HEADER SIGNALING PROTEIN 05-JAN-23 8FPW TITLE CRYSTAL STRUCTURE OF TUMOR RELATED RHOA MUTANT A161V IN COMPLEX WITH TITLE 2 GDP COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSFORMING PROTEIN RHOA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RHO CDNA CLONE 12,H12; COMPND 5 EC: 3.6.5.2; COMPND 6 ENGINEERED: YES; COMPND 7 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: RHOA, ARH12, ARHA, RHO12; SOURCE 6 EXPRESSION_SYSTEM: BACTERIA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 2; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_VARIANT: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX4T KEYWDS SMALL G PROTEINS, GTPASE, FAST-CYCLING MUTANT, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.LIN,Y.ZHENG REVDAT 2 04-SEP-24 8FPW 1 JRNL REVDAT 1 05-JUN-24 8FPW 0 JRNL AUTH Y.LIN,T.A.RAMELOT,S.SENYUZ,A.GURSOY,H.JANG,R.NUSSINOV, JRNL AUTH 2 O.KESKIN,Y.ZHENG JRNL TITL TUMOR-DERIVED RHOA MUTANTS INTERACT WITH EFFECTORS IN THE JRNL TITL 2 GDP-BOUND STATE. JRNL REF NAT COMMUN V. 15 7176 2024 JRNL REFN ESSN 2041-1723 JRNL PMID 39169042 JRNL DOI 10.1038/S41467-024-51445-Z REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 3 NUMBER OF REFLECTIONS : 35458 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.650 REMARK 3 FREE R VALUE TEST SET COUNT : 2005 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 26.9000 - 3.3700 0.95 2407 140 0.1636 0.2011 REMARK 3 2 3.3700 - 2.6800 1.00 2480 146 0.1741 0.2248 REMARK 3 3 2.6800 - 2.3400 0.99 2475 149 0.1867 0.1997 REMARK 3 4 2.3400 - 2.1300 0.99 2451 147 0.1738 0.1925 REMARK 3 5 2.1300 - 1.9700 0.99 2458 151 0.1698 0.2073 REMARK 3 6 1.9700 - 1.8600 0.99 2439 157 0.1744 0.1914 REMARK 3 7 1.8600 - 1.7600 0.99 2423 146 0.1772 0.2221 REMARK 3 8 1.7600 - 1.6900 0.98 2412 144 0.1759 0.1939 REMARK 3 9 1.6900 - 1.6200 0.98 2443 151 0.1773 0.2191 REMARK 3 10 1.6200 - 1.5700 0.98 2412 150 0.1782 0.2124 REMARK 3 11 1.5700 - 1.5200 0.98 2433 126 0.1919 0.1805 REMARK 3 12 1.5200 - 1.4700 0.98 2414 140 0.1978 0.2119 REMARK 3 13 1.4700 - 1.4400 0.91 2232 146 0.2414 0.2511 REMARK 3 14 1.4400 - 1.4000 0.80 1974 112 0.2650 0.3020 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.880 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.006 1562 REMARK 3 ANGLE : 0.993 2128 REMARK 3 CHIRALITY : 0.086 232 REMARK 3 PLANARITY : 0.007 278 REMARK 3 DIHEDRAL : 17.067 612 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 3.5875 2.4785 2.3990 REMARK 3 T TENSOR REMARK 3 T11: 0.0920 T22: 0.1210 REMARK 3 T33: 0.0827 T12: -0.0035 REMARK 3 T13: 0.0814 T23: -0.0078 REMARK 3 L TENSOR REMARK 3 L11: 0.8304 L22: 1.6306 REMARK 3 L33: 1.1904 L12: -0.0164 REMARK 3 L13: 0.0843 L23: -0.5583 REMARK 3 S TENSOR REMARK 3 S11: -0.0040 S12: -0.0454 S13: 0.0298 REMARK 3 S21: 0.0618 S22: -0.0233 S23: 0.0214 REMARK 3 S31: -0.0195 S32: -0.0377 S33: 0.0180 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 8FPW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JAN-23. REMARK 100 THE DEPOSITION ID IS D_1000270836. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-MAR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 31-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.22 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35470 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 26.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.10800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.37900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: PLATE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20-24% PEG8K, 15% DIOXANE, 0.1M TRIS REMARK 280 PH8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 43.42200 REMARK 290 SMTRY3 2 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: 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. (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 A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 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 LYS A 98 -55.92 -124.07 REMARK 500 LYS A 164 -6.85 81.64 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 531 DISTANCE = 5.92 ANGSTROMS 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 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 19 OG1 REMARK 620 2 PRO A 36 O 91.4 REMARK 620 3 GDP A 201 O3B 92.9 173.1 REMARK 620 4 HOH A 328 O 175.6 86.7 89.4 REMARK 620 5 HOH A 352 O 86.4 92.1 93.5 89.7 REMARK 620 6 HOH A 370 O 92.8 85.9 88.5 91.1 177.9 REMARK 620 N 1 2 3 4 5 DBREF 8FPW A 1 181 UNP P61586 RHOA_HUMAN 1 181 SEQADV 8FPW GLY A -1 UNP P61586 EXPRESSION TAG SEQADV 8FPW SER A 0 UNP P61586 EXPRESSION TAG SEQADV 8FPW ASN A 25 UNP P61586 PHE 25 ENGINEERED MUTATION SEQADV 8FPW VAL A 161 UNP P61586 ALA 161 ENGINEERED MUTATION SEQRES 1 A 183 GLY SER MET ALA ALA ILE ARG LYS LYS LEU VAL ILE VAL SEQRES 2 A 183 GLY ASP GLY ALA CYS GLY LYS THR CYS LEU LEU ILE VAL SEQRES 3 A 183 ASN SER LYS ASP GLN PHE PRO GLU VAL TYR VAL PRO THR SEQRES 4 A 183 VAL PHE GLU ASN TYR VAL ALA ASP ILE GLU VAL ASP GLY SEQRES 5 A 183 LYS GLN VAL GLU LEU ALA LEU TRP ASP THR ALA GLY GLN SEQRES 6 A 183 GLU ASP TYR ASP ARG LEU ARG PRO LEU SER TYR PRO ASP SEQRES 7 A 183 THR ASP VAL ILE LEU MET CYS PHE SER ILE ASP SER PRO SEQRES 8 A 183 ASP SER LEU GLU ASN ILE PRO GLU LYS TRP THR PRO GLU SEQRES 9 A 183 VAL LYS HIS PHE CYS PRO ASN VAL PRO ILE ILE LEU VAL SEQRES 10 A 183 GLY ASN LYS LYS ASP LEU ARG ASN ASP GLU HIS THR ARG SEQRES 11 A 183 ARG GLU LEU ALA LYS MET LYS GLN GLU PRO VAL LYS PRO SEQRES 12 A 183 GLU GLU GLY ARG ASP MET ALA ASN ARG ILE GLY ALA PHE SEQRES 13 A 183 GLY TYR MET GLU CYS SER VAL LYS THR LYS ASP GLY VAL SEQRES 14 A 183 ARG GLU VAL PHE GLU MET ALA THR ARG ALA ALA LEU GLN SEQRES 15 A 183 ALA HET GDP A 201 28 HET MG A 202 1 HET DIO A 203 6 HET DIO A 204 6 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM DIO 1,4-DIETHYLENE DIOXIDE FORMUL 2 GDP C10 H15 N5 O11 P2 FORMUL 3 MG MG 2+ FORMUL 4 DIO 2(C4 H8 O2) FORMUL 6 HOH *231(H2 O) HELIX 1 AA1 GLY A 17 VAL A 24 1 8 HELIX 2 AA2 GLN A 63 ASP A 67 5 5 HELIX 3 AA3 LEU A 69 TYR A 74 5 6 HELIX 4 AA4 SER A 88 LYS A 98 1 11 HELIX 5 AA5 LYS A 98 CYS A 107 1 10 HELIX 6 AA6 LYS A 118 ARG A 122 5 5 HELIX 7 AA7 ASP A 124 LYS A 133 1 10 HELIX 8 AA8 LYS A 140 GLY A 152 1 13 HELIX 9 AA9 GLY A 166 GLN A 180 1 15 SHEET 1 AA1 6 TYR A 42 VAL A 48 0 SHEET 2 AA1 6 LYS A 51 TRP A 58 -1 O LEU A 55 N ALA A 44 SHEET 3 AA1 6 ILE A 4 GLY A 12 1 N ILE A 4 O GLU A 54 SHEET 4 AA1 6 VAL A 79 SER A 85 1 O CYS A 83 N VAL A 11 SHEET 5 AA1 6 ILE A 112 ASN A 117 1 O ILE A 113 N ILE A 80 SHEET 6 AA1 6 GLY A 155 GLU A 158 1 O MET A 157 N GLY A 116 LINK OG1 THR A 19 MG MG A 202 1555 1555 2.06 LINK O PRO A 36 MG MG A 202 1555 1555 2.02 LINK O3B GDP A 201 MG MG A 202 1555 1555 2.03 LINK MG MG A 202 O HOH A 328 1555 1555 2.15 LINK MG MG A 202 O HOH A 352 1555 1555 2.04 LINK MG MG A 202 O HOH A 370 1555 1555 2.11 CRYST1 32.010 86.844 34.337 90.00 93.75 90.00 P 1 21 1 2 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 0.031240 0.000000 0.002047 0.00000 SCALE2 0.000000 0.011515 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029186 0.00000