HEADER RNA BINDING PROTEIN 01-SEP-21 7S17 TITLE CRYSTAL STRUCTURE OF HUMAN G3BP1-NTF2 WITH THREE MUTATIONS- F15W, TITLE 2 F33W, AND F124W COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAS GTPASE-ACTIVATING PROTEIN-BINDING PROTEIN 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: G3BP-1,ATP-DEPENDENT DNA HELICASE VIII,HDH VIII,GAP SH3 COMPND 5 DOMAIN-BINDING PROTEIN 1; COMPND 6 EC: 3.6.4.12,3.6.4.13; COMPND 7 ENGINEERED: YES; COMPND 8 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: G3BP1, G3BP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NTF2-LIKE DOMAIN, BINDING MUTANT, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.T.SHEEHAN,D.R.MADDEN REVDAT 3 25-OCT-23 7S17 1 REMARK REVDAT 2 11-JAN-23 7S17 1 JRNL REVDAT 1 12-OCT-22 7S17 0 JRNL AUTH C.T.SHEEHAN,T.H.HAMPTON,D.R.MADDEN JRNL TITL TRYPTOPHAN MUTATIONS IN G3BP1 TUNE THE STABILITY OF A JRNL TITL 2 CELLULAR SIGNALING HUB BY WEAKENING TRANSIENT INTERACTIONS JRNL TITL 3 WITH CAPRIN1 AND USP10. JRNL REF J.BIOL.CHEM. V. 298 02552 2022 JRNL REFN ESSN 1083-351X JRNL PMID 36183834 JRNL DOI 10.1016/J.JBC.2022.102552 REMARK 2 REMARK 2 RESOLUTION. 2.36 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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) : 2.36 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 11537 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.225 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.271 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 579 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 19.9100 - 3.7400 1.00 2863 145 0.1912 0.2360 REMARK 3 2 3.7400 - 2.9700 1.00 2724 145 0.2222 0.2872 REMARK 3 3 2.9700 - 2.6000 1.00 2700 144 0.2821 0.3060 REMARK 3 4 2.6000 - 2.3600 1.00 2671 145 0.2942 0.3424 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) : 0.362 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.062 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 43.95 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.70 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 2244 REMARK 3 ANGLE : 1.070 3039 REMARK 3 CHIRALITY : 0.066 319 REMARK 3 PLANARITY : 0.006 393 REMARK 3 DIHEDRAL : 20.301 816 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 : 1 REMARK 3 NCS GROUP : ens_1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "A" and (resid 1 through 38 or REMARK 3 resid 40 through 47 or resid 51 through REMARK 3 116 or resid 124 through 138)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 NCS OPERATOR : 2 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "B" and (resid 1 through 38 or REMARK 3 resid 40 through 138)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7S17 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-SEP-21. REMARK 100 THE DEPOSITION ID IS D_1000259433. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-MAR-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92011 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11543 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.360 REMARK 200 RESOLUTION RANGE LOW (A) : 19.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.0200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.36 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.50 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: PHASER REMARK 200 STARTING MODEL: 4FCJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 8000, 100 MM HEPES, PH 7.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K 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 21.32600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.86550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.83450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.86550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.32600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.83450 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 SER B 0 REMARK 465 ASN B 48 REMARK 465 GLY B 49 REMARK 465 LYS B 50 REMARK 465 GLU B 117 REMARK 465 GLY B 118 REMARK 465 SER B 119 REMARK 465 VAL B 120 REMARK 465 ALA B 121 REMARK 465 ASN B 122 REMARK 465 LYS B 123 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 ALA A 26 77.57 -163.83 REMARK 500 ASP A 46 -162.68 -129.95 REMARK 500 THR A 85 -168.48 -122.50 REMARK 500 ALA B 26 67.39 -158.56 REMARK 500 ASN B 69 73.93 39.42 REMARK 500 ASP B 88 23.05 48.11 REMARK 500 ASN B 101 75.68 41.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4FCJ RELATED DB: PDB REMARK 900 4FCJ CONTAINS WT VERSION OF THE SAME PROTEIN. DBREF 7S17 A 1 138 UNP Q13283 G3BP1_HUMAN 1 138 DBREF 7S17 B 1 138 UNP Q13283 G3BP1_HUMAN 1 138 SEQADV 7S17 SER A 0 UNP Q13283 EXPRESSION TAG SEQADV 7S17 TRP A 15 UNP Q13283 PHE 15 ENGINEERED MUTATION SEQADV 7S17 TRP A 33 UNP Q13283 PHE 33 ENGINEERED MUTATION SEQADV 7S17 TRP A 124 UNP Q13283 PHE 124 ENGINEERED MUTATION SEQADV 7S17 SER B 0 UNP Q13283 EXPRESSION TAG SEQADV 7S17 TRP B 15 UNP Q13283 PHE 15 ENGINEERED MUTATION SEQADV 7S17 TRP B 33 UNP Q13283 PHE 33 ENGINEERED MUTATION SEQADV 7S17 TRP B 124 UNP Q13283 PHE 124 ENGINEERED MUTATION SEQRES 1 A 139 SER MET VAL MET GLU LYS PRO SER PRO LEU LEU VAL GLY SEQRES 2 A 139 ARG GLU TRP VAL ARG GLN TYR TYR THR LEU LEU ASN GLN SEQRES 3 A 139 ALA PRO ASP MET LEU HIS ARG TRP TYR GLY LYS ASN SER SEQRES 4 A 139 SER TYR VAL HIS GLY GLY LEU ASP SER ASN GLY LYS PRO SEQRES 5 A 139 ALA ASP ALA VAL TYR GLY GLN LYS GLU ILE HIS ARG LYS SEQRES 6 A 139 VAL MET SER GLN ASN PHE THR ASN CYS HIS THR LYS ILE SEQRES 7 A 139 ARG HIS VAL ASP ALA HIS ALA THR LEU ASN ASP GLY VAL SEQRES 8 A 139 VAL VAL GLN VAL MET GLY LEU LEU SER ASN ASN ASN GLN SEQRES 9 A 139 ALA LEU ARG ARG PHE MET GLN THR PHE VAL LEU ALA PRO SEQRES 10 A 139 GLU GLY SER VAL ALA ASN LYS TRP TYR VAL HIS ASN ASP SEQRES 11 A 139 ILE PHE ARG TYR GLN ASP GLU VAL PHE SEQRES 1 B 139 SER MET VAL MET GLU LYS PRO SER PRO LEU LEU VAL GLY SEQRES 2 B 139 ARG GLU TRP VAL ARG GLN TYR TYR THR LEU LEU ASN GLN SEQRES 3 B 139 ALA PRO ASP MET LEU HIS ARG TRP TYR GLY LYS ASN SER SEQRES 4 B 139 SER TYR VAL HIS GLY GLY LEU ASP SER ASN GLY LYS PRO SEQRES 5 B 139 ALA ASP ALA VAL TYR GLY GLN LYS GLU ILE HIS ARG LYS SEQRES 6 B 139 VAL MET SER GLN ASN PHE THR ASN CYS HIS THR LYS ILE SEQRES 7 B 139 ARG HIS VAL ASP ALA HIS ALA THR LEU ASN ASP GLY VAL SEQRES 8 B 139 VAL VAL GLN VAL MET GLY LEU LEU SER ASN ASN ASN GLN SEQRES 9 B 139 ALA LEU ARG ARG PHE MET GLN THR PHE VAL LEU ALA PRO SEQRES 10 B 139 GLU GLY SER VAL ALA ASN LYS TRP TYR VAL HIS ASN ASP SEQRES 11 B 139 ILE PHE ARG TYR GLN ASP GLU VAL PHE FORMUL 3 HOH *17(H2 O) HELIX 1 AA1 SER A 7 ALA A 26 1 20 HELIX 2 AA2 PRO A 27 ARG A 32 5 6 HELIX 3 AA3 GLY A 57 GLN A 68 1 12 HELIX 4 AA4 SER B 7 ALA B 26 1 20 HELIX 5 AA5 PRO B 27 ARG B 32 5 6 HELIX 6 AA6 GLY B 57 GLN B 68 1 12 HELIX 7 AA7 ASP B 135 VAL B 137 5 3 SHEET 1 AA1 6 VAL A 55 TYR A 56 0 SHEET 2 AA1 6 TYR A 34 HIS A 42 -1 N TYR A 40 O VAL A 55 SHEET 3 AA1 6 TRP A 124 TYR A 133 1 O ASP A 129 N VAL A 41 SHEET 4 AA1 6 ARG A 106 PRO A 116 -1 N VAL A 113 O HIS A 127 SHEET 5 AA1 6 VAL A 90 SER A 99 -1 N VAL A 92 O PHE A 112 SHEET 6 AA1 6 HIS A 74 ALA A 84 -1 N LYS A 76 O LEU A 97 SHEET 1 AA2 6 VAL B 55 TYR B 56 0 SHEET 2 AA2 6 TYR B 34 HIS B 42 -1 N TYR B 40 O VAL B 55 SHEET 3 AA2 6 TYR B 125 TYR B 133 1 O ASP B 129 N VAL B 41 SHEET 4 AA2 6 ARG B 106 ALA B 115 -1 N VAL B 113 O HIS B 127 SHEET 5 AA2 6 GLY B 89 SER B 99 -1 N VAL B 90 O LEU B 114 SHEET 6 AA2 6 HIS B 74 THR B 85 -1 N LYS B 76 O LEU B 97 CRYST1 42.652 71.669 87.731 90.00 90.00 90.00 P 21 21 21 8 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 0.023446 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013953 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011398 0.00000 MTRIX1 1 0.654413 -0.067806 -0.753091 15.69116 1 MTRIX2 1 -0.070047 -0.997125 0.028910 -24.90614 1 MTRIX3 1 -0.752886 0.033832 -0.657280 36.81644 1