HEADER RNA BINDING PROTEIN/RNA 15-JUL-25 9VVA TITLE UP1 IN COMPLEX WITH RNA DINUCLEOTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN A1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HNRNP A1,HELIX-DESTABILIZING PROTEIN,SINGLE-STRAND RNA- COMPND 5 BINDING PROTEIN,HNRNP CORE PROTEIN A1; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RNA (26-MER); COMPND 9 CHAIN: B; COMPND 10 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-GOLD(DE3)PLYSS AG'; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_TAXID: 9606 KEYWDS RRM, RIBONUCLEOPROTEIN, RNA BINDING PROTEIN, RNA BINDING PROTEIN-RNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR L.PANCHARIYA,A.KUMAR,A.AROCKIASAMY,N.JAIN REVDAT 1 28-JAN-26 9VVA 0 JRNL AUTH L.PANCHARIYA,A.KUMAR,A.AROCKIASAMY,N.JAIN JRNL TITL UP1 IN COMPLEX WITH RNA DINUCLEOTIDE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.2_5419 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) : 34.02 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.100 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 3 NUMBER OF REFLECTIONS : 16732 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.160 REMARK 3 FREE R VALUE TEST SET COUNT : 863 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 34.0200 - 3.1800 0.96 2666 146 0.1478 0.1570 REMARK 3 2 3.1800 - 2.5200 0.95 2630 155 0.1840 0.1916 REMARK 3 3 2.5200 - 2.2100 0.95 2654 136 0.1806 0.2414 REMARK 3 4 2.2000 - 2.0000 0.96 2678 127 0.1763 0.2722 REMARK 3 5 2.0000 - 1.8600 0.95 2613 165 0.1790 0.2389 REMARK 3 6 1.8600 - 1.7500 0.95 2628 134 0.1862 0.2620 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) : 0.211 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.019 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.44 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 1560 REMARK 3 ANGLE : 0.803 2115 REMARK 3 CHIRALITY : 0.054 225 REMARK 3 PLANARITY : 0.007 273 REMARK 3 DIHEDRAL : 16.865 612 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 9VVA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-JUL-25. REMARK 100 THE DEPOSITION ID IS D_1300061575. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAY-24 REMARK 200 TEMPERATURE (KELVIN) : 173 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ELETTRA REMARK 200 BEAMLINE : 11.2C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16734 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 34.045 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.3000 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 (%) : 91.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.13300 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 (%): 15.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M POTASSIUM FORMATE, 20% W/V PEG REMARK 280 3350, PH 7.3, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 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 A -1 REMARK 465 ASN A 0 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 LYS A 3 REMARK 465 SER A 4 REMARK 465 GLU A 5 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 465 ARG A 196 REMARK 465 G B -14 REMARK 465 G B -13 REMARK 465 A B -12 REMARK 465 G B -11 REMARK 465 A B -10 REMARK 465 C B -9 REMARK 465 A B -8 REMARK 465 U B -7 REMARK 465 A B -6 REMARK 465 U B -5 REMARK 465 A B -4 REMARK 465 U B -3 REMARK 465 C B -2 REMARK 465 A B -1 REMARK 465 C B 0 REMARK 465 C B 4 REMARK 465 U B 5 REMARK 465 G B 6 REMARK 465 U B 7 REMARK 465 C B 8 REMARK 465 U B 9 REMARK 465 C B 10 REMARK 465 C B 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 A B 1 P OP1 OP2 REMARK 470 C B 3 C5' C4' O4' C3' O3' C2' O2' REMARK 470 C B 3 C1' N1 C2 O2 N3 C4 N4 REMARK 470 C B 3 C5 C6 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 43 109.39 -160.87 REMARK 500 LYS A 113 -148.37 57.34 REMARK 500 SER A 182 -155.43 -130.34 REMARK 500 REMARK 500 REMARK: NULL DBREF 9VVA A 1 196 UNP P09651 ROA1_HUMAN 1 196 DBREF 9VVA B -14 11 PDB 9VVA 9VVA -14 11 SEQADV 9VVA SER A -1 UNP P09651 EXPRESSION TAG SEQADV 9VVA ASN A 0 UNP P09651 EXPRESSION TAG SEQRES 1 A 198 SER ASN MET SER LYS SER GLU SER PRO LYS GLU PRO GLU SEQRES 2 A 198 GLN LEU ARG LYS LEU PHE ILE GLY GLY LEU SER PHE GLU SEQRES 3 A 198 THR THR ASP GLU SER LEU ARG SER HIS PHE GLU GLN TRP SEQRES 4 A 198 GLY THR LEU THR ASP CYS VAL VAL MET ARG ASP PRO ASN SEQRES 5 A 198 THR LYS ARG SER ARG GLY PHE GLY PHE VAL THR TYR ALA SEQRES 6 A 198 THR VAL GLU GLU VAL ASP ALA ALA MET ASN ALA ARG PRO SEQRES 7 A 198 HIS LYS VAL ASP GLY ARG VAL VAL GLU PRO LYS ARG ALA SEQRES 8 A 198 VAL SER ARG GLU ASP SER GLN ARG PRO GLY ALA HIS LEU SEQRES 9 A 198 THR VAL LYS LYS ILE PHE VAL GLY GLY ILE LYS GLU ASP SEQRES 10 A 198 THR GLU GLU HIS HIS LEU ARG ASP TYR PHE GLU GLN TYR SEQRES 11 A 198 GLY LYS ILE GLU VAL ILE GLU ILE MET THR ASP ARG GLY SEQRES 12 A 198 SER GLY LYS LYS ARG GLY PHE ALA PHE VAL THR PHE ASP SEQRES 13 A 198 ASP HIS ASP SER VAL ASP LYS ILE VAL ILE GLN LYS TYR SEQRES 14 A 198 HIS THR VAL ASN GLY HIS ASN CYS GLU VAL ARG LYS ALA SEQRES 15 A 198 LEU SER LYS GLN GLU MET ALA SER ALA SER SER SER GLN SEQRES 16 A 198 ARG GLY ARG SEQRES 1 B 26 G G A G A C A U A U A U C SEQRES 2 B 26 A C A G C C U G U C U C C FORMUL 3 HOH *149(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 GLN A 127 GLY A 129 5 3 HELIX 7 AA7 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 LEU A 16 O VAL A 60 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 5 ILE A 131 THR A 138 0 SHEET 2 AA3 5 LYS A 145 PHE A 153 -1 O PHE A 150 N GLU A 135 SHEET 3 AA3 5 LYS A 106 GLY A 110 -1 N VAL A 109 O ALA A 149 SHEET 4 AA3 5 HIS A 173 ALA A 180 -1 O GLU A 176 N GLY A 110 SHEET 5 AA3 5 HIS A 168 VAL A 170 -1 N HIS A 168 O CYS A 175 CISPEP 1 ARG A 75 PRO A 76 0 -0.68 CRYST1 36.935 37.967 38.599 64.38 67.63 84.78 P 1 1 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 0.027075 -0.002474 -0.011171 0.00000 SCALE2 0.000000 0.026448 -0.012667 0.00000 SCALE3 0.000000 0.000000 0.031063 0.00000 MASTER 260 0 0 7 11 0 0 6 1626 2 0 18 END