HEADER GENE REGULATION/RNA 25-SEP-01 1K1G TITLE STRUCTURAL BASIS FOR RECOGNITION OF THE INTRON BRANCH SITE RNA BY TITLE 2 SPLICING FACTOR 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*UP*AP*UP*AP*CP*UP*AP*AP*CP*AP*A)-3'; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: YEAST AND MAMMALIAN CONSENSUS BPS SEQUENCE; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: SF1-BO ISOFORM; COMPND 8 CHAIN: A; COMPND 9 FRAGMENT: RESIDUES 133-260, KH-QUA2 REGION; COMPND 10 SYNONYM: SPLICING FACTOR 1; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 5 ORGANISM_COMMON: HUMAN; SOURCE 6 ORGANISM_TAXID: 9606; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21 DE3; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: MODIFIED PET24D KEYWDS SPLICING, BRANCH POINT SEQUENCE, PROTEIN/RNA RECOGNITION, COMPLEX E, KEYWDS 2 KH DOMAIN, QUA2 HOMOLOGY, STAR PROTEINS, GENE REGULATION-RNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR Z.LIU,I.LUYTEN,M.J.BOTTOMLEY,A.C.MESSIAS,S.HOUNGNINOU-MOLANGO, AUTHOR 2 R.SPRANGERS,K.ZANIER,A.KRAMER,M.SATTLER REVDAT 4 22-MAY-24 1K1G 1 REMARK REVDAT 3 23-FEB-22 1K1G 1 REMARK SEQADV REVDAT 2 24-FEB-09 1K1G 1 VERSN REVDAT 1 07-NOV-01 1K1G 0 JRNL AUTH Z.LIU,I.LUYTEN,M.J.BOTTOMLEY,A.C.MESSIAS, JRNL AUTH 2 S.HOUNGNINOU-MOLANGO,R.SPRANGERS,K.ZANIER,A.KRAMER,M.SATTLER JRNL TITL STRUCTURAL BASIS FOR RECOGNITION OF THE INTRON BRANCH SITE JRNL TITL 2 RNA BY SPLICING FACTOR 1. JRNL REF SCIENCE V. 294 1098 2001 JRNL REFN ISSN 0036-8075 JRNL PMID 11691992 JRNL DOI 10.1126/SCIENCE.1064719 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.6, ARIA/CNS 1.0 REMARK 3 AUTHORS : BRUKER (XWINNMR), J. LINGE, M. NILGES (ARIA/CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 STRUCTURES WERE CALCULATED WITH A MIXED TORSION AND CARTESIAN ANGLE REMARK 3 DYNAMICS PROTOCOL USING ARIA/CNS. A REDUCED RELAXATION MATRIX REMARK 3 APPROACH REMARK 3 WAS USED FOR THE NOE CALIBRATION. THE STRUCTURES ARE CURRENTLY REMARK 3 BEING REMARK 3 REFINED USING RESIDUAL DIPOLAR COUPLINGS AND WILL BE UPDATED IN THE REMARK 3 FUTURE. REMARK 4 REMARK 4 1K1G COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-OCT-01. REMARK 100 THE DEPOSITION ID IS D_1000014440. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 295; 278 REMARK 210 PH : 6.5; 6.5 REMARK 210 IONIC STRENGTH : 50 MM NACL; 50 MM NACL REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM U-15N,13C SF1 KH REMARK 210 -QUA2/UNLABELED BPS IN 20 MM REMARK 210 PHOSPHATE BUFFER NA PH 6.5, 50 REMARK 210 MM NACL, 2 MM DTT; 1 MM U-15N, REMARK 210 13C SF1 KH-QUA2/UNLABELED BPS IN REMARK 210 20 MM PHOSPHATE BUFFER NA PH 6.5, REMARK 210 50 MM NACL, 2 MM DTT; 1 MM U- REMARK 210 15N SF1 KH-QUA2/UNLABELED BPS IN REMARK 210 20 MM PHOSPHATE BUFFER NA PH 6.5, REMARK 210 50 MM NACL, 2 MM DTT REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; REMARK 210 3D_13C/15N_EDITED/FILTERED_NOESY; 3D_15N-SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 1.8, XEASY 1.2, ARIA/CNS REMARK 210 1.0 REMARK 210 METHOD USED : RESTRAINED MOLECULAR DYNAMICS, REMARK 210 SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : 10 LOWEST ENERGY STRUCTURES REMARK 210 CONSISTENT WITH EXPERIMENTAL REMARK 210 DISTANCE AND DIHEDRAL ANGLE REMARK 210 RESTRAINTS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: BACKBONE AND SIDE CHAIN 1H, 15N AND 13C RESONANCES WERE REMARK 210 ASSIGNED USING STANDARD TRIPLE RESONANCE EXPERIMENTS. DISTANCE REMARK 210 RESTRAINTS WERE DERIVED FROM 13C- AND 15N-EDITED 3D NOESY REMARK 210 EXPERIMENTS. ASSIGNMENTS FOR THE RNA WERE OBTAINED FROM 2D REMARK 210 ISOTOPE-FILTERED EXPERIMENTS. INTERMOLECULAR DISTANCE RESTRAINTS REMARK 210 WERE MEASURED IN 3D 13C-EDITED/FILTERED EXPERIMENTS. DIHEDRAL REMARK 210 ANGLE RESTRAINTS FOR THE BACKBONE ANGLE PHI WERE DERIVED FROM REMARK 210 3J(HN,HA) COUPLING CONSTANTS MEASURED IN AN HNHA-J EXPERIMENT, REMARK 210 ADDITIONAL PHI/PSI RESTRAINTS WERE DERIVED FROM TALOS. HYDROGEN REMARK 210 BOND RESTRAINTS FOR SECONDARY STRUCTURE ELEMENTS IN THE PROTEIN REMARK 210 WERE DEFINED FROM SLOWLY EXCHANGING AMIDE PROTONS, IDENTIFIED REMARK 210 AFTER EXCHANGE OF THE H2O BUFFER TO D2O. 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 130 REMARK 465 ALA A 131 REMARK 465 MET A 132 REMARK 465 ALA A 133 REMARK 465 GLU A 256 REMARK 465 ASP A 257 REMARK 465 ASP A 258 REMARK 465 ASN A 259 REMARK 465 ARG A 260 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: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 1 A B 504 C2' A B 504 C1' -0.049 REMARK 500 2 A B 504 C2' A B 504 C1' -0.049 REMARK 500 5 A B 504 C2' A B 504 C1' -0.048 REMARK 500 7 A B 504 C2' A B 504 C1' -0.054 REMARK 500 8 A B 504 C2' A B 504 C1' -0.049 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 ASP A 138 109.01 -166.84 REMARK 500 1 PRO A 143 70.55 -68.04 REMARK 500 1 GLU A 146 -57.10 -122.77 REMARK 500 1 GLU A 149 -13.46 -164.84 REMARK 500 1 ILE A 150 -135.39 14.40 REMARK 500 1 ILE A 157 -68.40 -91.90 REMARK 500 1 ARG A 160 -44.02 78.64 REMARK 500 1 GLU A 170 -76.61 -79.71 REMARK 500 1 LYS A 180 -89.19 -61.27 REMARK 500 1 SER A 182 -47.61 -132.45 REMARK 500 1 LYS A 187 -160.94 -102.31 REMARK 500 1 ASP A 200 -75.73 -105.97 REMARK 500 1 PRO A 202 -73.22 -65.39 REMARK 500 1 LEU A 203 86.53 177.53 REMARK 500 1 ALA A 209 -161.42 -174.90 REMARK 500 1 THR A 232 150.75 -43.57 REMARK 500 1 PRO A 233 -175.34 -60.24 REMARK 500 1 GLN A 236 -84.48 -127.52 REMARK 500 1 ASN A 237 -49.30 74.22 REMARK 500 2 PRO A 148 -95.51 -50.93 REMARK 500 2 ILE A 150 -137.91 19.76 REMARK 500 2 ILE A 157 -66.19 -95.59 REMARK 500 2 ARG A 160 -42.12 79.40 REMARK 500 2 GLU A 170 -76.66 -81.83 REMARK 500 2 SER A 182 -86.94 -120.64 REMARK 500 2 LYS A 184 101.35 -58.44 REMARK 500 2 GLU A 185 -14.05 -165.96 REMARK 500 2 ARG A 190 -66.47 -98.42 REMARK 500 2 GLU A 199 -38.85 -160.85 REMARK 500 2 LEU A 203 102.13 176.29 REMARK 500 2 THR A 232 164.51 -49.99 REMARK 500 2 PRO A 233 143.49 -36.62 REMARK 500 2 GLN A 236 -86.29 -154.93 REMARK 500 2 ASN A 237 -86.01 59.03 REMARK 500 2 LYS A 241 9.33 -64.65 REMARK 500 3 PRO A 143 74.95 -68.45 REMARK 500 3 GLU A 146 -57.04 -129.73 REMARK 500 3 GLU A 149 -10.35 -168.51 REMARK 500 3 ILE A 150 -141.45 18.26 REMARK 500 3 ILE A 157 -69.01 -92.29 REMARK 500 3 ARG A 160 -48.27 80.19 REMARK 500 3 GLU A 170 -77.08 -75.73 REMARK 500 3 LYS A 180 90.04 -69.31 REMARK 500 3 SER A 182 -86.04 -121.68 REMARK 500 3 GLU A 185 15.32 -174.29 REMARK 500 3 LYS A 191 -164.07 53.57 REMARK 500 3 PRO A 197 171.32 -56.61 REMARK 500 3 PRO A 202 -70.57 -72.95 REMARK 500 3 LEU A 203 96.20 -178.85 REMARK 500 3 THR A 232 152.59 -48.09 REMARK 500 REMARK 500 THIS ENTRY HAS 184 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1K1G A 133 260 UNP Q15637 SF01_HUMAN 133 260 DBREF 1K1G B 501 511 PDB 1K1G 1K1G 501 511 SEQADV 1K1G GLY A 130 UNP Q15637 LYS 130 CLONING ARTIFACT SEQADV 1K1G ALA A 131 UNP Q15637 PRO 131 CLONING ARTIFACT SEQADV 1K1G MET A 132 UNP Q15637 PRO 132 CLONING ARTIFACT SEQRES 1 B 11 U A U A C U A A C A A SEQRES 1 A 131 GLY ALA MET ALA THR ARG VAL SER ASP LYS VAL MET ILE SEQRES 2 A 131 PRO GLN ASP GLU TYR PRO GLU ILE ASN PHE VAL GLY LEU SEQRES 3 A 131 LEU ILE GLY PRO ARG GLY ASN THR LEU LYS ASN ILE GLU SEQRES 4 A 131 LYS GLU CYS ASN ALA LYS ILE MET ILE ARG GLY LYS GLY SEQRES 5 A 131 SER VAL LYS GLU GLY LYS VAL GLY ARG LYS ASP GLY GLN SEQRES 6 A 131 MET LEU PRO GLY GLU ASP GLU PRO LEU HIS ALA LEU VAL SEQRES 7 A 131 THR ALA ASN THR MET GLU ASN VAL LYS LYS ALA VAL GLU SEQRES 8 A 131 GLN ILE ARG ASN ILE LEU LYS GLN GLY ILE GLU THR PRO SEQRES 9 A 131 GLU ASP GLN ASN ASP LEU ARG LYS MET GLN LEU ARG GLU SEQRES 10 A 131 LEU ALA ARG LEU ASN GLY THR LEU ARG GLU ASP ASP ASN SEQRES 11 A 131 ARG HELIX 1 1 GLU A 149 GLY A 158 1 10 HELIX 2 2 GLY A 161 CYS A 171 1 11 HELIX 3 3 THR A 211 LYS A 227 1 17 HELIX 4 4 ASN A 237 GLN A 243 5 7 HELIX 5 5 LEU A 244 ARG A 249 1 6 SHEET 1 A 3 VAL A 136 MET A 141 0 SHEET 2 A 3 LEU A 203 ALA A 209 -1 O ALA A 209 N VAL A 136 SHEET 3 A 3 LYS A 174 GLY A 179 -1 N ARG A 178 O HIS A 204 CRYST1 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