HEADER RNA BINDING PROTEIN 04-OCT-22 8B8S TITLE SOLUTION STRUCTURE OF TANDEM RRM1 AND RRM2 DOMAINS OF YEAST NPL3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE/ARGININE (SR)-TYPE SHUTTLING MRNA BINDING PROTEIN COMPND 3 NPL3; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: MITOCHONDRIAL TARGETING SUPPRESSOR 1 PROTEIN,NUCLEAR COMPND 6 POLYADENYLATED RNA-BINDING PROTEIN 1,NUCLEAR PROTEIN LOCALIZATION COMPND 7 PROTEIN 3,POLYADENYLATE-BINDING PROTEIN NPL3; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 STRAIN: ATCC 204508 / S288C; SOURCE 6 ATCC: 204508 / S288C; SOURCE 7 GENE: NPL3, MTR13, MTS1, NAB1, NOP3, YDR432W, D9461.19; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: EXPRESSION VECTOR; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PET FAMILY VECTOR KEYWDS SERINE/ARGININE (SR)-TYPE MRNA BINDING PROTEIN, PARAMAGNETIC KEYWDS 2 RELAXATION ENHANCEMENT (PRE) BASED SOLUTION NMR STRUCTURE, RNA KEYWDS 3 BINDING PROTEIN EXPDTA SOLUTION NMR; SOLUTION SCATTERING NUMMDL 10 AUTHOR N.KACHARIYA,M.SATTLER,P.KEIL,K.STRASSER REVDAT 4 19-JUN-24 8B8S 1 REMARK REVDAT 3 08-FEB-23 8B8S 1 JRNL REVDAT 2 11-JAN-23 8B8S 1 JRNL REVDAT 1 09-NOV-22 8B8S 0 JRNL AUTH P.KEIL,A.WULF,N.KACHARIYA,S.REUSCHER,K.HUHN,I.SILBERN, JRNL AUTH 2 J.ALTMULLER,M.KELLER,R.STEHLE,K.ZARNACK,M.SATTLER,H.URLAUB, JRNL AUTH 3 K.STRASSER JRNL TITL NPL3 FUNCTIONS IN MRNP ASSEMBLY BY RECRUITMENT OF MRNP JRNL TITL 2 COMPONENTS TO THE TRANSCRIPTION SITE AND THEIR TRANSFER ONTO JRNL TITL 3 THE MRNA. JRNL REF NUCLEIC ACIDS RES. V. 51 831 2023 JRNL REFN ESSN 1362-4962 JRNL PMID 36583366 JRNL DOI 10.1093/NAR/GKAC1206 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.KEIL,A.WULF,N.KACHARIYA,S.REUSCHER,K.HUHN,I.SILBERN, REMARK 1 AUTH 2 J.ALTMULLER,R.STEHLE,K.ZARNACK,M.SATTLER,H.URLAUB,K.STRASSER REMARK 1 TITL NPL3 FUNCTIONS IN MRNP ASSEMBLY BY RECRUITMENT OF MRNP REMARK 1 TITL 2 COMPONENTS TO THE TRANSCRIPTION SITE AND THEIR TRANSFER ONTO REMARK 1 TITL 3 THE MRNA REMARK 1 REF BIORXIV 2022 REMARK 1 REFN ISSN 2692-8205 REMARK 1 DOI 10.1101/2022.07.22.501171 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.21 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE ENSEMBLE STRUCTURES ARE BASED ON REMARK 3 TOTAL OF 100 DISTANCE RESTRAINS DERIVED FROM PRE EXPERIMENTS, REMARK 3 WHERE 69 AND 31 ARE INTRA- AND INTER-DOMAIN RESTRAINS. REMARK 4 REMARK 4 8B8S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-OCT-22. REMARK 100 THE DEPOSITION ID IS D_1292125681. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 70 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 150 UM [U-100% 15N] RRM1,2 OF REMARK 210 NPL3, 90% H2O/10% D2O; 1000 UM REMARK 210 [U-100% 13C; U-100% 15N] RRM1,2 REMARK 210 OF NPL3, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 3D HNCO; 3D HCACO; REMARK 210 3D H(CCO)NH; 3D C(CO)NH REMARK 210 SPECTROMETER FIELD STRENGTH : 950 MHZ; 900 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 3.5PL6, NMRPIPE, CCPNMR REMARK 210 ANALYSIS 2.5.0 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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 265 REMARK 265 EXPERIMENTAL DETAILS 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 O CYS A 211 OD2 ASP A 215 2.04 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 SER A 212 C - N - CA ANGL. DEV. = 18.3 DEGREES REMARK 500 2 SER A 212 C - N - CA ANGL. DEV. = 18.4 DEGREES REMARK 500 3 SER A 212 C - N - CA ANGL. DEV. = 18.3 DEGREES REMARK 500 4 SER A 212 C - N - CA ANGL. DEV. = 18.3 DEGREES REMARK 500 5 SER A 212 C - N - CA ANGL. DEV. = 18.2 DEGREES REMARK 500 6 SER A 212 C - N - CA ANGL. DEV. = 18.3 DEGREES REMARK 500 7 SER A 212 C - N - CA ANGL. DEV. = 18.3 DEGREES REMARK 500 8 SER A 212 C - N - CA ANGL. DEV. = 18.3 DEGREES REMARK 500 9 SER A 212 C - N - CA ANGL. DEV. = 18.2 DEGREES REMARK 500 10 SER A 212 C - N - CA ANGL. DEV. = 18.2 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 A 121 23.70 -142.36 REMARK 500 1 LEU A 122 -100.21 -73.99 REMARK 500 1 ASN A 124 -36.57 -179.85 REMARK 500 1 ARG A 126 118.55 178.97 REMARK 500 1 PRO A 133 -161.35 -69.72 REMARK 500 1 PRO A 147 60.42 -69.80 REMARK 500 1 PHE A 148 -41.56 -149.01 REMARK 500 1 PRO A 150 90.83 -69.74 REMARK 500 1 MET A 151 109.32 -59.20 REMARK 500 1 ASN A 158 93.83 -61.45 REMARK 500 1 GLU A 177 -61.88 -95.22 REMARK 500 1 PHE A 183 132.43 -171.85 REMARK 500 1 SER A 193 87.84 -40.09 REMARK 500 1 PRO A 196 -151.28 -100.23 REMARK 500 1 LYS A 198 153.25 59.82 REMARK 500 1 PRO A 208 66.36 -69.80 REMARK 500 1 CYS A 211 -108.14 5.05 REMARK 500 1 SER A 212 174.74 123.97 REMARK 500 1 ASN A 260 86.00 60.30 REMARK 500 1 PRO A 277 142.75 -33.25 REMARK 500 2 GLU A 121 -36.92 -139.22 REMARK 500 2 LEU A 122 -78.62 -120.85 REMARK 500 2 ASN A 124 -36.55 -164.20 REMARK 500 2 ARG A 126 118.67 179.05 REMARK 500 2 PRO A 133 -161.54 -69.65 REMARK 500 2 PRO A 147 60.34 -69.84 REMARK 500 2 PHE A 148 -41.48 -148.94 REMARK 500 2 PRO A 150 90.97 -69.80 REMARK 500 2 MET A 151 109.42 -59.40 REMARK 500 2 ASN A 158 93.89 -61.51 REMARK 500 2 GLU A 177 -61.81 -95.10 REMARK 500 2 PHE A 183 132.50 -171.92 REMARK 500 2 SER A 193 -32.89 -26.13 REMARK 500 2 LYS A 194 -168.76 -67.48 REMARK 500 2 PRO A 196 -139.15 -99.05 REMARK 500 2 ALA A 197 -157.92 -154.94 REMARK 500 2 LYS A 198 162.55 -46.97 REMARK 500 2 PRO A 208 66.29 -69.71 REMARK 500 2 CYS A 211 -107.92 5.04 REMARK 500 2 SER A 212 174.63 123.52 REMARK 500 2 ASN A 260 86.12 60.27 REMARK 500 2 PRO A 276 153.80 -49.39 REMARK 500 2 PRO A 278 -95.90 -101.17 REMARK 500 2 ILE A 279 -139.69 -125.74 REMARK 500 3 SER A 123 12.67 55.33 REMARK 500 3 ASN A 124 -36.61 -33.69 REMARK 500 3 ARG A 126 118.68 179.01 REMARK 500 3 PRO A 133 -161.53 -69.68 REMARK 500 3 PRO A 147 60.44 -69.88 REMARK 500 3 PHE A 148 -41.58 -149.01 REMARK 500 REMARK 500 THIS ENTRY HAS 213 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 1 GLY A 210 12.42 REMARK 500 2 GLY A 210 12.42 REMARK 500 3 GLY A 210 12.42 REMARK 500 4 GLY A 210 12.42 REMARK 500 5 GLY A 210 12.41 REMARK 500 6 GLY A 210 12.38 REMARK 500 7 GLY A 210 12.41 REMARK 500 8 GLY A 210 12.38 REMARK 500 9 GLY A 210 12.38 REMARK 500 10 GLY A 210 12.44 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: SASDQT5 RELATED DB: SASBDB REMARK 900 SASDQT5 ENTRY CONSTAIN SAME PROTEIN MOLECULAR SYSTEM (RRM1,2 OF REMARK 900 NPL3) REMARK 900 RELATED ID: 34761 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF TANDEM RRM1 AND RRM2 DOMAINS OF YEAST NPL3 DBREF 8B8S A 120 280 UNP Q01560 NOP3_YEAST 120 280 SEQRES 1 A 161 GLY GLU LEU SER ASN THR ARG LEU PHE VAL ARG PRO PHE SEQRES 2 A 161 PRO LEU ASP VAL GLN GLU SER GLU LEU ASN GLU ILE PHE SEQRES 3 A 161 GLY PRO PHE GLY PRO MET LYS GLU VAL LYS ILE LEU ASN SEQRES 4 A 161 GLY PHE ALA PHE VAL GLU PHE GLU GLU ALA GLU SER ALA SEQRES 5 A 161 ALA LYS ALA ILE GLU GLU VAL HIS GLY LYS SER PHE ALA SEQRES 6 A 161 ASN GLN PRO LEU GLU VAL VAL TYR SER LYS LEU PRO ALA SEQRES 7 A 161 LYS ARG TYR ARG ILE THR MET LYS ASN LEU PRO GLU GLY SEQRES 8 A 161 CYS SER TRP GLN ASP LEU LYS ASP LEU ALA ARG GLU ASN SEQRES 9 A 161 SER LEU GLU THR THR PHE SER SER VAL ASN THR ARG ASP SEQRES 10 A 161 PHE ASP GLY THR GLY ALA LEU GLU PHE PRO SER GLU GLU SEQRES 11 A 161 ILE LEU VAL GLU ALA LEU GLU ARG LEU ASN ASN ILE GLU SEQRES 12 A 161 PHE ARG GLY SER VAL ILE THR VAL GLU ARG ASP ASP ASN SEQRES 13 A 161 PRO PRO PRO ILE ARG HELIX 1 AA1 GLN A 137 GLY A 146 1 10 HELIX 2 AA2 GLU A 167 VAL A 178 1 12 HELIX 3 AA3 SER A 212 ASN A 223 1 12 HELIX 4 AA4 SER A 247 ASN A 259 1 13 SHEET 1 AA1 4 MET A 151 LEU A 157 0 SHEET 2 AA1 4 PHE A 160 PHE A 165 -1 O PHE A 162 N LYS A 155 SHEET 3 AA1 4 LEU A 127 VAL A 129 -1 N LEU A 127 O VAL A 163 SHEET 4 AA1 4 VAL A 190 TYR A 192 -1 O VAL A 191 N PHE A 128 SHEET 1 AA2 2 SER A 182 PHE A 183 0 SHEET 2 AA2 2 GLN A 186 PRO A 187 -1 O GLN A 186 N PHE A 183 SHEET 1 AA3 5 PHE A 229 VAL A 232 0 SHEET 2 AA3 5 GLY A 241 GLU A 244 -1 O ALA A 242 N SER A 231 SHEET 3 AA3 5 ARG A 201 LYS A 205 -1 N ILE A 202 O LEU A 243 SHEET 4 AA3 5 SER A 266 GLU A 271 -1 O GLU A 271 N THR A 203 SHEET 5 AA3 5 ILE A 261 PHE A 263 -1 N PHE A 263 O SER A 266 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 ENDMDL MODEL 2 ENDMDL MODEL 3 ENDMDL MODEL 4 ENDMDL MODEL 5 ENDMDL MODEL 6 ENDMDL MODEL 7 ENDMDL MODEL 8 ENDMDL MODEL 9 ENDMDL MODEL 10 ENDMDL MASTER 221 0 0 4 11 0 0 6 1285 1 0 13 END