HEADER SIGNALING PROTEIN 07-JUN-23 8JOG TITLE SOLUTION STRUCTURE OF RAS BINDING DOMEIN (RBD) IN C-RAF WITH NEGATIVE TITLE 2 ALLOSTERIC MODULATOR. COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAF PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTO-ONCOGENE C-RAF,CRAF,RAF-1; COMPND 5 EC: 2.7.11.1; COMPND 6 ENGINEERED: YES 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; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX6P-1 KEYWDS MAPK, SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR Y.MAKINO,S.MATSUMOTO,Y.YOSHIKAWA,T.KAWAMURA,T.KUMASAKA,F.SHIMA REVDAT 1 12-JUN-24 8JOG 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. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8JOG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1300038294. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 85 REMARK 210 PRESSURE : AMBIENT ATM REMARK 210 SAMPLE CONTENTS : 0.3 MM [U-100% 13C; U-100% 15N] REMARK 210 SERIN/THREONINE PROTEIN KINASE C- REMARK 210 RAF, 25 MM SODIUM PHOSPHATE, 50 REMARK 210 MM SODIUM CHLORIDE, 10 MM REMARK 210 MAGNESIUM DICHLORIDE, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D CBCA(CO)NH; 3D REMARK 210 HNCACB; 3D HN(CO)CA; 3D HNCO; 3D REMARK 210 HN(CA)CO; 3D 1H-15N NOESY; 3D 1H- REMARK 210 13C NOESY ALIPHATIC; 3D 1H-13C REMARK 210 NOESY AROMATIC; 3D HCCH-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : MAGRO-NMRVIEW, CYANA, NMRP REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : 20 REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 O ALA A 97 HA VAL A 128 1.45 REMARK 500 O LEU A 86 H GLY A 90 1.60 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 1 PRO A 47 -169.43 -76.56 REMARK 500 1 LEU A 48 104.47 42.42 REMARK 500 1 ASN A 64 30.26 73.42 REMARK 500 1 HIS A 105 -151.34 -97.24 REMARK 500 1 LYS A 108 -168.39 -107.21 REMARK 500 2 PRO A 47 -168.58 -76.03 REMARK 500 2 ASN A 56 82.79 65.34 REMARK 500 2 ASN A 64 31.63 74.15 REMARK 500 2 HIS A 105 -52.27 -147.82 REMARK 500 2 LYS A 108 -160.55 -128.31 REMARK 500 3 LEU A 48 -77.12 50.32 REMARK 500 3 ASN A 56 85.60 55.60 REMARK 500 3 GLU A 94 -163.14 56.49 REMARK 500 3 HIS A 103 -177.26 62.54 REMARK 500 4 PRO A 47 -168.17 -77.19 REMARK 500 4 ASN A 56 81.69 54.03 REMARK 500 4 HIS A 105 -91.30 -96.55 REMARK 500 4 LYS A 106 -57.73 -137.72 REMARK 500 4 LYS A 108 -162.51 -128.35 REMARK 500 5 PRO A 47 -167.71 -78.19 REMARK 500 5 ASN A 56 84.08 54.24 REMARK 500 6 PRO A 47 -168.16 -76.21 REMARK 500 6 ASN A 56 84.01 53.80 REMARK 500 6 HIS A 105 -156.06 -96.86 REMARK 500 6 LYS A 108 -145.33 -126.05 REMARK 500 7 SER A 52 -41.53 -130.23 REMARK 500 7 LYS A 53 -50.02 71.21 REMARK 500 7 ASN A 56 82.66 55.74 REMARK 500 7 GLU A 94 -164.35 59.16 REMARK 500 7 HIS A 105 -15.12 70.02 REMARK 500 7 LYS A 108 -79.44 -138.58 REMARK 500 8 PRO A 47 -168.11 -75.92 REMARK 500 8 ASN A 56 82.34 56.18 REMARK 500 8 ASN A 64 30.99 73.06 REMARK 500 8 HIS A 105 -57.81 74.74 REMARK 500 8 LYS A 108 47.34 -83.35 REMARK 500 9 PRO A 47 -168.23 -75.94 REMARK 500 9 ASN A 56 83.35 55.07 REMARK 500 9 HIS A 105 -163.25 -114.54 REMARK 500 10 PRO A 47 -167.76 -75.12 REMARK 500 10 ASN A 56 83.73 54.45 REMARK 500 10 GLU A 94 -165.86 57.90 REMARK 500 10 HIS A 103 -177.26 61.29 REMARK 500 10 LYS A 108 -157.02 -127.70 REMARK 500 11 LYS A 53 -41.02 -141.68 REMARK 500 11 ASN A 56 81.53 53.73 REMARK 500 11 HIS A 103 -157.16 -72.00 REMARK 500 11 LYS A 106 -89.63 64.49 REMARK 500 12 PRO A 47 -168.23 -76.94 REMARK 500 12 SER A 52 -45.48 -136.14 REMARK 500 REMARK 500 THIS ENTRY HAS 95 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8JOF RELATED DB: PDB REMARK 900 RELATED ID: 36570 RELATED DB: BMRB REMARK 900 RELATED ID: 36571 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF RAS BINDING DOMEIN (RBD) IN C-RAF WITH REMARK 900 NEGATIVE ALLOSTERIC MODULATOR. DBREF 8JOG A 51 131 UNP P04049 RAF1_HUMAN 51 131 SEQADV 8JOG GLY A 46 UNP P04049 EXPRESSION TAG SEQADV 8JOG PRO A 47 UNP P04049 EXPRESSION TAG SEQADV 8JOG LEU A 48 UNP P04049 EXPRESSION TAG SEQADV 8JOG GLY A 49 UNP P04049 EXPRESSION TAG SEQADV 8JOG SER A 50 UNP P04049 EXPRESSION TAG SEQRES 1 A 86 GLY PRO LEU GLY SER PRO SER LYS THR SER ASN THR ILE SEQRES 2 A 86 ARG VAL PHE LEU PRO ASN LYS GLN ARG THR VAL VAL ASN SEQRES 3 A 86 VAL ARG ASN GLY MET SER LEU HIS ASP CYS LEU MET LYS SEQRES 4 A 86 ALA LEU LYS VAL ARG GLY LEU GLN PRO GLU CYS CYS ALA SEQRES 5 A 86 VAL PHE ARG LEU LEU HIS GLU HIS LYS GLY LYS LYS ALA SEQRES 6 A 86 ARG LEU ASP TRP ASN THR ASP ALA ALA SER LEU ILE GLY SEQRES 7 A 86 GLU GLU LEU GLN VAL ASP PHE LEU HELIX 1 AA1 SER A 77 LYS A 87 1 11 HELIX 2 AA2 ASP A 117 ILE A 122 5 6 SHEET 1 AA1 2 ILE A 58 LEU A 62 0 SHEET 2 AA1 2 GLN A 66 VAL A 70 -1 O GLN A 66 N LEU A 62 SHEET 1 AA2 3 ALA A 110 ARG A 111 0 SHEET 2 AA2 3 ALA A 97 ARG A 100 -1 N ARG A 100 O ALA A 110 SHEET 3 AA2 3 LEU A 126 ASP A 129 -1 O ASP A 129 N ALA A 97 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 MODEL 1