HEADER SIGNALING PROTEIN 20-SEP-05 2B3A TITLE SOLUTION STRUCTURE OF THE RAS-BINDING DOMAIN OF THE RAL TITLE 2 GUANOSINE DISSOCIATION STIMULATOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAL GUANINE NUCLEOTIDE DISSOCIATION STIMULATOR; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RALGEF, RALGDS; COMPND 5 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: RALGDS, RGF; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-4T3 KEYWDS RAS BINDING DOMAIN, UBIQUITIN FOLD, SIGNAL TRANSDUCTION, KEYWDS 2 NMR, AUTOMATICALLY SOLVED, AUREMOL, SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR W.GRONWALD,T.MAURER,R.FUECHSL,S.WOHLGEMUTH,C.HERRMANN, AUTHOR 2 H.R.KALBITZER REVDAT 2 24-FEB-09 2B3A 1 VERSN REVDAT 1 26-SEP-06 2B3A 0 JRNL AUTH W.GRONWALD,T.MAURER,R.FUECHSL,S.WOHLGEMUTH, JRNL AUTH 2 C.HERRMANN,H.R.KALBITZER JRNL TITL NEW INSIGHTS INTO BINDING OF THE POSSIBLE CANCER JRNL TITL 2 TARGET RALGDS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.GEYER,C.HERRMANN,S.WOHLGEMUTH,A.WITTINGHOFER, REMARK 1 AUTH 2 H.R.KALBITZER REMARK 1 TITL STRUCTURE OF THE RAS-BINDING DOMAIN OF RALGEF AND REMARK 1 TITL 2 IMPLICATIONS FOR RAS BINDING AND SIGNALLING. REMARK 1 REF NAT.STRUCT.MOL.BIOL. V. 4 694 1997 REMARK 1 REFN ISSN 1545-9993 REMARK 1 REFERENCE 2 REMARK 1 AUTH L.HUANG,X.WENG,F.HOFER,G.S.MARTIN,S.H.KIM REMARK 1 TITL THREE-DIMENSIONAL STRUCTURE OF THE RAS-INTERACTING REMARK 1 TITL 2 DOMAIN OF RALGDS. REMARK 1 REF NAT.STRUCT.MOL.BIOL. V. 4 609 1997 REMARK 1 REFN ISSN 1545-9993 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XPLOR-NIH 2.9.6 REMARK 3 AUTHORS : SCHWIETERS REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL REMARK 3 OF 1680 RESTRAINTS, 1550 ARE NOE-DERIVED DISTANCE CONSTRAINTS, REMARK 3 104 DIHEDRAL ANGLE RESTRAINTS,26 DISTANCE RESTRAINTS FROM REMARK 3 HYDROGEN BONDS. REMARK 4 REMARK 4 2B3A COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-SEP-05. REMARK 100 THE RCSB ID CODE IS RCSB034622. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 20 MM POTASSIUM BUFFER REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 20 MM POTASSIUM BUFFER AT PH REMARK 210 7.0, 2 MM DITHIOERYTHRITOL REMARK 210 (DTE), 0.5 MM EDTA, 0.5 MM REMARK 210 NAN3, 0.1 MM 2,2-DIMETHYL-2- REMARK 210 SILAPENTANE SULFONIC ACID REMARK 210 (DSS) 1.0 MM RALGDS-RBD NON REMARK 210 LABELED; 20 MM POTASSIUM REMARK 210 BUFFER AT PH 7.0, 2 MM REMARK 210 DITHIOERYTHRITOL (DTE), 0.5 MM REMARK 210 EDTA, 0.5 MM NAN3, 0.1 MM 2,2- REMARK 210 DIMETHYL-2-SILAPENTANE REMARK 210 SULFONIC ACID (DSS) 2.9 MM REMARK 210 RALGDS-RBD 15N/13C LABELED; 20 REMARK 210 MM POTASSIUM BUFFER AT PH 7.0, REMARK 210 2 MM DITHIOERYTHRITOL (DTE), REMARK 210 0.5 MM EDTA, 0.5 MM NAN3, 0.1 REMARK 210 MM 2,2-DIMETHYL-2-SILAPENTANE REMARK 210 SULFONIC ACID (DSS) 1.0 MM REMARK 210 RALGDS-RBD NON LABELED REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, 3D_15N-SEPARATED_ REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ, 600 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 2.6, AUREMOL 2.2, CNS REMARK 210 1.1 REMARK 210 METHOD USED : SIMULATED ANNEALING FIRST IN REMARK 210 TORSION ANGLE SPACE FOLLOWED REMARK 210 BY SIMULATED ANNEALING IN REMARK 210 CARTESIAN SPACE. FINAL REMARK 210 REFINEMENT IN EXPLICIT SOLVENT REMARK 210 (H2O). REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 300 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: SEQUENTIAL ASSIGNMENT BASSED ON TRIPLE RESONANCE REMARK 210 SPECTRA, 2D 1H TOCSY, 3D 15N EDITED TOCSY, 3D 13C EDITED TOCSY 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 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 1 VAL A 41 CB VAL A 41 CG2 0.128 REMARK 500 1 TYR A 89 CB TYR A 89 CG 0.090 REMARK 500 2 VAL A 41 CB VAL A 41 CG2 0.127 REMARK 500 3 TYR A 89 CB TYR A 89 CG 0.095 REMARK 500 5 TYR A 89 CB TYR A 89 CG 0.100 REMARK 500 6 TYR A 89 CB TYR A 89 CG 0.092 REMARK 500 8 TYR A 89 CB TYR A 89 CG 0.101 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 ASP A 22 -57.42 -132.56 REMARK 500 1 ASN A 25 -47.30 61.36 REMARK 500 1 MET A 26 129.27 -179.79 REMARK 500 1 TYR A 27 -61.60 -128.01 REMARK 500 1 LEU A 51 46.28 -91.07 REMARK 500 1 LEU A 65 -93.35 -102.56 REMARK 500 1 ASP A 67 6.06 53.81 REMARK 500 1 ASP A 68 -77.78 -131.08 REMARK 500 1 SER A 85 -40.16 68.23 REMARK 500 1 ALA A 87 -73.56 -124.24 REMARK 500 1 TYR A 89 70.37 -108.76 REMARK 500 1 ARG A 96 79.28 -112.33 REMARK 500 2 ASN A 25 145.02 71.27 REMARK 500 2 MET A 26 117.56 73.77 REMARK 500 2 TYR A 27 -75.29 -149.92 REMARK 500 2 ASN A 50 65.43 63.79 REMARK 500 2 LEU A 65 -84.16 -109.71 REMARK 500 2 ASP A 68 -66.88 -157.10 REMARK 500 2 SER A 85 -60.58 61.08 REMARK 500 2 ASN A 88 157.57 69.88 REMARK 500 2 TYR A 89 64.88 -152.17 REMARK 500 3 ASN A 25 104.97 61.73 REMARK 500 3 MET A 26 131.94 76.17 REMARK 500 3 TYR A 27 -80.26 -145.99 REMARK 500 3 LEU A 65 -78.49 -118.89 REMARK 500 3 ASP A 68 -54.28 -176.08 REMARK 500 3 SER A 85 -36.48 62.23 REMARK 500 4 ASN A 23 58.40 -107.46 REMARK 500 4 ASN A 25 129.86 72.40 REMARK 500 4 MET A 26 129.08 79.60 REMARK 500 4 TYR A 27 -72.30 -136.98 REMARK 500 4 LEU A 65 -76.73 -104.65 REMARK 500 4 ASP A 67 -44.52 62.05 REMARK 500 4 ASP A 68 -54.14 -125.64 REMARK 500 4 ARG A 69 88.22 -65.01 REMARK 500 5 ASN A 23 -31.82 -38.63 REMARK 500 5 MET A 26 98.75 63.18 REMARK 500 5 TYR A 27 -89.27 -95.30 REMARK 500 5 ASN A 50 77.89 67.76 REMARK 500 5 LEU A 65 -76.58 -98.82 REMARK 500 5 ASP A 68 -58.46 -163.91 REMARK 500 5 SER A 85 -174.60 -176.24 REMARK 500 5 THR A 86 34.43 -87.07 REMARK 500 5 TYR A 89 59.15 -95.71 REMARK 500 6 ASP A 22 -43.21 -140.15 REMARK 500 6 ASN A 23 131.87 -177.41 REMARK 500 6 MET A 26 98.48 56.60 REMARK 500 6 TYR A 27 -69.75 -105.52 REMARK 500 6 ASN A 50 77.91 71.96 REMARK 500 6 SER A 66 -93.58 34.53 REMARK 500 6 ASP A 67 74.05 -170.13 REMARK 500 6 ASP A 68 -75.87 -170.18 REMARK 500 6 THR A 86 50.88 -166.85 REMARK 500 6 TYR A 89 75.94 -103.79 REMARK 500 7 ASP A 22 86.71 -167.00 REMARK 500 7 ASN A 25 -19.06 63.81 REMARK 500 7 MET A 26 -45.42 81.27 REMARK 500 7 TYR A 27 -87.73 61.87 REMARK 500 7 LEU A 65 -76.62 -109.04 REMARK 500 7 ASP A 68 -66.62 -162.80 REMARK 500 7 SER A 85 -55.35 64.15 REMARK 500 7 TYR A 89 78.51 -118.42 REMARK 500 8 MET A 26 95.76 74.99 REMARK 500 8 TYR A 27 -77.43 -111.72 REMARK 500 8 ASN A 50 69.49 66.28 REMARK 500 8 LEU A 65 -60.18 -95.48 REMARK 500 8 ASP A 68 -61.07 -176.20 REMARK 500 8 PRO A 74 -157.12 -97.20 REMARK 500 8 ASN A 84 -88.13 -83.79 REMARK 500 8 SER A 85 -41.69 71.60 REMARK 500 8 ASN A 88 155.67 72.06 REMARK 500 8 TYR A 89 60.21 -150.32 REMARK 500 9 ASN A 25 113.21 -166.04 REMARK 500 9 MET A 26 112.99 73.91 REMARK 500 9 TYR A 27 -101.41 -140.42 REMARK 500 9 GLU A 54 54.75 -100.90 REMARK 500 9 GLU A 55 150.70 -47.84 REMARK 500 9 LEU A 65 -78.35 -105.69 REMARK 500 9 ASP A 67 22.36 42.37 REMARK 500 9 ASP A 68 -65.56 -152.44 REMARK 500 9 SER A 85 -59.78 57.79 REMARK 500 9 ALA A 87 -69.37 -103.55 REMARK 500 9 TYR A 89 49.75 -158.44 REMARK 500 9 ARG A 96 -66.58 -107.42 REMARK 500 10 MET A 26 155.67 72.54 REMARK 500 10 TYR A 27 -75.16 -133.14 REMARK 500 10 LEU A 65 -68.19 -106.97 REMARK 500 10 ASP A 67 29.91 -67.70 REMARK 500 10 ASP A 68 -74.26 -138.43 REMARK 500 10 SER A 85 -70.06 69.60 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 3 ARG A 96 0.09 SIDE_CHAIN REMARK 500 10 ARG A 96 0.09 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 2B3A A 11 97 UNP Q12967 GNDS_HUMAN 798 884 SEQRES 1 A 87 ASP CYS CYS ILE ILE ARG VAL SER LEU ASP VAL ASP ASN SEQRES 2 A 87 GLY ASN MET TYR LYS SER ILE LEU VAL THR SER GLN ASP SEQRES 3 A 87 LYS ALA PRO ALA VAL ILE ARG LYS ALA MET ASP LYS HIS SEQRES 4 A 87 ASN LEU GLU GLU GLU GLU PRO GLU ASP TYR GLU LEU LEU SEQRES 5 A 87 GLN ILE LEU SER ASP ASP ARG LYS LEU LYS ILE PRO GLU SEQRES 6 A 87 ASN ALA ASN VAL PHE TYR ALA MET ASN SER THR ALA ASN SEQRES 7 A 87 TYR ASP PHE VAL LEU LYS LYS ARG THR HELIX 1 1 LYS A 37 HIS A 49 1 13 HELIX 2 2 ASN A 78 MET A 83 1 6 SHEET 1 A 5 LYS A 28 VAL A 32 0 SHEET 2 A 5 CYS A 13 LEU A 19 -1 N VAL A 17 O LYS A 28 SHEET 3 A 5 ASP A 90 LYS A 95 1 O PHE A 91 N SER A 18 SHEET 4 A 5 TYR A 59 ILE A 64 -1 N ILE A 64 O ASP A 90 SHEET 5 A 5 LYS A 70 ILE A 73 -1 O LEU A 71 N GLN A 63 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 237 0 0 2 5 0 0 6 0 0 0 7 END