HEADER RNA BINDING PROTEIN 26-OCT-21 7Q33 TITLE SOLUTION STRUCTURE OF RBM39 RRM2 BOUND TO 5'-AGCUUUG-3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA-BINDING PROTEIN 39; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CAPER ALPHA,CAPERALPHA,HEPATOCELLULAR CARCINOMA PROTEIN 1, COMPND 5 RNA-BINDING MOTIF PROTEIN 39,RNA-BINDING REGION-CONTAINING PROTEIN 2, COMPND 6 SPLICING FACTOR HCC1; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: RNA (5'-R(*AP*GP*CP*UP*UP*UP*G)-3'); COMPND 10 CHAIN: B; COMPND 11 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, HCC1, RNPC2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 EXPRESSION_SYSTEM: SYNTHETIC CONSTRUCT; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 32630 KEYWDS RNA BINDING, RRM, EXTENDED RNA BINDING SURFACE, RNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.CAMPAGNE,F.H.ALLAIN REVDAT 3 20-SEP-23 7Q33 1 JRNL REVDAT 2 13-SEP-23 7Q33 1 JRNL REVDAT 1 08-FEB-23 7Q33 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 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SA IN CARTESIAN SPACE REMARK 4 REMARK 4 7Q33 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-OCT-21. REMARK 100 THE DEPOSITION ID IS D_1292118916. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 60 REMARK 210 PRESSURE : ATM ATM REMARK 210 SAMPLE CONTENTS : 10 MM NAPO4, 50 MM SODIUM REMARK 210 CHLORIDE, 2 MM DTT, 1.2 MM 13C; REMARK 210 15N RBM39 RRM2, 1.2 MM AGCUUUG, REMARK 210 90% H2O/10% D2O; 10 MM NAPO4, 50 REMARK 210 MM SODIUM CHLORIDE, 2 MM DTT, REMARK 210 1.2 MM 13C; 15N RBM39 RRM2, 1.2 REMARK 210 MM AGCUUUG, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 3D HNCO; 3D H(CCO)NH; REMARK 210 3D C(CO)NH; 3D 1H-15N NOESY; 3D REMARK 210 1H-13C NOESY ALIPHATIC; 3D 1H- REMARK 210 13C NOESY AROMATIC; 2D F1FF2F REMARK 210 NOESY; 2D F2F NOESY; 2D F2F TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE NEO; AVANCE III HD REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CARA, CYANA, ATNOS REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 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: 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: 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 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 G B 702 C1' - O4' - C4' ANGL. DEV. = -4.3 DEGREES REMARK 500 1 G B 702 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 C B 703 C1' - O4' - C4' ANGL. DEV. = -7.4 DEGREES REMARK 500 1 C B 703 O4' - C1' - N1 ANGL. DEV. = 9.8 DEGREES REMARK 500 2 G B 702 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 C B 703 C1' - O4' - C4' ANGL. DEV. = -7.4 DEGREES REMARK 500 2 C B 703 O4' - C1' - N1 ANGL. DEV. = 9.6 DEGREES REMARK 500 3 C B 703 C1' - O4' - C4' ANGL. DEV. = -7.5 DEGREES REMARK 500 3 C B 703 O4' - C1' - N1 ANGL. DEV. = 6.3 DEGREES REMARK 500 4 G B 702 C1' - O4' - C4' ANGL. DEV. = -4.2 DEGREES REMARK 500 4 C B 703 C1' - O4' - C4' ANGL. DEV. = -5.0 DEGREES REMARK 500 5 G B 702 C1' - O4' - C4' ANGL. DEV. = -4.4 DEGREES REMARK 500 5 G B 702 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 5 C B 703 C1' - O4' - C4' ANGL. DEV. = -7.6 DEGREES REMARK 500 5 C B 703 O4' - C1' - N1 ANGL. DEV. = 8.8 DEGREES REMARK 500 6 C B 703 C1' - O4' - C4' ANGL. DEV. = -7.5 DEGREES REMARK 500 6 C B 703 O4' - C1' - N1 ANGL. DEV. = 7.0 DEGREES REMARK 500 7 C B 703 C1' - O4' - C4' ANGL. DEV. = -7.3 DEGREES REMARK 500 7 C B 703 O4' - C1' - N1 ANGL. DEV. = 6.2 DEGREES REMARK 500 8 C B 703 C1' - O4' - C4' ANGL. DEV. = -5.2 DEGREES REMARK 500 8 C B 703 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 9 G B 702 C1' - O4' - C4' ANGL. DEV. = -5.1 DEGREES REMARK 500 9 G B 702 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 9 C B 703 C5' - C4' - O4' ANGL. DEV. = 7.6 DEGREES REMARK 500 9 C B 703 C1' - O4' - C4' ANGL. DEV. = -7.8 DEGREES REMARK 500 9 C B 703 O4' - C1' - N1 ANGL. DEV. = 8.0 DEGREES REMARK 500 10 G B 702 C1' - O4' - C4' ANGL. DEV. = -5.3 DEGREES REMARK 500 10 G B 702 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 11 C B 703 C1' - O4' - C4' ANGL. DEV. = -7.3 DEGREES REMARK 500 11 C B 703 O4' - C1' - N1 ANGL. DEV. = 6.8 DEGREES REMARK 500 12 G B 702 C1' - O4' - C4' ANGL. DEV. = -4.9 DEGREES REMARK 500 12 C B 703 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 13 G B 702 C1' - O4' - C4' ANGL. DEV. = -5.7 DEGREES REMARK 500 13 G B 702 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 13 C B 703 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 13 U B 706 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 14 C B 703 C1' - O4' - C4' ANGL. DEV. = -5.0 DEGREES REMARK 500 15 G B 702 C1' - O4' - C4' ANGL. DEV. = -5.0 DEGREES REMARK 500 15 G B 702 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 15 C B 703 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 16 C B 703 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 17 G B 702 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 17 C B 703 C5' - C4' - O4' ANGL. DEV. = 6.0 DEGREES REMARK 500 17 C B 703 C1' - O4' - C4' ANGL. DEV. = -6.1 DEGREES REMARK 500 17 C B 703 O4' - C1' - N1 ANGL. DEV. = 7.9 DEGREES REMARK 500 18 G B 702 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 18 C B 703 C1' - O4' - C4' ANGL. DEV. = -7.9 DEGREES REMARK 500 18 C B 703 O4' - C1' - N1 ANGL. DEV. = 9.0 DEGREES REMARK 500 19 C B 703 C1' - O4' - C4' ANGL. DEV. = -5.9 DEGREES REMARK 500 19 C B 703 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 53 ANGLE DEVIATIONS. 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 329 9.26 -153.28 REMARK 500 1 LEU A 333 -12.62 -151.74 REMARK 500 2 SER A 290 -178.27 -69.86 REMARK 500 2 LEU A 333 -21.14 -162.76 REMARK 500 3 ALA A 247 21.78 -143.87 REMARK 500 3 ARG A 329 5.30 -150.14 REMARK 500 3 LEU A 333 -158.75 -149.73 REMARK 500 4 GLU A 334 12.17 55.52 REMARK 500 5 LEU A 308 -70.33 -67.40 REMARK 500 5 ARG A 329 -0.61 -151.65 REMARK 500 6 ALA A 247 23.97 -144.26 REMARK 500 6 ASN A 312 106.55 -59.59 REMARK 500 7 ASN A 312 109.30 -59.71 REMARK 500 8 ASN A 312 109.43 -59.39 REMARK 500 9 SER A 290 -179.54 -67.47 REMARK 500 9 GLU A 334 25.30 -75.12 REMARK 500 9 LEU A 335 -15.79 61.31 REMARK 500 10 ALA A 247 -169.88 55.57 REMARK 500 10 GLU A 334 15.98 55.65 REMARK 500 11 SER A 290 -178.59 -68.66 REMARK 500 11 LYS A 291 10.64 -141.85 REMARK 500 11 LEU A 308 -70.12 -67.17 REMARK 500 12 ASN A 312 108.04 -59.79 REMARK 500 12 LEU A 335 176.28 58.49 REMARK 500 13 LEU A 308 -70.07 -64.40 REMARK 500 13 ARG A 329 13.69 -154.72 REMARK 500 13 GLU A 334 14.18 54.73 REMARK 500 14 LEU A 308 -70.44 -63.16 REMARK 500 15 ALA A 247 23.67 -143.28 REMARK 500 15 LEU A 308 -70.18 -64.41 REMARK 500 15 ASN A 312 108.40 -59.27 REMARK 500 15 GLU A 315 69.34 -69.82 REMARK 500 16 ARG A 329 3.74 -157.46 REMARK 500 17 ALA A 247 20.85 -144.66 REMARK 500 17 SER A 290 -179.47 -68.84 REMARK 500 17 ASN A 312 107.98 -59.31 REMARK 500 18 LEU A 308 -70.43 -66.48 REMARK 500 19 LEU A 308 -70.56 -66.32 REMARK 500 19 ASN A 312 109.03 -59.69 REMARK 500 20 LEU A 335 157.09 62.24 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 1 C B 703 0.10 SIDE CHAIN REMARK 500 2 C B 703 0.11 SIDE CHAIN REMARK 500 3 C B 703 0.09 SIDE CHAIN REMARK 500 4 C B 703 0.07 SIDE CHAIN REMARK 500 6 C B 703 0.12 SIDE CHAIN REMARK 500 7 C B 703 0.10 SIDE CHAIN REMARK 500 8 C B 703 0.08 SIDE CHAIN REMARK 500 8 G B 707 0.06 SIDE CHAIN REMARK 500 11 C B 703 0.11 SIDE CHAIN REMARK 500 14 C B 703 0.07 SIDE CHAIN REMARK 500 18 C B 703 0.08 SIDE CHAIN REMARK 500 19 C B 703 0.06 SIDE CHAIN REMARK 500 20 C B 703 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34673 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF RBM39 RRM2 BOUND TO 5'-AGCUUUG-3 DBREF 7Q33 A 247 332 UNP Q14498 RBM39_HUMAN 247 332 DBREF 7Q33 B 701 707 PDB 7Q33 7Q33 701 707 SEQADV 7Q33 MET A 246 UNP Q14498 INITIATING METHIONINE SEQADV 7Q33 LEU A 333 UNP Q14498 EXPRESSION TAG SEQADV 7Q33 GLU A 334 UNP Q14498 EXPRESSION TAG SEQADV 7Q33 LEU A 335 UNP Q14498 EXPRESSION TAG SEQADV 7Q33 VAL A 336 UNP Q14498 EXPRESSION TAG SEQADV 7Q33 PRO A 337 UNP Q14498 EXPRESSION TAG SEQADV 7Q33 ARG A 338 UNP Q14498 EXPRESSION TAG SEQRES 1 A 93 MET ALA GLY PRO MET ARG LEU TYR VAL GLY SER LEU HIS SEQRES 2 A 93 PHE ASN ILE THR GLU ASP MET LEU ARG GLY ILE PHE GLU SEQRES 3 A 93 PRO PHE GLY ARG ILE GLU SER ILE GLN LEU MET MET ASP SEQRES 4 A 93 SER GLU THR GLY ARG SER LYS GLY TYR GLY PHE ILE THR SEQRES 5 A 93 PHE SER ASP SER GLU CYS ALA LYS LYS ALA LEU GLU GLN SEQRES 6 A 93 LEU ASN GLY PHE GLU LEU ALA GLY ARG PRO MET LYS VAL SEQRES 7 A 93 GLY HIS VAL THR GLU ARG THR ASP ALA LEU GLU LEU VAL SEQRES 8 A 93 PRO ARG SEQRES 1 B 7 A G C U U U G HELIX 1 AA1 THR A 262 GLU A 271 1 10 HELIX 2 AA2 PRO A 272 GLY A 274 5 3 HELIX 3 AA3 ASP A 300 ASN A 312 1 13 HELIX 4 AA4 ARG A 329 LEU A 333 5 5 SHEET 1 AA1 5 ILE A 276 MET A 283 0 SHEET 2 AA1 5 SER A 290 PHE A 298 -1 O THR A 297 N SER A 278 SHEET 3 AA1 5 MET A 250 GLY A 255 -1 N MET A 250 O PHE A 298 SHEET 4 AA1 5 ARG A 319 HIS A 325 -1 O GLY A 324 N TYR A 253 SHEET 5 AA1 5 PHE A 314 LEU A 316 -1 N PHE A 314 O MET A 321 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