HEADER TRANSCRIPTION 26-APR-11 2YH0 TITLE SOLUTION STRUCTURE OF THE CLOSED CONFORMATION OF HUMAN U2AF65 TANDEM TITLE 2 RRM1 AND RRM2 DOMAINS COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPLICING FACTOR U2AF 65 KDA SUBUNIT; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: TANDEM RRM1 AND RRM2 DOMAINS JOINED BY NATIVE LINKER, COMPND 5 RESIDUES 148-342; COMPND 6 SYNONYM: U2 AUXILIARY FACTOR 65 KDA SUBUNIT, HUMAN U2AF65, U2 SNRNP COMPND 7 AUXILIARY FACTOR LARGE SUBUNIT, HU2AF(65); COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: PLYSS; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PETM-11 KEYWDS PRE-MRNA SPLICING, TRANSCRIPTION, RNA BINDING PROTEIN, MRNA KEYWDS 2 PROCESSING EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR C.D.MACKERETH,T.MADL,B.SIMON,K.ZANIER,A.GASCH,M.SATTLER REVDAT 4 15-MAY-24 2YH0 1 REMARK REVDAT 3 25-SEP-19 2YH0 1 REMARK REVDAT 2 27-JUL-11 2YH0 1 JRNL ATOM MASTER REVDAT 1 20-JUL-11 2YH0 0 JRNL AUTH C.D.MACKERETH,T.MADL,S.BONNAL,B.SIMON,K.ZANIER,A.GASCH, JRNL AUTH 2 V.RYBIN,J.VALCARCEL,M.SATTLER JRNL TITL MULTI-DOMAIN CONFORMATIONAL SELECTION UNDERLIES PRE-MRNA JRNL TITL 2 SPLICING REGULATION BY U2AF JRNL REF NATURE V. 475 408 2011 JRNL REFN ISSN 0028-0836 JRNL PMID 21753750 JRNL DOI 10.1038/NATURE10171 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE, REMARK 3 SIMONSON,WARREN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: FINAL WATER REFINEMENT. THE STRUCTURE REMARK 3 WAS DETERMINED USING A MULTI-STEP PROTOCOL. FIRST WITH REMARK 3 REFINEMENT OF INDIVIDUAL STRUCTURED DOMAINS FOR RRM1 AND RRM2 OF REMARK 3 U2AF65. THE INITIAL COORDINATES OF THE ISOLATED DOMAINS WERE REMARK 3 BASED ON PDB ID 2G4B BY SICKMIER ET AL. 2006. MOL. CELL 23, 49- REMARK 3 59. SECOND STEP IS ADDITION AND RANDOMIZATION OF FLEXIBLE AND REMARK 3 LINKER RESIDUES. THE THIRD STEP IS MODEL CALCULATION USING RDC REMARK 3 ORIENTATION, PRE-BASED DISTANCE, TALOS DIHEDRAL AND HYDROGEN REMARK 3 BOND RESTRAINTS WITH THE RRM1 AND RRM2 DOMAINS RESTRAINED TO REMARK 3 THEIR INITIAL STARTING STRUCTURES. STRUCTURE CALCULATION REMARK 3 INCLUDED DISTANCE RESTRAINTS BASED ON PARAMAGNETIC RELAXATION REMARK 3 ENHANCEMENT DATA FROM SEVEN INDEPENDENT CYSTEINE MUTANTS (N155C, REMARK 3 A164C, A171C, T209C, D273C, A287C AND A318C) COVALENTLY MODIFIED REMARK 3 BY 3-(2- IODOACETAMIDO)-2,2,5,5, TETRAMETHYL-1- PYRROLIDINYLOXY REMARK 3 RADICAL (IODOACETAMIDO-PROXYL). REMARK 4 REMARK 4 2YH0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-APR-11. REMARK 100 THE DEPOSITION ID IS D_1290048117. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 295.0 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 70 REMARK 210 PRESSURE : 1.0 ATM REMARK 210 SAMPLE CONTENTS : 90% WATER/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 1H; 15N HSQC (PRE) REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY REMARK 210 METHOD USED : MODIFIED ARIA REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 500 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-10 REMARK 465 RES C SSSEQI REMARK 465 GLY A 145 REMARK 465 ALA A 146 REMARK 465 MET A 147 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 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 1 GLU A 240 -169.07 -162.08 REMARK 500 1 SER A 243 -75.62 -146.20 REMARK 500 1 VAL A 244 -44.70 -160.80 REMARK 500 1 TYR A 245 -90.69 63.39 REMARK 500 1 SER A 336 -82.51 -86.56 REMARK 500 1 VAL A 337 107.10 63.52 REMARK 500 1 ALA A 339 98.89 -169.62 REMARK 500 2 ASN A 196 61.52 66.76 REMARK 500 2 GLN A 233 89.73 63.08 REMARK 500 2 LEU A 235 92.20 63.34 REMARK 500 2 PRO A 242 -151.48 -72.07 REMARK 500 2 PRO A 247 -179.03 -66.99 REMARK 500 2 SER A 336 -38.17 -147.04 REMARK 500 2 VAL A 337 81.95 55.29 REMARK 500 2 LYS A 340 -72.33 70.55 REMARK 500 3 LEU A 235 83.48 61.22 REMARK 500 3 MET A 238 -60.10 -108.08 REMARK 500 3 VAL A 244 -59.96 -120.21 REMARK 500 3 VAL A 250 -41.78 -175.91 REMARK 500 3 SER A 251 74.77 56.68 REMARK 500 4 ARG A 149 -24.64 75.99 REMARK 500 4 ASN A 196 61.35 60.04 REMARK 500 4 GLN A 233 70.16 53.34 REMARK 500 4 LEU A 235 136.78 73.80 REMARK 500 4 ASN A 241 -52.88 -165.84 REMARK 500 4 ALA A 295 -68.90 -98.03 REMARK 500 4 VAL A 337 -60.46 71.13 REMARK 500 4 LYS A 340 101.63 66.34 REMARK 500 5 ASN A 196 61.86 62.20 REMARK 500 5 LEU A 235 -55.79 -163.24 REMARK 500 5 MET A 238 -70.61 -71.47 REMARK 500 5 TYR A 245 -80.19 -98.43 REMARK 500 5 VAL A 249 86.49 64.91 REMARK 500 5 SER A 251 -177.05 64.92 REMARK 500 5 SER A 257 45.87 -90.19 REMARK 500 5 VAL A 337 -65.64 71.64 REMARK 500 6 SER A 204 -161.88 -125.44 REMARK 500 6 GLU A 240 79.04 61.25 REMARK 500 6 VAL A 249 74.41 51.69 REMARK 500 6 VAL A 250 90.71 65.02 REMARK 500 6 ASP A 256 98.03 64.44 REMARK 500 6 SER A 336 -71.97 -64.29 REMARK 500 7 LEU A 187 -61.63 -90.98 REMARK 500 7 SER A 204 -165.30 -125.84 REMARK 500 7 HIS A 230 -74.45 -75.55 REMARK 500 7 SER A 243 78.30 61.31 REMARK 500 7 VAL A 254 86.77 63.18 REMARK 500 7 ALA A 258 -45.42 -169.17 REMARK 500 7 SER A 336 -56.33 -154.73 REMARK 500 7 VAL A 337 -60.73 72.47 REMARK 500 REMARK 500 THIS ENTRY HAS 69 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2U2F RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE SECOND RIBONUCLEIC ACID- BINDING DOMAIN REMARK 900 OF HU2AF65 REMARK 900 RELATED ID: 1U2F RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE FIRST RIBONUCLEIC ACID-BINDING DOMAIN OF REMARK 900 HU2AF65 REMARK 900 RELATED ID: 1OPI RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE THIRD RNA RECOGNITION MOTIF ( RRM)OF REMARK 900 U2AF65 IN COMPLEX WITH AN N-TERMINAL SF1 PEPTIDE REMARK 900 RELATED ID: 1O0P RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE THIRD RNA RECOGNITION MOTIF ( RRM)OF REMARK 900 U2AF65 IN COMPLEX WITH AN N-TERMINAL SF1 PEPTIDE REMARK 900 RELATED ID: 2G4B RELATED DB: PDB REMARK 900 STRUCTURE OF U2AF65 VARIANT WITH POLYURIDINE TRACT REMARK 900 RELATED ID: 1JMT RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF A CORE U2AF65/U2AF35 HETERODIMER REMARK 900 RELATED ID: 2YH4 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE OPEN CONFORMATION OF HUMAN U2AF65 TANDEM REMARK 900 RRM1 AND RRM2 DOMAINS REMARK 900 RELATED ID: 2YH1 RELATED DB: PDB REMARK 900 MODEL OF HUMAN U2AF65 TANDEM RRM1 AND RRM2 DOMAINS WITH EIGHT-SITE REMARK 900 URIDINE BINDING REMARK 900 RELATED ID: 17622 RELATED DB: BMRB DBREF 2YH0 A 148 342 UNP P26368 U2AF2_HUMAN 148 342 SEQADV 2YH0 GLY A 145 UNP P26368 EXPRESSION TAG SEQADV 2YH0 ALA A 146 UNP P26368 EXPRESSION TAG SEQADV 2YH0 MET A 147 UNP P26368 EXPRESSION TAG SEQRES 1 A 198 GLY ALA MET ALA ARG ARG LEU TYR VAL GLY ASN ILE PRO SEQRES 2 A 198 PHE GLY ILE THR GLU GLU ALA MET MET ASP PHE PHE ASN SEQRES 3 A 198 ALA GLN MET ARG LEU GLY GLY LEU THR GLN ALA PRO GLY SEQRES 4 A 198 ASN PRO VAL LEU ALA VAL GLN ILE ASN GLN ASP LYS ASN SEQRES 5 A 198 PHE ALA PHE LEU GLU PHE ARG SER VAL ASP GLU THR THR SEQRES 6 A 198 GLN ALA MET ALA PHE ASP GLY ILE ILE PHE GLN GLY GLN SEQRES 7 A 198 SER LEU LYS ILE ARG ARG PRO HIS ASP TYR GLN PRO LEU SEQRES 8 A 198 PRO GLY MET SER GLU ASN PRO SER VAL TYR VAL PRO GLY SEQRES 9 A 198 VAL VAL SER THR VAL VAL PRO ASP SER ALA HIS LYS LEU SEQRES 10 A 198 PHE ILE GLY GLY LEU PRO ASN TYR LEU ASN ASP ASP GLN SEQRES 11 A 198 VAL LYS GLU LEU LEU THR SER PHE GLY PRO LEU LYS ALA SEQRES 12 A 198 PHE ASN LEU VAL LYS ASP SER ALA THR GLY LEU SER LYS SEQRES 13 A 198 GLY TYR ALA PHE CYS GLU TYR VAL ASP ILE ASN VAL THR SEQRES 14 A 198 ASP GLN ALA ILE ALA GLY LEU ASN GLY MET GLN LEU GLY SEQRES 15 A 198 ASP LYS LYS LEU LEU VAL GLN ARG ALA SER VAL GLY ALA SEQRES 16 A 198 LYS ASN ALA HELIX 1 1 THR A 161 GLY A 176 1 16 HELIX 2 2 VAL A 205 MET A 212 1 8 HELIX 3 3 ALA A 213 ASP A 215 5 3 HELIX 4 4 ASN A 271 SER A 281 1 11 HELIX 5 5 ASN A 311 ASN A 321 1 11 SHEET 1 AA 5 VAL A 186 ASN A 192 0 SHEET 2 AA 5 PHE A 197 PHE A 202 -1 O PHE A 197 N ASN A 192 SHEET 3 AA 5 ARG A 150 GLY A 154 -1 O LEU A 151 N LEU A 200 SHEET 4 AA 5 GLN A 222 ARG A 227 -1 O LYS A 225 N GLY A 154 SHEET 5 AA 5 ILE A 217 PHE A 219 -1 O ILE A 217 N LEU A 224 SHEET 1 AB 4 LEU A 285 LYS A 292 0 SHEET 2 AB 4 SER A 299 TYR A 307 -1 N LYS A 300 O VAL A 291 SHEET 3 AB 4 LYS A 260 GLY A 264 -1 O LEU A 261 N CYS A 305 SHEET 4 AB 4 LEU A 331 ARG A 334 -1 O LEU A 331 N GLY A 264 SHEET 1 AC 2 GLN A 324 LEU A 325 0 SHEET 2 AC 2 LYS A 328 LYS A 329 -1 O LYS A 328 N LEU A 325 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1