HEADER SIGNALING PROTEIN 06-JUN-23 8JNB TITLE CRAF RAS-BINDING DOMAIN CHIMERA, LIGAND COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAF PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE, CRAF; COMPND 3 CHAIN: B; COMPND 4 SYNONYM: PROTO-ONCOGENE C-RAF,CRAF,RAF-1,PROTO-ONCOGENE B-RAF,P94,V- COMPND 5 RAF MURINE SARCOMA VIRAL ONCOGENE HOMOLOG B1; COMPND 6 EC: 2.7.11.1; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 OTHER_DETAILS: 102-LHEHKGKKARLD-113 REPLACED WITH QDGEKKPIG (201-209) COMPND 10 FROM P15056 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: RAF1, RAF, BRAF, BRAF1, RAFB1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX-6P-1 KEYWDS RAF, CRAF, CHIMERA, BETA-GRASP, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.KAWAMURA,T.KUMASAKA REVDAT 1 19-JUN-24 8JNB 0 JRNL AUTH Y.YOSHIKAWA,Y.MAKINO,H.KUBOTA,T.KAWAMURA,S.MATSUMOTO,H.YUKI, JRNL AUTH 2 A.SHIBAIKE,M.OKAMURA,T.OKADA,T.KATAOKA,T.HONMA,T.KUMASAKA, JRNL AUTH 3 H.KOYAMA,F.SHIMA JRNL TITL SMALL-MOLECULE RAS/RAF-BINDING INHIBITORS ALLOSTERICALLY JRNL TITL 2 DISRUPT RAF CONFORMATION AND EXERT EFFICACY AGAINST JRNL TITL 3 BROAD-SPECTRUM RAS-DRIVEN CANCERS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.62 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17_3644 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.62 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.89 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 11694 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 587 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 34.8900 - 2.5700 1.00 2914 155 0.1888 0.2323 REMARK 3 2 2.5700 - 2.0400 0.99 2787 146 0.2195 0.2342 REMARK 3 3 2.0400 - 1.7800 0.99 2736 145 0.2108 0.2651 REMARK 3 4 1.7800 - 1.6200 0.96 2670 141 0.2689 0.3105 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.209 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.905 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.51 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.32 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.011 681 REMARK 3 ANGLE : 1.632 930 REMARK 3 CHIRALITY : 0.079 105 REMARK 3 PLANARITY : 0.007 118 REMARK 3 DIHEDRAL : 21.329 243 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8JNB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1300038217. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-DEC-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL38B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI(111) SILICON CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS FEB 3, 2021 REMARK 200 DATA SCALING SOFTWARE : XDS FEB 3, 2021 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11698 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.620 REMARK 200 RESOLUTION RANGE LOW (A) : 34.890 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.04916 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.62 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.4 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 0.89840 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.020 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.5M AMMONIUM SULFATE, 1.0M LITHIUM REMARK 280 SULFATE, 0.1M SODIUM CITRATE, PH 5.6, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 19.87300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 19.87300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 32.50950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.88750 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 32.50950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.88750 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 19.87300 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 32.50950 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 34.88750 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 19.87300 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 32.50950 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 34.88750 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 GLY B 45 REMARK 465 PRO B 46 REMARK 465 LEU B 47 REMARK 465 GLY B 48 REMARK 465 SER B 49 REMARK 465 ASP B 50 REMARK 465 PRO B 51 REMARK 465 SER B 52 REMARK 465 LYS B 53 REMARK 465 THR B 54 REMARK 465 SER B 55 REMARK 465 ASP B 106 REMARK 465 GLY B 107 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG B 73 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 92 CG CD OE1 NE2 REMARK 470 GLU B 108 CG CD OE1 OE2 REMARK 470 LYS B 110 CG CD CE NZ 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 CYS B 81 CB CYS B 81 SG -0.124 REMARK 500 REMARK 500 REMARK: NULL DBREF 8JNB B 50 101 UNP P04049 RAF1_HUMAN 50 101 DBREF 8JNB B 102 113 UNP P15056 BRAF_HUMAN 201 209 DBREF 8JNB B 114 141 UNP P04049 RAF1_HUMAN 114 141 SEQADV 8JNB GLY B 45 UNP P04049 EXPRESSION TAG SEQADV 8JNB PRO B 46 UNP P04049 EXPRESSION TAG SEQADV 8JNB LEU B 47 UNP P04049 EXPRESSION TAG SEQADV 8JNB GLY B 48 UNP P04049 EXPRESSION TAG SEQADV 8JNB SER B 49 UNP P04049 EXPRESSION TAG SEQADV 8JNB SER B 65 UNP P04049 LYS 65 ENGINEERED MUTATION SEQADV 8JNB TYR B 99 UNP P04049 PHE 99 ENGINEERED MUTATION SEQADV 8JNB TRP B 120 UNP P04049 SER 120 ENGINEERED MUTATION SEQADV 8JNB GLU B 129 UNP P04049 ASP 129 ENGINEERED MUTATION SEQRES 1 B 94 GLY PRO LEU GLY SER ASP PRO SER LYS THR SER ASN THR SEQRES 2 B 94 ILE ARG VAL PHE LEU PRO ASN SER GLN ARG THR VAL VAL SEQRES 3 B 94 ASN VAL ARG ASN GLY MET SER LEU HIS ASP CYS LEU MET SEQRES 4 B 94 LYS ALA LEU LYS VAL ARG GLY LEU GLN PRO GLU CYS CYS SEQRES 5 B 94 ALA VAL TYR ARG LEU GLN ASP GLY GLU LYS LYS PRO ILE SEQRES 6 B 94 GLY TRP ASN THR ASP ALA ALA TRP LEU ILE GLY GLU GLU SEQRES 7 B 94 LEU GLN VAL GLU PHE LEU ASP HIS VAL PRO LEU THR THR SEQRES 8 B 94 HIS ASN PHE HET USX B 201 27 HETNAM USX 2-[4-[[(2S)-1-ETHANOYL-3-OXIDANYLIDENE-2H-INDOL-2- HETNAM 2 USX YL]METHYL]-2-METHOXY-PHENOXY]ETHANAMIDE FORMUL 2 USX C20 H20 N2 O5 FORMUL 3 HOH *73(H2 O) HELIX 1 AA1 SER B 77 VAL B 88 1 12 HELIX 2 AA2 GLN B 92 GLU B 94 5 3 HELIX 3 AA3 ASP B 117 ILE B 122 5 6 SHEET 1 AA1 5 ARG B 67 ASN B 71 0 SHEET 2 AA1 5 THR B 57 PHE B 61 -1 N VAL B 60 O THR B 68 SHEET 3 AA1 5 GLU B 125 PHE B 130 1 O LEU B 126 N PHE B 61 SHEET 4 AA1 5 CYS B 96 LEU B 101 -1 N ALA B 97 O GLU B 129 SHEET 5 AA1 5 LYS B 110 ILE B 112 -1 O LYS B 110 N ARG B 100 LINK SG CYS B 95 C8 USX B 201 1555 1555 1.76 CRYST1 65.019 69.775 39.746 90.00 90.00 90.00 C 2 2 21 8 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 0.015380 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014332 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025160 0.00000