HEADER DE NOVO PROTEIN 20-JUN-24 9CC6 TITLE DE NOVO DESIGN OF HIGH-AFFINITY PROTEIN BINDERS TO RNA BINDING DOMAIN TITLE 2 OF G3BP1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: G3BP1 BINDER; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: RAS GTPASE-ACTIVATING PROTEIN-BINDING PROTEIN 1; COMPND 7 CHAIN: B; COMPND 8 SYNONYM: G3BP-1,ATP-DEPENDENT DNA HELICASE VIII,HDH VIII,GAP SH3 COMPND 9 DOMAIN-BINDING PROTEIN 1; COMPND 10 EC: 3.6.4.12,3.6.4.13; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606 KEYWDS PROTEIN DESIGN, DIFFUSION, DEEP LEARNING, DE NOVO PROTEIN, BINDERS, KEYWDS 2 IDP, IDR, PHASE SEPARATION EXPDTA X-RAY DIFFRACTION AUTHOR A.K.BERA,C.LIU,A.KANG,D.BAKER REVDAT 3 27-AUG-25 9CC6 1 JRNL REVDAT 2 13-AUG-25 9CC6 1 JRNL REVDAT 1 14-MAY-25 9CC6 0 JRNL AUTH C.LIU,K.WU,H.CHOI,H.L.HAN,X.ZHANG,J.L.WATSON,G.AHN, JRNL AUTH 2 J.Z.ZHANG,S.SHIJO,L.L.GOOD,C.M.FISCHER,A.K.BERA,A.KANG, JRNL AUTH 3 E.BRACKENBROUGH,B.COVENTRY,D.R.HICK,S.QAMAR,X.LI, JRNL AUTH 4 J.DECARREAU,S.R.GERBEN,W.YANG,I.GORESHNIK,D.VAFEADOS,X.WANG, JRNL AUTH 5 M.LAMB,A.MURRAY,S.KENNY,M.S.BAUER,A.N.HOOFNAGLE,P.ZHU, JRNL AUTH 6 T.P.J.KNOWLES,D.BAKER JRNL TITL DIFFUSING PROTEIN BINDERS TO INTRINSICALLY DISORDERED JRNL TITL 2 PROTEINS. JRNL REF NATURE V. 644 809 2025 JRNL REFN ESSN 1476-4687 JRNL PMID 40739343 JRNL DOI 10.1038/S41586-025-09248-9 REMARK 2 REMARK 2 RESOLUTION. 2.40 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.02 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 3 NUMBER OF REFLECTIONS : 4698 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) : 0.221 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.260 REMARK 3 FREE R VALUE TEST SET COUNT : 482 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 37.0200 - 3.4600 0.95 1455 166 0.1975 0.2156 REMARK 3 2 3.4600 - 2.4800 0.96 1431 162 0.2358 0.2994 REMARK 3 3 2.4800 - 2.4000 0.89 1330 154 0.2835 0.3632 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) : 0.334 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.464 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.45 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.04 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 : 0.003 1206 REMARK 3 ANGLE : 0.569 1636 REMARK 3 CHIRALITY : 0.043 194 REMARK 3 PLANARITY : 0.007 217 REMARK 3 DIHEDRAL : 25.436 481 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 9CC6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JUN-24. REMARK 100 THE DEPOSITION ID IS D_1000285016. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAY-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.96862 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 : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4698 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 37.020 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.03300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.62300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 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 (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05 M CALCIUM CHLORIDE DIHYDRATE, 0.1 REMARK 280 M BIS-TRIS PH 6.5, AND 30% V/V POLYETHYLENE GLYCOL MONOMETHYL REMARK 280 ETHER 550, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 21.19100 REMARK 290 SMTRY3 2 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: 1750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 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 MET A -2 REMARK 465 SER A -1 REMARK 465 GLY A 0 REMARK 465 GLY A 140 REMARK 465 SER A 141 REMARK 465 HIS A 142 REMARK 465 HIS A 143 REMARK 465 HIS A 144 REMARK 465 HIS A 145 REMARK 465 HIS A 146 REMARK 465 HIS A 147 REMARK 465 LYS B 140 REMARK 465 ARG B 152 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 GLU A 90 CG CD OE1 OE2 REMARK 470 THR A 106 OG1 CG2 REMARK 470 GLU A 126 CG CD OE1 OE2 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 29 95.30 -66.89 REMARK 500 THR A 107 147.03 68.49 REMARK 500 REMARK 500 REMARK: NULL DBREF 9CC6 A -2 147 PDB 9CC6 9CC6 -2 147 DBREF 9CC6 B 140 152 UNP Q13283 G3BP1_HUMAN 453 465 SEQRES 1 A 150 MET SER GLY MET PRO PRO ARG VAL ARG ARG ARG VAL GLU SEQRES 2 A 150 GLU LEU LEU ARG ARG ALA ARG GLU LEU ALA GLU GLU LEU SEQRES 3 A 150 GLY ILE ARG VAL GLU VAL LEU GLU VAL ASP PRO GLU TYR SEQRES 4 A 150 GLU LEU GLU LEU THR ALA VAL ILE THR LEU ALA ILE LEU SEQRES 5 A 150 ALA VAL LEU ALA PRO PRO GLU ARG GLN ASP GLU VAL LEU SEQRES 6 A 150 GLU LEU LEU ARG GLU THR LEU LYS THR LEU SER GLU VAL SEQRES 7 A 150 VAL GLU SER LEU ALA VAL SER ILE TRP ALA PRO PRO GLU SEQRES 8 A 150 ARG GLU GLU ALA ALA ARG ARG VAL GLU ARG LEU VAL GLU SEQRES 9 A 150 GLU ALA PHE ASN THR THR PRO GLU THR ARG GLU ARG ALA SEQRES 10 A 150 ARG LYS LEU ARG ASP GLU ALA ARG ARG ASP ALA GLU PRO SEQRES 11 A 150 ASP GLU VAL VAL VAL ALA VAL HIS LEU VAL PRO LYS GLY SEQRES 12 A 150 SER HIS HIS HIS HIS HIS HIS SEQRES 1 B 13 LYS PRO GLY PHE GLY VAL GLY ARG GLY LEU ALA PRO ARG FORMUL 3 HOH *7(H2 O) HELIX 1 AA1 PRO A 2 GLY A 24 1 23 HELIX 2 AA2 TYR A 36 ALA A 53 1 18 HELIX 3 AA3 PRO A 54 GLU A 56 5 3 HELIX 4 AA4 ARG A 57 SER A 73 1 17 HELIX 5 AA5 PRO A 86 GLU A 88 5 3 HELIX 6 AA6 ARG A 89 PHE A 104 1 16 HELIX 7 AA7 THR A 107 ARG A 123 1 17 SHEET 1 AA1 4 ARG A 26 VAL A 32 0 SHEET 2 AA1 4 PHE B 143 LEU B 149 -1 O VAL B 145 N GLU A 31 SHEET 3 AA1 4 VAL A 130 PRO A 138 -1 N VAL A 134 O GLY B 144 SHEET 4 AA1 4 VAL A 76 TRP A 84 -1 N ALA A 80 O HIS A 135 CRYST1 38.426 42.382 40.633 90.00 105.53 90.00 P 1 21 1 2 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 0.026024 0.000000 0.007232 0.00000 SCALE2 0.000000 0.023595 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025543 0.00000 TER 1119 LYS A 139 TER 1192 PRO B 151 HETATM 1193 O HOH A 201 18.246 -14.489 20.055 1.00 34.76 O HETATM 1194 O HOH A 202 5.646 -12.548 19.235 1.00 40.52 O HETATM 1195 O HOH A 203 -1.218 -12.204 -6.435 1.00 44.67 O HETATM 1196 O HOH A 204 7.470 7.343 24.637 1.00 35.59 O HETATM 1197 O HOH A 205 7.498 -13.662 17.084 1.00 49.66 O HETATM 1198 O HOH A 206 21.961 -5.195 -1.705 1.00 41.72 O HETATM 1199 O HOH B 201 6.690 4.660 -3.531 1.00 53.42 O MASTER 235 0 0 7 4 0 0 6 1197 2 0 13 END