 1 N TYR A 5 O GLU A 757 SHEET 4 AA1 6 SER A 15 THR A 22 -1 O ILE A 21 N SER A 6 SHEET 5 AA1 6 GLY A 49 LEU A 52 -1 O LEU A 51 N VAL A 16 SHEET 6 AA1 6 ASN A1093 LYS A1096 1 O VAL A1095 N LEU A 52 SHEET 1 AA2 2 SER A 29 LYS A 31 0 SHEET 2 AA2 2 LYS A 44 ASN A 46 -1 O LYS A 45 N LYS A 30 SHEET 1 AA3 6 LEU A 35 GLY A 36 0 SHEET 2 AA3 6 GLU A1357 ARG A1359 1 O ARG A1359 N LEU A 35 SHEET 3 AA3 6 ALA A1345 GLN A1350 -1 N HIS A1349 O THR A1358 SHEET 4 AA3 6 LEU A1203 LEU A1206 -1 N LEU A1203 O ILE A1348 SHEET 5 AA3 6 ARG A1210 LEU A1214 -1 O ARG A1210 N LEU A1206 SHEET 6 AA3 6 LEU A1220 GLN A1221 -1 O GLN A1221 N MET A1213 SHEET 1 AA4 3 ALA A 538 PHE A 539 0 SHEET 2 AA4 3 LYS A 528 VAL A 530 -1 N TYR A 529 O ALA A 538 SHEET 3 AA4 3 GLU A 579 SER A 581 -1 O SER A 581 N LYS A 528 SHEET 1 AA5 2 VAL A 838 ALA A 840 0 SHEET 2 AA5 2 LYS A 855 LEU A 857 -1 O VAL A 856 N ASP A 839 SHEET 1 AA6 2 LYS A1107 ILE A1110 0 SHEET 2 AA6 2 PHE A1134 ASP A1135 -1 O ASP A1135 N LYS A1107 SHEET 1 AA7 3 LYS A1161 THR A1167 0 SHEET 2 AA7 3 VAL A1139 VAL A1146 -1 N TYR A1141 O ILE A1166 SHEET 3 AA7 3 ILE A1196 LEU A1198 -1 O LEU A1198 N SER A1142 SHEET 1 AA8 2 GLU A1150 LYS A1151 0 SHEET 2 AA8 2 LYS A1156 LEU A1157 -1 O LYS A1156 N LYS A1151 LINK OD1 ASP A 839 MG MG A1402 1555 1555 2.37 LINK OD2 ASP A 861 MG MG A1402 1555 1555 2.15 LINK OD2 ASP A 986 MG MG A1401 1555 1555 2.01 LINK MG MG A1401 OP2 DA D 34 1555 1555 1.84 LINK OP1 DA D 34 MG MG D 101 1555 1555 2.14 SITE 1 AC1 4 HIS A 982 HIS A 983 ASP A 986 DA D 34 SITE 1 AC2 2 ASP A 839 ASP A 861 SITE 1 AC3 2 ARG A 925 DA D 34 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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