HEADER CELL INVASION 30-JUN-25 9VNH TITLE STRUCTURE OF WILD-TYPE RHOA IN COMPLEX WITH GDP AND 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 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, RHOA, WILD-TYPE, GDP BOUND, CELL INVASION EXPDTA X-RAY DIFFRACTION AUTHOR H.WU,C.LUO REVDAT 1 01-APR-26 9VNH 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. 1.79 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) : 1.79 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.4 REMARK 3 NUMBER OF REFLECTIONS : 15278 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1528 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 22.5400 - 3.9700 0.99 1448 161 0.1720 0.2166 REMARK 3 2 3.9700 - 3.1600 0.99 1374 152 0.1510 0.1870 REMARK 3 3 3.1600 - 2.7600 0.99 1358 152 0.1801 0.2302 REMARK 3 4 2.7600 - 2.5100 0.99 1339 148 0.1890 0.2691 REMARK 3 5 2.5100 - 2.3300 0.98 1326 147 0.1759 0.2826 REMARK 3 6 2.3300 - 2.1900 0.99 1311 146 0.1752 0.2103 REMARK 3 7 2.1900 - 2.0800 0.98 1319 147 0.1835 0.2481 REMARK 3 8 2.0800 - 1.9900 0.98 1281 142 0.1879 0.2162 REMARK 3 9 1.9900 - 1.9100 0.93 1235 138 0.2052 0.2485 REMARK 3 10 1.9100 - 1.8500 0.74 982 109 0.2171 0.2742 REMARK 3 11 1.8500 - 1.7900 0.59 777 86 0.2698 0.3129 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.100 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 1483 REMARK 3 ANGLE : 0.951 2014 REMARK 3 CHIRALITY : 0.059 221 REMARK 3 PLANARITY : 0.007 260 REMARK 3 DIHEDRAL : 15.378 566 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 9VNH 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_1300061085. 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 : 8.5 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 : 15301 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.790 REMARK 200 RESOLUTION RANGE LOW (A) : 25.260 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 200 DATA REDUNDANCY : 12.50 REMARK 200 R MERGE (I) : 0.23600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.79 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.12400 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 (%): 39.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM CHLORIDE, 0.01 M REMARK 280 CALCIUM CHLORIDE DIHYDRATE, 0.05 M TRIS HYDROCHLORIDE PH 8.5, 30% REMARK 280 W/V POLYETHYLENE GLYCOL 4000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 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 15.93500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.39000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.88500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.39000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.93500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.88500 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: 9290 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 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 GLN A 63 153.54 74.49 REMARK 500 LYS A 98 -54.38 -127.87 REMARK 500 LYS A 164 -5.35 77.48 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 ARG A 68 0.14 SIDE CHAIN REMARK 500 ARG A 129 0.18 SIDE CHAIN 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 89.6 REMARK 620 3 GDP A 201 O1B 83.8 167.6 REMARK 620 4 HOH A 320 O 84.1 97.6 92.2 REMARK 620 5 HOH A 328 O 86.3 85.5 83.6 169.9 REMARK 620 6 HOH A 340 O 177.3 93.2 93.5 95.4 94.1 REMARK 620 N 1 2 3 4 5 DBREF 9VNH A 1 181 UNP P61586 RHOA_HUMAN 1 181 SEQADV 9VNH GLY A 0 UNP P61586 EXPRESSION TAG 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 TYR 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 *153(H2 O) HELIX 1 AA1 GLY A 17 ASP A 28 1 12 HELIX 2 AA2 GLY A 62 ARG A 70 1 9 HELIX 3 AA3 PRO A 71 TYR A 74 5 4 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 LEU A 8 O ALA A 56 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 2.08 LINK O THR A 37 MG MG A 202 1555 1555 2.30 LINK O1B GDP A 201 MG MG A 202 1555 1555 2.30 LINK MG MG A 202 O HOH A 320 1555 1555 2.16 LINK MG MG A 202 O HOH A 328 1555 1555 2.28 LINK MG MG A 202 O HOH A 340 1555 1555 2.02 CRYST1 31.870 63.770 82.780 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 0.031377 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015681 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012080 0.00000 CONECT 129 1454 CONECT 274 1454 CONECT 1426 1427 1428 1429 1430 CONECT 1427 1426 1454 CONECT 1428 1426 CONECT 1429 1426 CONECT 1430 1426 1431 CONECT 1431 1430 1432 1433 1434 CONECT 1432 1431 CONECT 1433 1431 CONECT 1434 1431 1435 CONECT 1435 1434 1436 CONECT 1436 1435 1437 1438 CONECT 1437 1436 1442 CONECT 1438 1436 1439 1440 CONECT 1439 1438 CONECT 1440 1438 1441 1442 CONECT 1441 1440 CONECT 1442 1437 1440 1443 CONECT 1443 1442 1444 1453 CONECT 1444 1443 1445 CONECT 1445 1444 1446 CONECT 1446 1445 1447 1453 CONECT 1447 1446 1448 1449 CONECT 1448 1447 CONECT 1449 1447 1450 CONECT 1450 1449 1451 1452 CONECT 1451 1450 CONECT 1452 1450 1453 CONECT 1453 1443 1446 1452 CONECT 1454 129 274 1427 1474 CONECT 1454 1482 1494 CONECT 1474 1454 CONECT 1482 1454 CONECT 1494 1454 MASTER 266 0 2 9 6 0 0 6 1600 1 35 14 END