HEADER RNA BINDING PROTEIN/RNA 30-MAY-17 5W0H TITLE STRUCTURE OF U2AF65 (U2AF2) RRM2 AT 1.11 ANGSTROM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPLICING FACTOR U2AF 65 KDA SUBUNIT; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RNA RECOGNITION MOTIF 2 (RRM2), RESIDUES 258-336; COMPND 5 SYNONYM: U2 AUXILIARY FACTOR 65 KDA SUBUNIT,HU2AF65,U2 SNRNP COMPND 6 AUXILIARY FACTOR LARGE SUBUNIT; COMPND 7 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: U2AF2, U2AF65; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-6P KEYWDS RNA SPLICING FACTOR, RNA RECOGNITION MOTIF, POLYPYRIMIDINE TRACT, RNA KEYWDS 2 BINDING PROTEIN, RNA BINDING PROTEIN-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.A.AGRAWAL,J.L.JENKINS,C.L.KIELKOPF REVDAT 3 04-OCT-23 5W0H 1 REMARK REVDAT 2 23-MAR-22 5W0H 1 REMARK REVDAT 1 11-APR-18 5W0H 0 JRNL AUTH E.GLASSER,A.A.AGRAWAL,J.L.JENKINS,C.L.KIELKOPF JRNL TITL CANCER-ASSOCIATED MUTATIONS MAPPED ON HIGH-RESOLUTION JRNL TITL 2 STRUCTURES OF THE U2AF2 RNA RECOGNITION MOTIFS. JRNL REF BIOCHEMISTRY V. 56 4757 2017 JRNL REFN ISSN 1520-4995 JRNL PMID 28850223 JRNL DOI 10.1021/ACS.BIOCHEM.7B00551 REMARK 2 REMARK 2 RESOLUTION. 1.11 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.11 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.69 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 3 NUMBER OF REFLECTIONS : 36085 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.154 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.168 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.370 REMARK 3 FREE R VALUE TEST SET COUNT : 1938 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 20.6922 - 2.6797 1.00 2696 154 0.1754 0.1828 REMARK 3 2 2.6797 - 2.1276 1.00 2573 146 0.1747 0.1818 REMARK 3 3 2.1276 - 1.8589 0.86 2177 123 0.1453 0.1383 REMARK 3 4 1.8589 - 1.6890 1.00 2533 144 0.1359 0.1600 REMARK 3 5 1.6890 - 1.5680 1.00 2524 144 0.1121 0.1298 REMARK 3 6 1.5680 - 1.4756 1.00 2494 142 0.1128 0.1477 REMARK 3 7 1.4756 - 1.4017 0.99 2482 140 0.1212 0.1736 REMARK 3 8 1.4017 - 1.3407 0.99 2465 136 0.1204 0.1387 REMARK 3 9 1.3407 - 1.2891 0.98 2439 140 0.1329 0.1862 REMARK 3 10 1.2891 - 1.2446 0.97 2420 138 0.1276 0.1395 REMARK 3 11 1.2446 - 1.2057 0.97 2423 139 0.1325 0.2057 REMARK 3 12 1.2057 - 1.1712 0.96 2416 137 0.1320 0.1529 REMARK 3 13 1.1712 - 1.1404 0.96 2368 135 0.1554 0.1541 REMARK 3 14 1.1404 - 1.1126 0.87 2137 120 0.2027 0.2218 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.320 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.44 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.50 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 : 0.007 733 REMARK 3 ANGLE : 0.885 999 REMARK 3 CHIRALITY : 0.078 110 REMARK 3 PLANARITY : 0.007 134 REMARK 3 DIHEDRAL : 15.828 289 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 5W0H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-MAY-17. REMARK 100 THE DEPOSITION ID IS D_1000228195. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-MAY-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : F1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9779 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36104 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.110 REMARK 200 RESOLUTION RANGE LOW (A) : 20.690 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.11 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.13 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.27800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.500 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: 2G4B RRM2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 26% (W/V) PEG 8000, 0.1 M NAOAC, 0.2 REMARK 280 MM TCEP, 10% (V/V) DIOXANE, 0.2 UL BIGCHAP, 0.05 M POTASSIUM REMARK 280 PHOSPHATE MONOBASIC, PH 5.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K 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 16.71500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.36100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.10150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.36100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.71500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.10150 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 253 REMARK 465 PRO A 254 REMARK 465 LEU A 255 REMARK 465 GLY A 256 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 OD1 ASP A 314 HH22 ARG A 334 1.60 REMARK 500 O HOH A 429 O HOH A 512 2.08 REMARK 500 O HOH A 420 O HOH A 526 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 536 DISTANCE = 6.42 ANGSTROMS REMARK 525 HOH A 537 DISTANCE = 6.43 ANGSTROMS REMARK 525 HOH A 538 DISTANCE = 6.58 ANGSTROMS REMARK 525 HOH A 539 DISTANCE = 7.06 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5W0G RELATED DB: PDB DBREF 5W0H A 258 336 UNP P26368 U2AF2_HUMAN 258 336 SEQADV 5W0H GLY A 253 UNP P26368 EXPRESSION TAG SEQADV 5W0H PRO A 254 UNP P26368 EXPRESSION TAG SEQADV 5W0H LEU A 255 UNP P26368 EXPRESSION TAG SEQADV 5W0H GLY A 256 UNP P26368 EXPRESSION TAG SEQADV 5W0H SER A 257 UNP P26368 EXPRESSION TAG SEQRES 1 A 84 GLY PRO LEU GLY SER ALA HIS LYS LEU PHE ILE GLY GLY SEQRES 2 A 84 LEU PRO ASN TYR LEU ASN ASP ASP GLN VAL LYS GLU LEU SEQRES 3 A 84 LEU THR SER PHE GLY PRO LEU LYS ALA PHE ASN LEU VAL SEQRES 4 A 84 LYS ASP SER ALA THR GLY LEU SER LYS GLY TYR ALA PHE SEQRES 5 A 84 CYS GLU TYR VAL ASP ILE ASN VAL THR ASP GLN ALA ILE SEQRES 6 A 84 ALA GLY LEU ASN GLY MET GLN LEU GLY ASP LYS LYS LEU SEQRES 7 A 84 LEU VAL GLN ARG ALA SER FORMUL 2 HOH *139(H2 O) HELIX 1 AA1 ASN A 271 SER A 281 1 11 HELIX 2 AA2 ASP A 309 ASN A 321 1 13 SHEET 1 AA1 4 LEU A 285 LYS A 292 0 SHEET 2 AA1 4 SER A 299 TYR A 307 -1 O GLU A 306 N LYS A 286 SHEET 3 AA1 4 LYS A 260 GLY A 264 -1 N ILE A 263 O ALA A 303 SHEET 4 AA1 4 LEU A 331 ARG A 334 -1 O LEU A 331 N GLY A 264 SHEET 1 AA2 2 GLN A 324 LEU A 325 0 SHEET 2 AA2 2 LYS A 328 LYS A 329 -1 O LYS A 328 N LEU A 325 CRYST1 33.430 38.203 72.722 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 0.029913 0.000000 0.000000 0.00000 SCALE2 0.000000 0.026176 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013751 0.00000