HEADER SIGNALING PROTEIN 28-APR-11 2LCF TITLE SOLUTION STRUCTURE OF GPPNHP-BOUND H-RAST35S MUTANT PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: GTPASE HRAS; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-166; COMPND 5 SYNONYM: H-RAS-1, HA-RAS, TRANSFORMING PROTEIN P21, C-H-RAS, P21RAS, COMPND 6 GTPASE HRAS, N-TERMINALLY PROCESSED; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: HRAS; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PGEX-6P KEYWDS RAS, SIGNALING PROTEIN, GTP-BOUND FORM, CONFORMATIONAL STATES EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.ARAKI,F.SHIMA,Y.YOSHIKAWA,S.MURAOKA,Y.IJIRI,Y.NAGAHARA,T.SHIRONO, AUTHOR 2 T.KATAOKA,A.TAMURA REVDAT 3 01-MAY-24 2LCF 1 REMARK LINK REVDAT 2 01-JAN-20 2LCF 1 JRNL REMARK SEQADV REVDAT 1 28-SEP-11 2LCF 0 JRNL AUTH M.ARAKI,F.SHIMA,Y.YOSHIKAWA,S.MURAOKA,Y.IJIRI,Y.NAGAHARA, JRNL AUTH 2 T.SHIRONO,T.KATAOKA,A.TAMURA JRNL TITL SOLUTION STRUCTURE OF THE STATE 1 CONFORMER OF GTP-BOUND JRNL TITL 2 H-RAS PROTEIN AND DISTINCT DYNAMIC PROPERTIES BETWEEN THE JRNL TITL 3 STATE 1 AND STATE 2 CONFORMERS. JRNL REF J.BIOL.CHEM. V. 286 39644 2011 JRNL REFN ESSN 1083-351X JRNL PMID 21930707 JRNL DOI 10.1074/JBC.M111.227074 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.1, CNS 1.2 REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), REMARK 3 BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANNEAL.INP REMARK 4 REMARK 4 2LCF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-MAY-11. REMARK 100 THE DEPOSITION ID IS D_1000102225. 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 : 0.24 REMARK 210 PRESSURE : AMBIENT ATM REMARK 210 SAMPLE CONTENTS : 1-2MM [U-98% 13C; U-98% 15N] REMARK 210 HRAS-1, 1-2MM REMARK 210 PHOSPHOAMINOPHOSPHONIC ACID- REMARK 210 GUANYLATE ESTER-2, 10MM REMARK 210 MAGNESIUM ION-3, 150MM SODIUM REMARK 210 CHLORIDE-4, 25MM SODIUM REMARK 210 PHOSPHATE-5, 90% H2O/10% D2O; 1- REMARK 210 2MM [U-98% 15N] HRAS-6, 1-2MM REMARK 210 PHOSPHOAMINOPHOSPHONIC ACID- REMARK 210 GUANYLATE ESTER-7, 10MM REMARK 210 MAGNESIUM ION-8, 150MM SODIUM REMARK 210 CHLORIDE-9, 25MM SODIUM REMARK 210 PHOSPHATE-10, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-13C HSQC; 3D CBCA(CO)NH; REMARK 210 3D HNCO; 3D HNCA; 3D HBHA(CO)NH; REMARK 210 3D HN(CO)CA; 3D H(CCO)NH; 3D REMARK 210 HCCH-TOCSY; 3D 1H-13C NOESY; 3D REMARK 210 HCCH-COSY; 2D 1H-15N HSQC; 3D 1H- REMARK 210 15N NOESY; 3D 1H-15N TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, SPARKY REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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: 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 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 GLY A -5 REMARK 465 PRO A -4 REMARK 465 LEU A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 ASP A 0 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 ILE A 24 -71.10 -111.03 REMARK 500 1 ASN A 26 74.64 65.11 REMARK 500 1 GLU A 31 31.70 -166.42 REMARK 500 1 SER A 35 130.89 62.74 REMARK 500 1 GLN A 61 70.50 45.14 REMARK 500 1 GLU A 63 87.51 56.46 REMARK 500 1 TYR A 64 34.35 -169.15 REMARK 500 1 SER A 106 141.51 -177.73 REMARK 500 1 LEU A 120 162.67 -49.23 REMARK 500 1 ARG A 149 64.06 68.02 REMARK 500 2 ASP A 30 23.13 -150.10 REMARK 500 2 GLU A 31 76.45 -173.63 REMARK 500 2 SER A 35 91.68 56.74 REMARK 500 2 ASP A 38 45.58 -103.28 REMARK 500 2 SER A 39 -178.26 -54.05 REMARK 500 2 ASP A 57 76.28 -109.65 REMARK 500 2 GLN A 61 98.24 73.14 REMARK 500 2 SER A 65 -36.74 179.28 REMARK 500 2 ASN A 116 172.15 -55.41 REMARK 500 2 ALA A 121 39.06 -95.57 REMARK 500 2 ALA A 122 34.56 -143.48 REMARK 500 2 ARG A 149 60.35 65.99 REMARK 500 3 ASN A 26 76.67 -62.83 REMARK 500 3 PHE A 28 132.94 75.46 REMARK 500 3 ASP A 30 -36.56 176.31 REMARK 500 3 SER A 35 96.22 59.59 REMARK 500 3 GLN A 61 -65.62 -109.70 REMARK 500 3 GLU A 62 -156.10 -61.28 REMARK 500 3 TYR A 64 -86.26 -143.84 REMARK 500 3 SER A 106 139.31 -170.68 REMARK 500 3 ARG A 149 65.51 63.45 REMARK 500 4 ILE A 24 -69.58 -106.56 REMARK 500 4 ASN A 26 75.11 65.68 REMARK 500 4 ASP A 30 -37.93 178.68 REMARK 500 4 GLU A 31 50.31 -94.20 REMARK 500 4 ASP A 57 69.65 -114.31 REMARK 500 4 SER A 106 122.06 -178.48 REMARK 500 4 LEU A 120 178.37 -52.93 REMARK 500 4 ARG A 149 37.30 70.10 REMARK 500 5 PHE A 28 -85.17 -53.58 REMARK 500 5 VAL A 29 148.06 178.94 REMARK 500 5 ASP A 30 -36.45 173.70 REMARK 500 5 SER A 35 103.94 62.17 REMARK 500 5 GLU A 63 86.15 52.89 REMARK 500 5 SER A 65 -45.16 -135.97 REMARK 500 5 ALA A 122 36.90 -144.83 REMARK 500 5 ARG A 149 73.77 57.39 REMARK 500 6 ALA A 11 -172.44 -176.59 REMARK 500 6 ILE A 24 -71.21 -116.45 REMARK 500 6 ASN A 26 69.15 69.63 REMARK 500 REMARK 500 THIS ENTRY HAS 197 RAMACHANDRAN OUTLIERS. 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 A 246 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 17 OG REMARK 620 2 GNP A 219 O2G 165.7 REMARK 620 3 GNP A 219 O2B 81.3 91.1 REMARK 620 4 HOH A 252 O 87.5 81.3 96.3 REMARK 620 5 HOH A 258 O 91.7 99.0 80.4 176.7 REMARK 620 6 HOH A 264 O 92.1 95.9 172.9 86.2 97.0 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GNP A 219 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 246 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17610 RELATED DB: BMRB DBREF 2LCF A 1 166 UNP P01112 RASH_HUMAN 1 166 SEQADV 2LCF GLY A -5 UNP P01112 EXPRESSION TAG SEQADV 2LCF PRO A -4 UNP P01112 EXPRESSION TAG SEQADV 2LCF LEU A -3 UNP P01112 EXPRESSION TAG SEQADV 2LCF GLY A -2 UNP P01112 EXPRESSION TAG SEQADV 2LCF SER A -1 UNP P01112 EXPRESSION TAG SEQADV 2LCF ASP A 0 UNP P01112 EXPRESSION TAG SEQADV 2LCF SER A 35 UNP P01112 THR 35 ENGINEERED MUTATION SEQRES 1 A 172 GLY PRO LEU GLY SER ASP MET THR GLU TYR LYS LEU VAL SEQRES 2 A 172 VAL VAL GLY ALA GLY GLY VAL GLY LYS SER ALA LEU THR SEQRES 3 A 172 ILE GLN LEU ILE GLN ASN HIS PHE VAL ASP GLU TYR ASP SEQRES 4 A 172 PRO SER ILE GLU ASP SER TYR ARG LYS GLN VAL VAL ILE SEQRES 5 A 172 ASP GLY GLU THR CYS LEU LEU ASP ILE LEU ASP THR ALA SEQRES 6 A 172 GLY GLN GLU GLU TYR SER ALA MET ARG ASP GLN TYR MET SEQRES 7 A 172 ARG THR GLY GLU GLY PHE LEU CYS VAL PHE ALA ILE ASN SEQRES 8 A 172 ASN THR LYS SER PHE GLU ASP ILE HIS GLN TYR ARG GLU SEQRES 9 A 172 GLN ILE LYS ARG VAL LYS ASP SER ASP ASP VAL PRO MET SEQRES 10 A 172 VAL LEU VAL GLY ASN LYS CYS ASP LEU ALA ALA ARG THR SEQRES 11 A 172 VAL GLU SER ARG GLN ALA GLN ASP LEU ALA ARG SER TYR SEQRES 12 A 172 GLY ILE PRO TYR ILE GLU THR SER ALA LYS THR ARG GLN SEQRES 13 A 172 GLY VAL GLU ASP ALA PHE TYR THR LEU VAL ARG GLU ILE SEQRES 14 A 172 ARG GLN HIS HET GNP A 219 45 HET MG A 246 1 HETNAM GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER HETNAM MG MAGNESIUM ION FORMUL 2 GNP C10 H17 N6 O13 P3 FORMUL 3 MG MG 2+ FORMUL 4 HOH *3(H2 O) HELIX 1 1 GLY A 15 GLN A 25 1 11 HELIX 2 2 TYR A 64 ARG A 73 1 10 HELIX 3 3 ASN A 86 ASP A 105 1 20 HELIX 4 4 GLU A 126 GLY A 138 1 13 HELIX 5 5 GLY A 151 HIS A 166 1 16 SHEET 1 A 6 TYR A 40 VAL A 45 0 SHEET 2 A 6 THR A 50 ASP A 57 -1 O CYS A 51 N VAL A 44 SHEET 3 A 6 GLU A 3 VAL A 9 1 N LEU A 6 O LEU A 56 SHEET 4 A 6 GLY A 77 ALA A 83 1 O LEU A 79 N VAL A 9 SHEET 5 A 6 MET A 111 ASN A 116 1 O VAL A 112 N CYS A 80 SHEET 6 A 6 TYR A 141 GLU A 143 1 O ILE A 142 N GLY A 115 LINK OG SER A 17 MG MG A 246 1555 1555 2.27 LINK O2G GNP A 219 MG MG A 246 1555 1555 2.02 LINK O2B GNP A 219 MG MG A 246 1555 1555 2.25 LINK MG MG A 246 O HOH A 252 1555 1555 2.22 LINK MG MG A 246 O HOH A 258 1555 1555 2.23 LINK MG MG A 246 O HOH A 264 1555 1555 2.19 SITE 1 AC1 16 GLY A 12 GLY A 13 SER A 17 PHE A 28 SITE 2 AC1 16 VAL A 29 TYR A 32 SER A 35 ASN A 116 SITE 3 AC1 16 LYS A 117 ASP A 119 LEU A 120 ALA A 146 SITE 4 AC1 16 LYS A 147 MG A 246 HOH A 252 HOH A 258 SITE 1 AC2 5 SER A 17 GNP A 219 HOH A 252 HOH A 258 SITE 2 AC2 5 HOH A 264 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