HEADER CELL INVASION 30-JUN-25 9VNI TITLE STRUCTURE OF THE RHOA Y42C MUTANT FEATURING THR37 COORDINATION OF TITLE 2 MAGNESIUM ION 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; COMPND 8 OTHER_DETAILS: Y42C MUTANT 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: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SMALL GTPASE, Y42C MUTANT, GDP BOUND, CELL INVASION EXPDTA X-RAY DIFFRACTION AUTHOR H.WU,C.LUO REVDAT 1 01-APR-26 9VNI 0 JRNL AUTH H.WU,Z.LIU,H.JIANG,H.ZHAO,C.DONG,Y.LU,S.ZU,Y.GUO,C.LAI, JRNL AUTH 2 P.LUO,K.XU,Y.YANG,Y.YANG,Z.SUN,Q.HUANG,H.XIONG,L.ZHOU,Y.LUO, JRNL AUTH 3 Y.ZENG,D.DU,Z.LIANG,W.XIAO,S.ZHAO,W.ZHANG,Y.TANG,C.XIAO, JRNL AUTH 4 K.CHEN,X.YANG,F.WANG,C.LUO JRNL TITL DISCOVERING TARGETABLE CONFORMATION OF RHOA MUTANT BY JRNL TITL 2 INTEGRATING NATIVE MASS SPECTROMETRY, ULTRAVIOLET JRNL TITL 3 PHOTODISSOCIATION, AND X-RAY DIFFRACTION. JRNL REF J.AM.CHEM.SOC. 2026 JRNL REFN ESSN 1520-5126 JRNL PMID 41837560 JRNL DOI 10.1021/JACS.5C20067 REMARK 2 REMARK 2 RESOLUTION. 1.83 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.21.1_5286: ???) 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) : 1.83 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.42 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 15204 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1521 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 28.4200 - 4.0700 0.99 1329 149 0.1803 0.2072 REMARK 3 2 4.0700 - 3.2300 1.00 1274 140 0.1674 0.2607 REMARK 3 3 3.2300 - 2.8200 1.00 1253 141 0.1941 0.2350 REMARK 3 4 2.8200 - 2.5600 1.00 1246 137 0.2009 0.2535 REMARK 3 5 2.5600 - 2.3800 1.00 1237 138 0.1939 0.2401 REMARK 3 6 2.3800 - 2.2400 1.00 1242 138 0.2006 0.2597 REMARK 3 7 2.2400 - 2.1300 1.00 1202 134 0.1988 0.2329 REMARK 3 8 2.1300 - 2.0300 1.00 1241 138 0.2209 0.2870 REMARK 3 9 2.0300 - 1.9600 1.00 1218 134 0.2442 0.2884 REMARK 3 10 1.9600 - 1.8900 1.00 1228 137 0.2481 0.2953 REMARK 3 11 1.8900 - 1.8300 1.00 1213 135 0.2678 0.3297 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.130 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 : 0.007 1432 REMARK 3 ANGLE : 0.943 1941 REMARK 3 CHIRALITY : 0.057 215 REMARK 3 PLANARITY : 0.007 248 REMARK 3 DIHEDRAL : 16.366 545 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 9VNI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 04-JUL-25. REMARK 100 THE DEPOSITION ID IS D_1300061090. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAR-25 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97946 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15240 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.830 REMARK 200 RESOLUTION RANGE LOW (A) : 28.420 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 12.60 REMARK 200 R MERGE (I) : 0.37100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.83 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.88 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.68400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% V/V 2-PROPANOL, 0.1 M SODIUM REMARK 280 ACETATE TRIHYDRATE PH 4.0, 22% W/V POLYETHYLENE GLYCOL 6000, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 15.89500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 40.92000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.71500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 40.92000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.89500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.71500 REMARK 290 SMTRY3 4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 KCAL/MOL 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 0 REMARK 465 MET A 1 REMARK 465 GLU A 32 REMARK 465 VAL A 33 REMARK 465 GLN A 63 REMARK 465 GLU A 64 REMARK 465 ASP A 65 REMARK 465 ALA A 181 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 -55.95 -134.72 REMARK 500 LYS A 164 -4.06 76.46 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 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 19 OG1 REMARK 620 2 THR A 37 O 89.2 REMARK 620 3 GDP A 201 O2B 89.4 174.1 REMARK 620 4 HOH A 323 O 174.2 86.8 95.1 REMARK 620 5 HOH A 328 O 84.1 92.4 93.2 92.0 REMARK 620 6 HOH A 331 O 88.6 84.4 89.8 95.1 172.0 REMARK 620 N 1 2 3 4 5 DBREF 9VNI A 1 181 UNP P61586 RHOA_HUMAN 1 181 SEQADV 9VNI GLY A 0 UNP P61586 EXPRESSION TAG SEQADV 9VNI CYS A 42 UNP P61586 TYR 42 ENGINEERED MUTATION SEQRES 1 A 182 GLY MET ALA ALA ILE ARG LYS LYS LEU VAL ILE VAL GLY SEQRES 2 A 182 ASP GLY ALA CYS GLY LYS THR CYS LEU LEU ILE VAL PHE SEQRES 3 A 182 SER LYS ASP GLN PHE PRO GLU VAL TYR VAL PRO THR VAL SEQRES 4 A 182 PHE GLU ASN CYS VAL ALA ASP ILE GLU VAL ASP GLY LYS SEQRES 5 A 182 GLN VAL GLU LEU ALA LEU TRP ASP THR ALA GLY GLN GLU SEQRES 6 A 182 ASP TYR ASP ARG LEU ARG PRO LEU SER TYR PRO ASP THR SEQRES 7 A 182 ASP VAL ILE LEU MET CYS PHE SER ILE ASP SER PRO ASP SEQRES 8 A 182 SER LEU GLU ASN ILE PRO GLU LYS TRP THR PRO GLU VAL SEQRES 9 A 182 LYS HIS PHE CYS PRO ASN VAL PRO ILE ILE LEU VAL GLY SEQRES 10 A 182 ASN LYS LYS ASP LEU ARG ASN ASP GLU HIS THR ARG ARG SEQRES 11 A 182 GLU LEU ALA LYS MET LYS GLN GLU PRO VAL LYS PRO GLU SEQRES 12 A 182 GLU GLY ARG ASP MET ALA ASN ARG ILE GLY ALA PHE GLY SEQRES 13 A 182 TYR MET GLU CYS SER ALA LYS THR LYS ASP GLY VAL ARG SEQRES 14 A 182 GLU VAL PHE GLU MET ALA THR ARG ALA ALA LEU GLN ALA HET GDP A 201 28 HET MG A 202 1 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 2 GDP C10 H15 N5 O11 P2 FORMUL 3 MG MG 2+ FORMUL 4 HOH *99(H2 O) HELIX 1 AA1 GLY A 17 ASP A 28 1 12 HELIX 2 AA2 LEU A 69 TYR A 74 5 6 HELIX 3 AA3 SER A 88 LYS A 98 1 11 HELIX 4 AA4 LYS A 98 CYS A 107 1 10 HELIX 5 AA5 LYS A 118 ARG A 122 5 5 HELIX 6 AA6 ASP A 124 LYS A 133 1 10 HELIX 7 AA7 LYS A 140 GLY A 152 1 13 HELIX 8 AA8 GLY A 166 GLN A 180 1 15 SHEET 1 AA1 6 CYS 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 ASN A 117 N PHE A 84 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 2.01 LINK O THR A 37 MG MG A 202 1555 1555 2.16 LINK O2B GDP A 201 MG MG A 202 1555 1555 2.06 LINK MG MG A 202 O HOH A 323 1555 1555 2.18 LINK MG MG A 202 O HOH A 328 1555 1555 1.98 LINK MG MG A 202 O HOH A 331 1555 1555 2.09 CRYST1 31.790 63.430 81.840 90.00 90.00 90.00 P 21 21 21 4 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 0.031456 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015765 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012219 0.00000 CONECT 129 1406 CONECT 258 1406 CONECT 1378 1379 1380 1381 1382 CONECT 1379 1378 CONECT 1380 1378 1406 CONECT 1381 1378 CONECT 1382 1378 1383 CONECT 1383 1382 1384 1385 1386 CONECT 1384 1383 CONECT 1385 1383 CONECT 1386 1383 1387 CONECT 1387 1386 1388 CONECT 1388 1387 1389 1390 CONECT 1389 1388 1394 CONECT 1390 1388 1391 1392 CONECT 1391 1390 CONECT 1392 1390 1393 1394 CONECT 1393 1392 CONECT 1394 1389 1392 1395 CONECT 1395 1394 1396 1405 CONECT 1396 1395 1397 CONECT 1397 1396 1398 CONECT 1398 1397 1399 1405 CONECT 1399 1398 1400 1401 CONECT 1400 1399 CONECT 1401 1399 1402 CONECT 1402 1401 1403 1404 CONECT 1403 1402 CONECT 1404 1402 1405 CONECT 1405 1395 1398 1404 CONECT 1406 129 258 1380 1429 CONECT 1406 1434 1437 CONECT 1429 1406 CONECT 1434 1406 CONECT 1437 1406 MASTER 252 0 2 8 6 0 0 6 1498 1 35 14 END