HEADER RNA BINDING PROTEIN 26-NOV-21 7QDD TITLE NMR STRUCTURE OF NPL3 RRM1 BOUND TO THE AUCCAA RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*AP*UP*CP*CP*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; COMPND 12 OTHER_DETAILS: RECOMBINANT PROTEIN 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, U2 SNRNA, RRM, SPLIT-ICRAC, YEAST, PROTEIN-RNA COMPLEX, RNA KEYWDS 2 BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR A.CLERY,F.H.-T.ALLAIN,A.MOURSY REVDAT 2 10-JAN-24 7QDD 1 JRNL REVDAT 1 26-OCT-22 7QDD 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 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.MOURSY,A.CLERY,S.GERHARDY,K.M.BETZ,S.RAO,S.CAMPAGNE, REMARK 1 AUTH 2 I.BEUSCH,M.M.DUSZCZYK,M.D.ROBINSON,V.G.PANSE,F.H.T.ALLAIN REMARK 1 TITL THE STRUCTURE OF YEAST NPL3 BOUND TO RNA REVEALS A REMARK 1 TITL 2 COOPERATIVE SEQUENCE-SPECIFIC RECOGNITION AND AN RNA REMARK 1 TITL 3 CHAPERONE ROLE IN SPLICING REMARK 1 REF BIORXIV 2022 REMARK 1 REFN ISSN 2692-8205 REMARK 1 DOI 10.1101/2022.05.24.493251 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 7QDD 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_1292119248. 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 RRM1, 90% REMARK 210 H2O/10% D2O; 0.9 MM [U-100% 13C; REMARK 210 U-100% 15N] NPL3 RRM1, 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 F1FF2F; 2D NOESY F2F; 3D HNCACB REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 700 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; AVANCE III HD 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: 1500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 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: 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 B 135 12.38 -146.62 REMARK 500 1 PRO B 147 7.97 -61.62 REMARK 500 2 ASP B 135 10.07 -140.78 REMARK 500 2 PRO B 147 11.71 -62.02 REMARK 500 2 ALA B 197 -25.85 -168.66 REMARK 500 3 ASP B 135 14.19 -148.77 REMARK 500 3 PRO B 147 7.81 -61.73 REMARK 500 4 GLN B 118 -11.38 -145.88 REMARK 500 4 ASP B 135 14.50 -144.31 REMARK 500 4 PRO B 147 10.83 -61.67 REMARK 500 4 PHE B 183 -29.86 -146.55 REMARK 500 4 ALA B 184 54.88 -143.63 REMARK 500 4 TYR B 200 -19.21 -143.46 REMARK 500 5 ASP B 135 17.04 -144.75 REMARK 500 5 PRO B 147 10.56 -61.76 REMARK 500 6 ASP B 135 13.32 -140.17 REMARK 500 6 PRO B 147 11.30 -61.61 REMARK 500 6 PHE B 183 -34.55 -147.98 REMARK 500 7 GLN B 118 -22.09 -158.93 REMARK 500 7 PRO B 147 9.93 -61.17 REMARK 500 7 TYR B 200 0.04 -69.66 REMARK 500 8 GLU B 121 27.11 -76.05 REMARK 500 8 ASP B 135 16.59 -148.11 REMARK 500 8 PRO B 147 20.12 -72.15 REMARK 500 8 PHE B 183 -32.25 -153.68 REMARK 500 9 HIS B 116 3.15 -152.76 REMARK 500 9 GLU B 121 27.80 -73.24 REMARK 500 9 ASP B 135 15.28 -148.77 REMARK 500 9 PRO B 147 8.53 -61.33 REMARK 500 9 PHE B 183 -30.76 -153.16 REMARK 500 9 ALA B 184 56.06 -141.48 REMARK 500 9 ALA B 197 13.49 57.50 REMARK 500 10 HIS B 115 28.66 -78.62 REMARK 500 10 ASP B 135 15.34 -147.31 REMARK 500 10 PRO B 147 7.44 -60.85 REMARK 500 10 PRO B 196 -168.81 -67.98 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 111 0.07 SIDE CHAIN REMARK 500 8 C A 111 0.06 SIDE CHAIN REMARK 500 8 A A 112 0.06 SIDE CHAIN REMARK 500 10 C A 111 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34691 RELATED DB: BMRB REMARK 900 NMR STRUCTURE OF NPL3 RRM1 BOUND TO THE AUCCAA RNA DBREF 7QDD A 108 113 PDB 7QDD 7QDD 108 113 DBREF 7QDD B 114 201 UNP Q01560 NOP3_YEAST 114 201 SEQRES 1 A 6 A U C C A A SEQRES 1 B 88 MET HIS HIS ARG GLN GLU GLY GLU LEU SER ASN THR ARG SEQRES 2 B 88 LEU PHE VAL ARG PRO PHE PRO LEU ASP VAL GLN GLU SER SEQRES 3 B 88 GLU LEU ASN GLU ILE PHE GLY PRO PHE GLY PRO MET LYS SEQRES 4 B 88 GLU VAL LYS ILE LEU ASN GLY PHE ALA PHE VAL GLU PHE SEQRES 5 B 88 GLU GLU ALA GLU SER ALA ALA LYS ALA ILE GLU GLU VAL SEQRES 6 B 88 HIS GLY LYS SER PHE ALA ASN GLN PRO LEU GLU VAL VAL SEQRES 7 B 88 TYR SER LYS LEU PRO ALA LYS ARG TYR ARG HELIX 1 AA1 GLN B 137 GLY B 146 1 10 HELIX 2 AA2 PRO B 147 GLY B 149 5 3 HELIX 3 AA3 GLU B 167 HIS B 179 1 13 SHEET 1 AA1 4 MET B 151 LEU B 157 0 SHEET 2 AA1 4 PHE B 160 PHE B 165 -1 O GLU B 164 N GLU B 153 SHEET 3 AA1 4 LEU B 122 ARG B 130 -1 N LEU B 127 O VAL B 163 SHEET 4 AA1 4 GLU B 189 LYS B 194 -1 O VAL B 191 N PHE B 128 SHEET 1 AA2 2 SER B 182 PHE B 183 0 SHEET 2 AA2 2 GLN B 186 PRO B 187 -1 O GLN B 186 N PHE B 183 CISPEP 1 ARG B 130 PRO B 131 1 -5.66 CISPEP 2 ARG B 130 PRO B 131 2 -4.29 CISPEP 3 ARG B 130 PRO B 131 3 -5.14 CISPEP 4 ARG B 130 PRO B 131 4 -5.15 CISPEP 5 ARG B 130 PRO B 131 5 -5.28 CISPEP 6 ARG B 130 PRO B 131 6 -4.31 CISPEP 7 ARG B 130 PRO B 131 7 -5.40 CISPEP 8 ARG B 130 PRO B 131 8 -4.53 CISPEP 9 ARG B 130 PRO B 131 9 -4.04 CISPEP 10 ARG B 130 PRO B 131 10 -4.55 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