HEADER ONCOPROTEIN 21-MAR-24 9B4Q TITLE CRYSTAL STRUCTURE OF RRAS2 (RAS-RELATED PROTEIN) BOUND TO GMPPNP COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAS-RELATED PROTEIN R-RAS2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RAS-LIKE PROTEIN TC21,TERATOCARCINOMA ONCOGENE; COMPND 5 EC: 3.6.5.-; 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: RRAS2, TC21; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RAS, RRAS2, TC21, ONCOPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.J.CZYZYK,D.K.SIMANSHU REVDAT 1 22-JAN-25 9B4Q 0 JRNL AUTH D.CZYZYK,W.YAN,S.MESSING,W.GILLETTE,T.TSUJI,M.YAMAGUCHI, JRNL AUTH 2 S.FURUZONO,D.M.TURNER,D.ESPOSITO,D.V.NISSLEY,F.MCCORMICK, JRNL AUTH 3 D.K.SIMANSHU JRNL TITL STRUCTURAL INSIGHTS INTO ISOFORM-SPECIFIC RAS-PI3K ALPHA JRNL TITL 2 INTERACTIONS AND THE ROLE OF RAS IN PI3K ALPHA ACTIVATION. JRNL REF NAT COMMUN V. 16 525 2025 JRNL REFN ESSN 2041-1723 JRNL PMID 39788953 JRNL DOI 10.1038/S41467-024-55766-X REMARK 2 REMARK 2 RESOLUTION. 1.46 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.21_5207: ???) 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) : 1.46 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.52 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 29153 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) : 0.182 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1456 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 45.5200 - 3.1400 1.00 2955 154 0.1577 0.1853 REMARK 3 2 3.1400 - 2.4900 1.00 2833 144 0.1804 0.1998 REMARK 3 3 2.4900 - 2.1800 1.00 2796 153 0.1658 0.1823 REMARK 3 4 2.1800 - 1.9800 1.00 2760 148 0.1602 0.2202 REMARK 3 5 1.9800 - 1.8400 1.00 2760 141 0.1833 0.2668 REMARK 3 6 1.8400 - 1.7300 1.00 2755 149 0.2109 0.2562 REMARK 3 7 1.7300 - 1.6400 0.99 2725 142 0.2104 0.2715 REMARK 3 8 1.6400 - 1.5700 0.99 2698 148 0.2487 0.2836 REMARK 3 9 1.5700 - 1.5100 1.00 2748 136 0.3448 0.3822 REMARK 3 10 1.5100 - 1.4600 0.98 2667 141 0.5214 0.6004 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.620 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 : 0.012 1483 REMARK 3 ANGLE : 1.316 2017 REMARK 3 CHIRALITY : 0.143 220 REMARK 3 PLANARITY : 0.012 260 REMARK 3 DIHEDRAL : 13.717 574 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): -9.0766 15.2320 -17.2461 REMARK 3 T TENSOR REMARK 3 T11: 0.1662 T22: 0.1673 REMARK 3 T33: 0.1191 T12: -0.0048 REMARK 3 T13: 0.0083 T23: -0.0078 REMARK 3 L TENSOR REMARK 3 L11: 2.5564 L22: 3.1901 REMARK 3 L33: 0.9612 L12: -0.2913 REMARK 3 L13: -0.0359 L23: -0.2902 REMARK 3 S TENSOR REMARK 3 S11: 0.0298 S12: -0.0511 S13: -0.0434 REMARK 3 S21: 0.1991 S22: 0.0308 S23: 0.1585 REMARK 3 S31: 0.0351 S32: -0.0789 S33: 0.0035 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 9B4Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-MAR-24. REMARK 100 THE DEPOSITION ID IS D_1000282566. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-JUL-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29226 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.460 REMARK 200 RESOLUTION RANGE LOW (A) : 45.520 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 12.60 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.4600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.46 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.54 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.23000 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS, 5%W/V PGA-LM, 30%W/V PEG REMARK 280 MME 550, PH 7.8, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 19.64950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.04450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.39850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.04450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.64950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.39850 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 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 11 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 GLN A 12 CG CD OE1 NE2 REMARK 470 HIS A 133 CG ND1 CD2 CE1 NE2 REMARK 470 GLN A 179 CG CD OE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 412 O HOH A 429 2.15 REMARK 500 O HOH A 431 O HOH A 438 2.18 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 SER A 28 OG REMARK 620 2 THR A 46 OG1 82.4 REMARK 620 3 GNP A 201 O2G 175.4 93.2 REMARK 620 4 GNP A 201 O1B 93.8 173.7 90.6 REMARK 620 5 HOH A 338 O 88.3 96.1 90.6 88.8 REMARK 620 6 HOH A 339 O 90.0 88.6 91.5 86.3 174.7 REMARK 620 N 1 2 3 4 5 DBREF 9B4Q A 11 179 UNP P62070 RRAS2_HUMAN 11 179 SEQRES 1 A 169 GLY GLN GLU LYS TYR ARG LEU VAL VAL VAL GLY GLY GLY SEQRES 2 A 169 GLY VAL GLY LYS SER ALA LEU THR ILE GLN PHE ILE GLN SEQRES 3 A 169 SER TYR PHE VAL THR ASP TYR ASP PRO THR ILE GLU ASP SEQRES 4 A 169 SER TYR THR LYS GLN CYS VAL ILE ASP ASP ARG ALA ALA SEQRES 5 A 169 ARG LEU ASP ILE LEU ASP THR ALA GLY GLN GLU GLU PHE SEQRES 6 A 169 GLY ALA MET ARG GLU GLN TYR MET ARG THR GLY GLU GLY SEQRES 7 A 169 PHE LEU LEU VAL PHE SER VAL THR ASP ARG GLY SER PHE SEQRES 8 A 169 GLU GLU ILE TYR LYS PHE GLN ARG GLN ILE LEU ARG VAL SEQRES 9 A 169 LYS ASP ARG ASP GLU PHE PRO MET ILE LEU ILE GLY ASN SEQRES 10 A 169 LYS ALA ASP LEU ASP HIS GLN ARG GLN VAL THR GLN GLU SEQRES 11 A 169 GLU GLY GLN GLN LEU ALA ARG GLN LEU LYS VAL THR TYR SEQRES 12 A 169 MET GLU ALA SER ALA LYS ILE ARG MET ASN VAL ASP GLN SEQRES 13 A 169 ALA PHE HIS GLU LEU VAL ARG VAL ILE ARG LYS PHE GLN HET GNP A 201 32 HET MG A 202 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 *175(H2 O) HELIX 1 AA1 GLY A 26 SER A 37 1 12 HELIX 2 AA2 GLN A 72 ALA A 77 5 6 HELIX 3 AA3 MET A 78 GLY A 86 1 9 HELIX 4 AA4 ASP A 97 ASP A 116 1 20 HELIX 5 AA5 LEU A 131 ARG A 135 5 5 HELIX 6 AA6 THR A 138 LEU A 149 1 12 HELIX 7 AA7 ASN A 163 GLN A 179 1 17 SHEET 1 AA1 6 GLU A 48 ILE A 57 0 SHEET 2 AA1 6 ARG A 60 THR A 69 -1 O ASP A 68 N ASP A 49 SHEET 3 AA1 6 LYS A 14 VAL A 20 1 N VAL A 19 O LEU A 67 SHEET 4 AA1 6 GLY A 88 SER A 94 1 O VAL A 92 N VAL A 20 SHEET 5 AA1 6 MET A 122 ASN A 127 1 O ILE A 125 N LEU A 91 SHEET 6 AA1 6 THR A 152 GLU A 155 1 O THR A 152 N LEU A 124 LINK OG SER A 28 MG MG A 202 1555 1555 2.13 LINK OG1 THR A 46 MG MG A 202 1555 1555 2.02 LINK O2G GNP A 201 MG MG A 202 1555 1555 2.07 LINK O1B GNP A 201 MG MG A 202 1555 1555 2.04 LINK MG MG A 202 O HOH A 338 1555 1555 2.06 LINK MG MG A 202 O HOH A 339 1555 1555 2.09 CRYST1 39.299 62.797 66.089 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 0.025446 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015924 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015131 0.00000