HEADER CELL INVASION 17-FEB-22 7WZC TITLE AN OPEN CONFORMATION FORM2 OF SWITCH II FOR RHOA GDP-BOUND STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSFORMING PROTEIN RHOA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C16V,C20S,C83V,C159T; COMPND 5 SYNONYM: RHO CDNA CLONE 12,H12; COMPND 6 EC: 3.6.5.2; COMPND 7 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, RHO FAMILY MEMBER, CELL INVASION EXPDTA X-RAY DIFFRACTION AUTHOR H.JIANG,C.LUO REVDAT 3 29-NOV-23 7WZC 1 REMARK REVDAT 2 06-SEP-23 7WZC 1 JRNL REVDAT 1 22-FEB-23 7WZC 0 JRNL AUTH H.JIANG,S.ZU,Y.LU,Z.SUN,A.ADEERJIANG,Q.GUO,H.ZHANG,C.DONG, JRNL AUTH 2 Q.WU,H.DING,D.DU,M.WANG,C.LIU,Y.TANG,Z.LIANG,C.LUO JRNL TITL A RHOA STRUCTURE WITH SWITCH II FLIPPED OUTWARD REVEALED THE JRNL TITL 2 CONFORMATIONAL DYNAMICS OF SWITCH II REGION. JRNL REF J.STRUCT.BIOL. V. 215 07942 2023 JRNL REFN ESSN 1095-8657 JRNL PMID 36781028 JRNL DOI 10.1016/J.JSB.2023.107942 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 16629 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.955 REMARK 3 FREE R VALUE TEST SET COUNT : 824 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 41.6815 - 3.2694 1.00 2820 148 0.1729 0.2252 REMARK 3 2 3.2694 - 2.5951 1.00 2688 140 0.2081 0.2622 REMARK 3 3 2.5951 - 2.2671 1.00 2626 148 0.2186 0.2793 REMARK 3 4 2.2671 - 2.0598 1.00 2639 144 0.2278 0.2852 REMARK 3 5 2.0598 - 1.9122 1.00 2641 127 0.2464 0.3599 REMARK 3 6 1.9122 - 1.7995 0.91 2391 117 0.2511 0.2984 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) : 0.251 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.859 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.73 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 : 0.008 1480 REMARK 3 ANGLE : 0.892 2013 REMARK 3 CHIRALITY : 0.051 227 REMARK 3 PLANARITY : 0.006 257 REMARK 3 DIHEDRAL : 13.831 888 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 7WZC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-FEB-22. REMARK 100 THE DEPOSITION ID IS D_1300027742. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-MAY-18 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 : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9789 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 : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16632 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.799 REMARK 200 RESOLUTION RANGE LOW (A) : 41.682 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 12.70 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 30.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: 1FTN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MES, PH6.0, 30% PEG 600, 5% PEG REMARK 280 1000, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 289K 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 15.74350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.68150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.17900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.68150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.74350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.17900 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: 820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 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 ALA A 181 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 PHE A -2 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLN A 29 CG CD OE1 NE2 REMARK 470 TYR A 34 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU A 47 CG CD OE1 OE2 REMARK 470 LYS A 51 CG CD CE NZ REMARK 470 ASP A 65 CG OD1 OD2 REMARK 470 ARG A 68 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 93 CG CD OE1 OE2 REMARK 470 GLU A 125 CG CD OE1 OE2 REMARK 470 ARG A 168 CG CD NE CZ NH1 NH2 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 VAL A 33 -58.21 -126.95 REMARK 500 TYR A 34 73.67 -119.80 REMARK 500 ASN A 41 2.28 86.94 REMARK 500 GLU A 64 -125.04 50.36 REMARK 500 LYS A 98 -57.50 -124.07 REMARK 500 LYS A 164 -2.35 80.13 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 203 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 19 OG1 REMARK 620 2 THR A 37 O 88.7 REMARK 620 3 GDP A 202 O1B 89.0 173.4 REMARK 620 4 HOH A 321 O 83.9 94.1 91.8 REMARK 620 5 HOH A 337 O 173.4 92.3 90.6 89.5 REMARK 620 6 HOH A 342 O 95.0 85.4 88.6 178.8 91.6 REMARK 620 N 1 2 3 4 5 DBREF 7WZC A 1 181 UNP P61586 RHOA_HUMAN 1 181 SEQADV 7WZC TYR A -3 UNP P61586 EXPRESSION TAG SEQADV 7WZC PHE A -2 UNP P61586 EXPRESSION TAG SEQADV 7WZC GLN A -1 UNP P61586 EXPRESSION TAG SEQADV 7WZC GLY A 0 UNP P61586 EXPRESSION TAG SEQADV 7WZC VAL A 16 UNP P61586 CYS 16 ENGINEERED MUTATION SEQADV 7WZC SER A 20 UNP P61586 CYS 20 ENGINEERED MUTATION SEQADV 7WZC VAL A 83 UNP P61586 CYS 83 ENGINEERED MUTATION SEQADV 7WZC THR A 159 UNP P61586 CYS 159 ENGINEERED MUTATION SEQRES 1 A 185 TYR PHE GLN GLY MET ALA ALA ILE ARG LYS LYS LEU VAL SEQRES 2 A 185 ILE VAL GLY ASP GLY ALA VAL GLY LYS THR SER LEU LEU SEQRES 3 A 185 ILE VAL PHE SER LYS ASP GLN PHE PRO GLU VAL TYR VAL SEQRES 4 A 185 PRO THR VAL PHE GLU ASN TYR VAL ALA ASP ILE GLU VAL SEQRES 5 A 185 ASP GLY LYS GLN VAL GLU LEU ALA LEU TRP ASP THR ALA SEQRES 6 A 185 GLY GLN GLU ASP TYR ASP ARG LEU ARG PRO LEU SER TYR SEQRES 7 A 185 PRO ASP THR ASP VAL ILE LEU MET VAL PHE SER ILE ASP SEQRES 8 A 185 SER PRO ASP SER LEU GLU ASN ILE PRO GLU LYS TRP THR SEQRES 9 A 185 PRO GLU VAL LYS HIS PHE CYS PRO ASN VAL PRO ILE ILE SEQRES 10 A 185 LEU VAL GLY ASN LYS LYS ASP LEU ARG ASN ASP GLU HIS SEQRES 11 A 185 THR ARG ARG GLU LEU ALA LYS MET LYS GLN GLU PRO VAL SEQRES 12 A 185 LYS PRO GLU GLU GLY ARG ASP MET ALA ASN ARG ILE GLY SEQRES 13 A 185 ALA PHE GLY TYR MET GLU THR SER ALA LYS THR LYS ASP SEQRES 14 A 185 GLY VAL ARG GLU VAL PHE GLU MET ALA THR ARG ALA ALA SEQRES 15 A 185 LEU GLN ALA HET GOL A 201 14 HET GDP A 202 40 HET MG A 203 1 HETNAM GOL GLYCEROL HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 GDP C10 H15 N5 O11 P2 FORMUL 4 MG MG 2+ FORMUL 5 HOH *117(H2 O) HELIX 1 AA1 GLY A 17 ASP A 28 1 12 HELIX 2 AA2 GLN A 63 ARG A 70 1 8 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 ASN A 123 5 6 HELIX 7 AA7 ASP A 124 LYS A 133 1 10 HELIX 8 AA8 LYS A 140 ILE A 151 1 12 HELIX 9 AA9 GLY A 166 GLN A 180 1 15 SHEET 1 AA1 6 VAL A 43 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 VAL 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 GLY A 155 N LEU A 114 LINK OG1 THR A 19 MG MG A 203 1555 1555 2.03 LINK O THR A 37 MG MG A 203 1555 1555 2.12 LINK O1B GDP A 202 MG MG A 203 1555 1555 2.09 LINK MG MG A 203 O HOH A 321 1555 1555 2.22 LINK MG MG A 203 O HOH A 337 1555 1555 2.18 LINK MG MG A 203 O HOH A 342 1555 1555 2.09 CRYST1 31.487 66.358 83.363 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 0.031759 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015070 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011996 0.00000