HEADER RNA BINDING PROTEIN 26-NOV-21 7QDE TITLE NMR STRUCTURE OF NPL3 RRM12 BOUND TO THE AUCCAGUGGAA RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*AP*UP*CP*CP*AP*GP*UP*GP*GP*AP*A)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: SYNTHETIC RNA FROM HORIZON; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: NUCLEOLAR PROTEIN 3; COMPND 8 CHAIN: B; COMPND 9 SYNONYM: MITOCHONDRIAL TARGETING SUPPRESSOR 1 PROTEIN,NUCLEAR COMPND 10 POLYADENYLATED RNA-BINDING PROTEIN 1; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / SOURCE 7 S288C); SOURCE 8 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 9 ORGANISM_TAXID: 559292; SOURCE 10 STRAIN: ATCC 204508 / S288C; SOURCE 11 GENE: NPL3, MTR13, MTS1, NAB1, NOP3, YDR432W, D9461.19; SOURCE 12 EXPRESSION_SYSTEM: UNIDENTIFIED PLASMID; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 45202 KEYWDS SPLICING, U2SNRNA, RRM, YEAST, PROTEIN-RNA COMPLEX, RNA BINDING KEYWDS 2 PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR F.H.-T.ALLAIN,A.CLERY,A.MOURSY REVDAT 2 10-JAN-24 7QDE 1 JRNL REVDAT 1 21-DEC-22 7QDE 0 JRNL AUTH A.MOURSY,A.CLERY,S.GERHARDY,K.M.BETZ,S.RAO,J.MAZUR, JRNL AUTH 2 S.CAMPAGNE,I.BEUSCH,M.M.DUSZCZYK,M.D.ROBINSON,V.G.PANSE, JRNL AUTH 3 F.H.ALLAIN JRNL TITL RNA RECOGNITION BY NPL3P REVEALS U2 SNRNA-BINDING COMPATIBLE JRNL TITL 2 WITH A CHAPERONE ROLE DURING SPLICING. JRNL REF NAT COMMUN V. 14 7166 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 37935663 JRNL DOI 10.1038/S41467-023-42962-4 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: NULL REMARK 4 REMARK 4 7QDE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-NOV-21. REMARK 100 THE DEPOSITION ID IS D_1292119302. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 313 REMARK 210 PH : 6.9 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : 0 PA REMARK 210 SAMPLE CONTENTS : 0.9 MM [U-15N] NPL3 RRM12, 90% REMARK 210 H2O/10% D2O; 0.9 MM [U-100% 13C; REMARK 210 U-100% 15N] NPL3 RRM12, 90% H2O/ REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 2D NOESY; 2D NOESY REMARK 210 F1F2F; 2D NOESY F2F; 3D HNCACB REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 700 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA, SPARKY REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL 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 4 C A 106 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 6 C A 106 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 8 C A 106 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 9 U A 104 O4' - C1' - N1 ANGL. DEV. = 4.5 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 GLU B 119 -33.48 -139.90 REMARK 500 1 GLU B 121 53.40 -111.55 REMARK 500 1 ARG B 130 -51.55 -134.55 REMARK 500 1 PRO B 133 -88.01 -68.94 REMARK 500 1 LEU B 134 -36.12 -172.54 REMARK 500 1 GLN B 137 57.98 31.28 REMARK 500 1 MET B 151 98.54 34.72 REMARK 500 1 ASN B 158 106.18 -55.52 REMARK 500 1 HIS B 179 29.70 -76.11 REMARK 500 1 LYS B 181 -156.69 -142.47 REMARK 500 1 ALA B 184 34.18 -156.84 REMARK 500 1 GLU B 189 41.87 -147.30 REMARK 500 1 ASN B 206 -156.61 -159.82 REMARK 500 1 ASN B 223 -63.04 -108.86 REMARK 500 1 SER B 224 -39.50 -171.59 REMARK 500 1 VAL B 232 52.57 -141.66 REMARK 500 1 PHE B 237 86.83 54.44 REMARK 500 1 GLU B 262 91.89 63.89 REMARK 500 1 THR B 269 47.91 -97.34 REMARK 500 1 ASP B 274 70.90 52.90 REMARK 500 1 ARG B 281 171.05 59.54 REMARK 500 2 SER B 123 21.44 -69.79 REMARK 500 2 ARG B 130 -51.90 -139.09 REMARK 500 2 PRO B 133 -88.61 -72.76 REMARK 500 2 LEU B 134 -38.44 -172.85 REMARK 500 2 VAL B 136 28.56 -74.03 REMARK 500 2 GLU B 140 -16.52 -141.65 REMARK 500 2 MET B 151 97.60 34.27 REMARK 500 2 ASN B 158 106.76 -51.42 REMARK 500 2 HIS B 179 25.77 -77.83 REMARK 500 2 LYS B 181 -157.75 -142.22 REMARK 500 2 ALA B 184 37.21 -158.74 REMARK 500 2 GLU B 189 36.18 -150.89 REMARK 500 2 SER B 193 -167.53 -79.68 REMARK 500 2 ASN B 206 -143.28 -155.90 REMARK 500 2 ASN B 223 -67.76 -129.70 REMARK 500 2 SER B 224 -37.43 -170.12 REMARK 500 2 PHE B 237 94.49 56.70 REMARK 500 2 GLU B 262 88.75 66.33 REMARK 500 2 THR B 269 42.54 -99.57 REMARK 500 2 ARG B 280 -25.06 -158.06 REMARK 500 3 ARG B 117 20.50 -72.39 REMARK 500 3 THR B 125 -43.26 -130.48 REMARK 500 3 ARG B 130 -52.11 -138.25 REMARK 500 3 PRO B 131 43.36 -71.19 REMARK 500 3 PRO B 133 -88.61 -71.05 REMARK 500 3 LEU B 134 -36.52 -171.94 REMARK 500 3 GLN B 137 57.53 32.67 REMARK 500 3 MET B 151 96.57 33.20 REMARK 500 3 ASN B 158 106.16 -58.83 REMARK 500 REMARK 500 THIS ENTRY HAS 205 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 1 C A 106 0.14 SIDE CHAIN REMARK 500 2 C A 106 0.06 SIDE CHAIN REMARK 500 3 C A 106 0.08 SIDE CHAIN REMARK 500 4 C A 106 0.10 SIDE CHAIN REMARK 500 4 G A 111 0.06 SIDE CHAIN REMARK 500 5 C A 106 0.10 SIDE CHAIN REMARK 500 6 C A 106 0.10 SIDE CHAIN REMARK 500 7 C A 106 0.08 SIDE CHAIN REMARK 500 7 G A 111 0.06 SIDE CHAIN REMARK 500 8 C A 106 0.13 SIDE CHAIN REMARK 500 9 U A 104 0.06 SIDE CHAIN REMARK 500 9 C A 106 0.13 SIDE CHAIN REMARK 500 9 G A 111 0.09 SIDE CHAIN REMARK 500 10 C A 106 0.11 SIDE CHAIN REMARK 500 10 G A 111 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34692 RELATED DB: BMRB REMARK 900 NMR STRUCTURE OF NPL3 RRM12 BOUND TO THE AUCCAGUGGAA RNA DBREF 7QDE A 103 113 PDB 7QDE 7QDE 103 113 DBREF 7QDE B 114 282 UNP Q01560 NOP3_YEAST 114 282 SEQRES 1 A 11 A U C C A G U G G A A SEQRES 1 B 169 MET HIS HIS ARG GLN GLU GLY GLU LEU SER ASN THR ARG SEQRES 2 B 169 LEU PHE VAL ARG PRO PHE PRO LEU ASP VAL GLN GLU SER SEQRES 3 B 169 GLU LEU ASN GLU ILE PHE GLY PRO PHE GLY PRO MET LYS SEQRES 4 B 169 GLU VAL LYS ILE LEU ASN GLY PHE ALA PHE VAL GLU PHE SEQRES 5 B 169 GLU GLU ALA GLU SER ALA ALA LYS ALA ILE GLU GLU VAL SEQRES 6 B 169 HIS GLY LYS SER PHE ALA ASN GLN PRO LEU GLU VAL VAL SEQRES 7 B 169 TYR SER LYS LEU PRO ALA LYS ARG TYR ARG ILE THR MET SEQRES 8 B 169 LYS ASN LEU PRO GLU GLY CYS SER TRP GLN ASP LEU LYS SEQRES 9 B 169 ASP LEU ALA ARG GLU ASN SER LEU GLU THR THR PHE SER SEQRES 10 B 169 SER VAL ASN THR ARG ASP PHE ASP GLY THR GLY ALA LEU SEQRES 11 B 169 GLU PHE PRO SER GLU GLU ILE LEU VAL GLU ALA LEU GLU SEQRES 12 B 169 ARG LEU ASN ASN ILE GLU PHE ARG GLY SER VAL ILE THR SEQRES 13 B 169 VAL GLU ARG ASP ASP ASN PRO PRO PRO ILE ARG ARG SER HELIX 1 AA1 GLU B 140 PHE B 145 1 6 HELIX 2 AA2 GLU B 167 HIS B 179 1 13 HELIX 3 AA3 SER B 212 GLU B 222 1 11 HELIX 4 AA4 SER B 247 LEU B 258 1 12 SHEET 1 AA1 4 GLU B 153 LEU B 157 0 SHEET 2 AA1 4 PHE B 160 GLU B 164 -1 O PHE B 160 N LEU B 157 SHEET 3 AA1 4 LEU B 127 VAL B 129 -1 N LEU B 127 O VAL B 163 SHEET 4 AA1 4 VAL B 191 TYR B 192 -1 O VAL B 191 N PHE B 128 SHEET 1 AA2 3 TYR B 200 MET B 204 0 SHEET 2 AA2 3 GLY B 241 PHE B 245 -1 O PHE B 245 N TYR B 200 SHEET 3 AA2 3 PHE B 229 SER B 231 -1 N PHE B 229 O GLU B 244 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