HEADER RNA BINDING PROTEIN 16-DEC-24 9HQL TITLE UP1 IN COMPLEX WITH Z1152242726 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN A1, N-TERMINALLY COMPND 3 PROCESSED; COMPND 4 CHAIN: A; COMPND 5 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: HNRNPA1, HNRPA1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PETM-14 KEYWDS FRAGMENT SCREENING, HNRNP A1, UP1, RNA/DNA BINDING PROTEIN, UP1- KEYWDS 2 FRAGMENT COMPLEX, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.DUNNETT,F.PRISCHI REVDAT 1 25-DEC-24 9HQL 0 SPRSDE 25-DEC-24 9HQL 9F4E JRNL AUTH L.DUNNETT,F.PRISCHI JRNL TITL ENHANCED IDENTIFICATION OF SMALL MOLECULES BINDING TO HNRNP JRNL TITL 2 A1 VIA IN SILICO HOTSPOT AND CRYPTIC POCKETS MAPPING COUPLED JRNL TITL 3 WITH X-RAY FRAGMENT SCREENING JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 55.59 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 3 NUMBER OF REFLECTIONS : 17901 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 890 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 55.5900 - 3.1800 0.96 2907 157 0.1748 0.1785 REMARK 3 2 3.1800 - 2.5200 0.97 2845 134 0.1919 0.2218 REMARK 3 3 2.5200 - 2.2100 0.96 2876 137 0.1831 0.2197 REMARK 3 4 2.2000 - 2.0000 0.96 2793 160 0.1949 0.2176 REMARK 3 5 2.0000 - 1.8600 0.96 2807 142 0.2023 0.2393 REMARK 3 6 1.8600 - 1.7500 0.96 2783 160 0.2697 0.3290 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) : 0.234 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.632 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.38 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.17 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 : 0.006 1363 REMARK 3 ANGLE : 0.876 1831 REMARK 3 CHIRALITY : 0.057 196 REMARK 3 PLANARITY : 0.008 238 REMARK 3 DIHEDRAL : 16.322 518 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 9HQL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-DEC-24. REMARK 100 THE DEPOSITION ID IS D_1292144052. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUN-18 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 : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91587 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17906 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 55.590 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 1.800 REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.8 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 : 2.500 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 (%): 40.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL, PH 8.50, 25% PEG-4000, REMARK 280 8% 2-METHYL-2,4-PENTANEDIOL, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 289K 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 21.96000 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: MONOMERIC 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 -2 REMARK 465 PRO A -1 REMARK 465 MET A 0 REMARK 465 GLY A 1 REMARK 465 SER A 2 REMARK 465 LYS A 3 REMARK 465 SER A 4 REMARK 465 GLU A 5 REMARK 465 SER A 6 REMARK 465 PRO A 7 REMARK 465 SER A 91 REMARK 465 ARG A 92 REMARK 465 GLU A 93 REMARK 465 ASP A 94 REMARK 465 SER A 95 REMARK 465 GLN A 96 REMARK 465 ARG A 97 REMARK 465 PRO A 98 REMARK 465 GLY A 99 REMARK 465 ALA A 100 REMARK 465 HIS A 101 REMARK 465 SER A 182 REMARK 465 LYS A 183 REMARK 465 GLN A 184 REMARK 465 GLU A 185 REMARK 465 MET A 186 REMARK 465 ALA A 187 REMARK 465 SER A 188 REMARK 465 ALA A 189 REMARK 465 SER A 190 REMARK 465 SER A 191 REMARK 465 SER A 192 REMARK 465 GLN A 193 REMARK 465 ARG A 194 REMARK 465 GLY A 195 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 24 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 380 O HOH A 415 2455 1.92 REMARK 500 REMARK 500 REMARK: NULL 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 CYS A 43 115.48 -163.62 REMARK 500 LYS A 113 -161.83 59.57 REMARK 500 REMARK 500 REMARK: NULL DBREF 9HQL A 2 195 UNP P09651 ROA1_HUMAN 2 195 SEQADV 9HQL GLY A -2 UNP P09651 EXPRESSION TAG SEQADV 9HQL PRO A -1 UNP P09651 EXPRESSION TAG SEQADV 9HQL MET A 0 UNP P09651 EXPRESSION TAG SEQADV 9HQL GLY A 1 UNP P09651 EXPRESSION TAG SEQRES 1 A 198 GLY PRO MET GLY SER LYS SER GLU SER PRO LYS GLU PRO SEQRES 2 A 198 GLU GLN LEU ARG LYS LEU PHE ILE GLY GLY LEU SER PHE SEQRES 3 A 198 GLU THR THR ASP GLU SER LEU ARG SER HIS PHE GLU GLN SEQRES 4 A 198 TRP GLY THR LEU THR ASP CYS VAL VAL MET ARG ASP PRO SEQRES 5 A 198 ASN THR LYS ARG SER ARG GLY PHE GLY PHE VAL THR TYR SEQRES 6 A 198 ALA THR VAL GLU GLU VAL ASP ALA ALA MET ASN ALA ARG SEQRES 7 A 198 PRO HIS LYS VAL ASP GLY ARG VAL VAL GLU PRO LYS ARG SEQRES 8 A 198 ALA VAL SER ARG GLU ASP SER GLN ARG PRO GLY ALA HIS SEQRES 9 A 198 LEU THR VAL LYS LYS ILE PHE VAL GLY GLY ILE LYS GLU SEQRES 10 A 198 ASP THR GLU GLU HIS HIS LEU ARG ASP TYR PHE GLU GLN SEQRES 11 A 198 TYR GLY LYS ILE GLU VAL ILE GLU ILE MET THR ASP ARG SEQRES 12 A 198 GLY SER GLY LYS LYS ARG GLY PHE ALA PHE VAL THR PHE SEQRES 13 A 198 ASP ASP HIS ASP SER VAL ASP LYS ILE VAL ILE GLN LYS SEQRES 14 A 198 TYR HIS THR VAL ASN GLY HIS ASN CYS GLU VAL ARG LYS SEQRES 15 A 198 ALA LEU SER LYS GLN GLU MET ALA SER ALA SER SER SER SEQRES 16 A 198 GLN ARG GLY HET VZM A 201 17 HETNAM VZM N-(6-METHOXYPYRIDIN-3-YL)-N'-THIOPHEN-2-YLUREA FORMUL 2 VZM C11 H11 N3 O2 S FORMUL 3 HOH *202(H2 O) HELIX 1 AA1 PRO A 10 LEU A 13 5 4 HELIX 2 AA2 THR A 26 GLU A 35 1 10 HELIX 3 AA3 GLN A 36 GLY A 38 5 3 HELIX 4 AA4 THR A 64 ALA A 74 1 11 HELIX 5 AA5 GLU A 117 GLU A 126 1 10 HELIX 6 AA6 ASP A 155 GLN A 165 1 11 SHEET 1 AA1 4 LEU A 40 ARG A 47 0 SHEET 2 AA1 4 SER A 54 TYR A 62 -1 O ARG A 55 N MET A 46 SHEET 3 AA1 4 LYS A 15 GLY A 19 -1 N ILE A 18 O GLY A 58 SHEET 4 AA1 4 GLU A 85 ARG A 88 -1 O LYS A 87 N PHE A 17 SHEET 1 AA2 2 LYS A 78 VAL A 79 0 SHEET 2 AA2 2 ARG A 82 VAL A 83 -1 O ARG A 82 N VAL A 79 SHEET 1 AA3 4 ILE A 131 THR A 138 0 SHEET 2 AA3 4 LYS A 145 PHE A 153 -1 O PHE A 150 N GLU A 135 SHEET 3 AA3 4 LYS A 106 GLY A 110 -1 N VAL A 109 O ALA A 149 SHEET 4 AA3 4 GLU A 176 LYS A 179 -1 O GLU A 176 N GLY A 110 SHEET 1 AA4 2 THR A 169 VAL A 170 0 SHEET 2 AA4 2 HIS A 173 ASN A 174 -1 O HIS A 173 N VAL A 170 CISPEP 1 ARG A 75 PRO A 76 0 0.14 CRYST1 37.900 43.920 55.730 90.00 94.05 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 0.026385 0.000000 0.001868 0.00000 SCALE2 0.000000 0.022769 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017989 0.00000