HEADER RNA BINDING PROTEIN 22-MAR-22 7ZAP TITLE SOLUTION STRUCTURE OF RBM39 RRM1 BOUND TO U1 SNRNA STEM LOOP 3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA-BINDING PROTEIN 39; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RNA-BINDING REGION (RNP1,RRM) CONTAINING 2,ISOFORM CRA_F; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: U1 SNRNA SL3; COMPND 8 CHAIN: B; COMPND 9 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: RBM39, RNPC2, HCG_38221; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS RBM39, RRM, STEM LOOP RECOGNITION, RNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.CAMPAGNE,F.H.ALLAIN REVDAT 3 20-SEP-23 7ZAP 1 JRNL REVDAT 2 13-SEP-23 7ZAP 1 JRNL REVDAT 1 29-MAR-23 7ZAP 0 JRNL AUTH S.CAMPAGNE,D.JUTZI,F.MALARD,M.MATOGA,K.ROMANE,M.FELDMULLER, JRNL AUTH 2 M.COLOMBO,M.D.RUEPP,F.H.ALLAIN JRNL TITL MOLECULAR BASIS OF RNA-BINDING AND AUTOREGULATION BY THE JRNL TITL 2 CANCER-ASSOCIATED SPLICING FACTOR RBM39. JRNL REF NAT COMMUN V. 14 5366 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 37666821 JRNL DOI 10.1038/S41467-023-40254-5 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 21 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7ZAP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-MAR-22. REMARK 100 THE DEPOSITION ID IS D_1292120350. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 313 REMARK 210 PH : 5.5 REMARK 210 IONIC STRENGTH : 10 REMARK 210 PRESSURE : ATMOSPHERIC ATM REMARK 210 SAMPLE CONTENTS : 10 MM SODIUM PHOSPHATE, 3 MM REMARK 210 DTT, 1.2 MM [U-13C; U-15N] RBM39 REMARK 210 RRM1, 1.5 MM U1 SNRNA SL3, 90% REMARK 210 H2O/10% D2O; 10 MM SODIUM REMARK 210 PHOSPHATE, 3 MM DTT, 1.2 MM [U- REMARK 210 13C; U-15N] RBM39 RRM1, 1.5 MM REMARK 210 U1 SNRNA SL3, 100% D2O; 10 MM REMARK 210 SODIUM PHOSPHATE, 3 MM DTT, 1.2 REMARK 210 MM [U-13C; U-15N] RBM39 RRM1, REMARK 210 1.5 MM U1 SNRNA SL3, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCACB; 3D CBCA(CO)NH; 3D REMARK 210 HNCO; 3D H(CCO)NH; 3D C(CO)NH; REMARK 210 3D 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 3D HCCH-TOCSY; 3D REMARK 210 EDITED FILTERED 1H-13C NOESY REMARK 210 HSQC; 2D 1H-1H F1F NOESY; 2D 1H- REMARK 210 1H F2FF1F NOESY; 2D 1H-1H NOESY; REMARK 210 3D 1H-13C EDITED-FILTERED NOESY REMARK 210 HSQC; 3D HCCH-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 700 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III HD; AVANCE NEO REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 3.1, CARA, ATNOS, TOPSPIN REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 500 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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: 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 1 U B 107 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 7 U B 107 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 9 U B 107 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 17 U B 107 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 19 U B 107 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 20 U B 107 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES 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 ARG A 188 -73.58 -96.00 REMARK 500 1 ASN A 189 15.38 47.08 REMARK 500 1 SER A 193 84.54 49.48 REMARK 500 2 SER A 186 21.64 -141.58 REMARK 500 2 ARG A 188 -73.19 -71.79 REMARK 500 2 ASN A 189 -23.10 58.91 REMARK 500 2 SER A 193 92.07 39.53 REMARK 500 3 ARG A 188 -66.52 -90.34 REMARK 500 3 ASN A 189 17.69 45.30 REMARK 500 3 SER A 193 89.77 43.74 REMARK 500 3 LYS A 194 16.69 58.44 REMARK 500 4 ARG A 188 -73.88 -98.26 REMARK 500 4 ASN A 189 7.47 46.56 REMARK 500 4 SER A 193 80.43 51.72 REMARK 500 5 ASN A 144 84.30 -150.62 REMARK 500 5 ASN A 189 26.26 -74.69 REMARK 500 5 SER A 193 89.45 40.47 REMARK 500 6 ASN A 189 -25.77 58.66 REMARK 500 6 SER A 193 92.81 40.61 REMARK 500 7 ARG A 188 -62.25 -98.05 REMARK 500 7 ASN A 189 19.10 47.68 REMARK 500 7 SER A 193 78.46 49.19 REMARK 500 7 LYS A 194 17.48 58.24 REMARK 500 8 ARG A 188 -76.57 -89.44 REMARK 500 8 ASN A 189 17.39 42.72 REMARK 500 8 SER A 193 94.22 34.91 REMARK 500 9 ARG A 188 -73.25 -96.97 REMARK 500 9 ASN A 189 -20.07 57.05 REMARK 500 9 ARG A 191 -5.55 -58.78 REMARK 500 10 ARG A 188 -73.61 -98.25 REMARK 500 10 ASN A 189 12.71 48.46 REMARK 500 10 SER A 193 77.70 43.03 REMARK 500 10 LYS A 194 18.61 59.68 REMARK 500 11 ASN A 189 6.43 50.77 REMARK 500 11 SER A 193 93.55 39.49 REMARK 500 12 ASN A 189 88.16 44.47 REMARK 500 12 SER A 190 176.19 67.04 REMARK 500 12 SER A 193 94.71 41.97 REMARK 500 13 ARG A 188 -73.82 -97.44 REMARK 500 13 ASN A 189 14.54 44.48 REMARK 500 13 SER A 193 87.94 43.36 REMARK 500 14 SER A 186 26.35 -145.51 REMARK 500 15 ARG A 188 -68.05 -97.79 REMARK 500 15 ASN A 189 -9.64 55.01 REMARK 500 15 SER A 193 70.65 49.08 REMARK 500 16 ARG A 188 -73.81 -97.83 REMARK 500 16 ASN A 189 -6.00 51.96 REMARK 500 16 SER A 193 79.32 49.28 REMARK 500 16 LEU A 219 32.84 37.65 REMARK 500 17 ASN A 144 49.35 -140.07 REMARK 500 REMARK 500 THIS ENTRY HAS 64 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 12 C B 100 0.07 SIDE CHAIN REMARK 500 16 U B 105 0.07 SIDE CHAIN REMARK 500 17 U B 107 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34715 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF RBM39 RRM1 BOUND TO U1 SNRNA STEM LOOP 3 DBREF 7ZAP A 142 237 UNP G3XAC6 G3XAC6_HUMAN 142 237 DBREF 7ZAP B 91 118 PDB 7ZAP 7ZAP 91 118 SEQADV 7ZAP MET A 141 UNP G3XAC6 INITIATING METHIONINE SEQRES 1 A 97 MET ILE ASP ASN LEU THR PRO GLU GLU ARG ASP ALA ARG SEQRES 2 A 97 THR VAL PHE CYS MET GLN LEU ALA ALA ARG ILE ARG PRO SEQRES 3 A 97 ARG ASP LEU GLU GLU PHE PHE SER THR VAL GLY LYS VAL SEQRES 4 A 97 ARG ASP VAL ARG MET ILE SER ASP ARG ASN SER ARG ARG SEQRES 5 A 97 SER LYS GLY ILE ALA TYR VAL GLU PHE VAL ASP VAL SER SEQRES 6 A 97 SER VAL PRO LEU ALA ILE GLY LEU THR GLY GLN ARG VAL SEQRES 7 A 97 LEU GLY VAL PRO ILE ILE VAL GLN ALA SER GLN ALA GLU SEQRES 8 A 97 LYS ASN ARG ALA ALA ALA SEQRES 1 B 28 G G G A U U U C C C C A A SEQRES 2 B 28 A U G U G G G A A A C U C SEQRES 3 B 28 C C HELIX 1 AA1 ARG A 150 ALA A 152 5 3 HELIX 2 AA2 PRO A 166 SER A 174 1 9 HELIX 3 AA3 ASP A 203 SER A 205 5 3 HELIX 4 AA4 SER A 206 LEU A 213 1 8 HELIX 5 AA5 ALA A 230 ALA A 235 1 6 SHEET 1 AA1 4 VAL A 179 ILE A 185 0 SHEET 2 AA1 4 ILE A 196 PHE A 201 -1 O TYR A 198 N ARG A 183 SHEET 3 AA1 4 THR A 154 MET A 158 -1 N VAL A 155 O VAL A 199 SHEET 4 AA1 4 ILE A 224 ALA A 227 -1 O GLN A 226 N PHE A 156 SHEET 1 AA2 2 ARG A 217 VAL A 218 0 SHEET 2 AA2 2 VAL A 221 PRO A 222 -1 O VAL A 221 N VAL A 218 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