HEADER RNA BINDING PROTEIN 08-MAY-13 2M88 TITLE NMR STRUCTURE OF A TWO-DOMAIN RNA-BINDING FRAGMENT OF NRD1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN NRD1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 307-491; COMPND 5 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 GENE: NRD1, YNL251C, N0868; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS NRD1 COMPLEX, RNA PROCESSING AND DEGRADATION, RRM STRUCTURE, RNA KEYWDS 2 BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR V.BACIKOVA,J.PASULKA,K.KUBICEK,R.STEFL REVDAT 5 14-JUN-23 2M88 1 REMARK SEQADV REVDAT 4 16-JUL-14 2M88 1 JRNL REVDAT 3 09-JUL-14 2M88 1 JRNL REVDAT 2 21-MAY-14 2M88 1 JRNL REVDAT 1 14-MAY-14 2M88 0 JRNL AUTH V.BACIKOVA,J.PASULKA,K.KUBICEK,R.STEFL JRNL TITL STRUCTURE AND SEMI-SEQUENCE-SPECIFIC RNA BINDING OF NRD1. JRNL REF NUCLEIC ACIDS RES. V. 42 8024 2014 JRNL REFN ISSN 0305-1048 JRNL PMID 24860164 JRNL DOI 10.1093/NAR/GKU446 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SPARKY, AMBER, CYANA REMARK 3 AUTHORS : GODDARD (SPARKY), CASE, DARDEN, CHEATHAM, III, REMARK 3 SIMMERLING, WANG, DUKE, LUO, ... AND KOLLMAN REMARK 3 (AMBER), GUNTERT, MUMENTHALER AND WUTHRICH (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2M88 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-MAY-13. REMARK 100 THE DEPOSITION ID IS D_1000103332. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293; 293; 293 REMARK 210 PH : 8; 8; 8 REMARK 210 IONIC STRENGTH : NULL; NULL; NULL REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 0.4 MM [U-13C; U-15N] NRD1, 50 REMARK 210 MM SODIUM PHOSPHATE, 300 MM REMARK 210 SODIUM CHLORIDE, 10 MM BETA- REMARK 210 MERCAPTOETHANOL, 90% H2O/10% D2O; REMARK 210 0.4 MM [U-100% 13C; U-100% 15N; REMARK 210 U-80% 2H] NRD1, 50 MM SODIUM REMARK 210 PHOSPHATE, 300 MM SODIUM REMARK 210 CHLORIDE, 10 MM BETA- REMARK 210 MERCAPTOETHANOL, 90% H2O/10% D2O; REMARK 210 0.4 MM [U-13C; U-15N; U-2H] REMARK 210 NRD1, 50 MM SODIUM PHOSPHATE, REMARK 210 300 MM SODIUM CHLORIDE, 10 MM REMARK 210 BETA-MERCAPTOETHANOL, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCA; 3D REMARK 210 HN(CO)CA; 3D HNCACB; 3D HN(COCA) REMARK 210 CB; 3D HNCO; 3D HCACO; 4D HCCH REMARK 210 METHYL NOESY; 3D HCCCONH; 3D CCH REMARK 210 TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ; 950 MHZ; 900 REMARK 210 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY, PROCHECK, WHAT IF, REMARK 210 CYANA, MOLMOL, TOPSPIN REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 SIMULATED ANNEALING, MOLECULAR REMARK 210 DYNAMICS, SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 80 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: 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 MET A 0 REMARK 465 LEU A 186 REMARK 465 GLU A 187 REMARK 465 HIS A 188 REMARK 465 HIS A 189 REMARK 465 HIS A 190 REMARK 465 HIS A 191 REMARK 465 HIS A 192 REMARK 465 HIS A 193 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 PRO A 1 CA - N - CD ANGL. DEV. = -9.7 DEGREES REMARK 500 2 PRO A 1 CA - N - CD ANGL. DEV. = -9.9 DEGREES REMARK 500 3 PRO A 1 CA - N - CD ANGL. DEV. = -9.7 DEGREES REMARK 500 4 PRO A 1 CA - N - CD ANGL. DEV. = -9.7 DEGREES REMARK 500 6 PRO A 1 CA - N - CD ANGL. DEV. = -9.9 DEGREES REMARK 500 7 PRO A 1 CA - N - CD ANGL. DEV. = -9.9 DEGREES REMARK 500 8 PRO A 1 CA - N - CD ANGL. DEV. = -9.7 DEGREES REMARK 500 9 PRO A 1 CA - N - CD ANGL. DEV. = -9.7 DEGREES REMARK 500 11 PRO A 1 CA - N - CD ANGL. DEV. = -9.9 DEGREES REMARK 500 12 PRO A 1 CA - N - CD ANGL. DEV. = -9.7 DEGREES REMARK 500 13 PRO A 1 CA - N - CD ANGL. DEV. = -9.8 DEGREES REMARK 500 14 PRO A 1 CA - N - CD ANGL. DEV. = -9.9 DEGREES REMARK 500 15 PRO A 1 CA - N - CD ANGL. DEV. = -9.7 DEGREES REMARK 500 16 PRO A 1 CA - N - CD ANGL. DEV. = -9.8 DEGREES REMARK 500 17 PRO A 1 CA - N - CD ANGL. DEV. = -9.7 DEGREES REMARK 500 18 PRO A 1 CA - N - CD ANGL. DEV. = -9.6 DEGREES REMARK 500 19 PRO A 1 CA - N - CD ANGL. DEV. = -9.7 DEGREES REMARK 500 20 PRO A 1 CA - N - CD ANGL. DEV. = -9.7 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 3 55.07 -93.42 REMARK 500 1 SER A 18 24.94 -164.06 REMARK 500 1 ASP A 20 33.29 -72.67 REMARK 500 1 LYS A 29 26.81 -142.92 REMARK 500 1 THR A 34 -174.50 53.42 REMARK 500 1 ASN A 66 149.93 65.58 REMARK 500 1 LYS A 90 14.99 -143.63 REMARK 500 1 CYS A 109 39.67 -79.18 REMARK 500 1 MET A 121 21.02 -79.82 REMARK 500 1 SER A 134 55.62 -147.52 REMARK 500 1 ALA A 135 -42.15 -132.29 REMARK 500 1 THR A 140 116.69 66.46 REMARK 500 1 PRO A 144 0.64 -61.94 REMARK 500 1 VAL A 150 20.77 43.83 REMARK 500 2 SER A 7 51.63 -92.72 REMARK 500 2 VAL A 17 98.90 -61.74 REMARK 500 2 SER A 21 34.44 -78.31 REMARK 500 2 ASN A 66 153.72 64.66 REMARK 500 2 SER A 67 32.66 -78.82 REMARK 500 2 ASP A 108 33.37 -81.88 REMARK 500 2 CYS A 109 40.73 -86.50 REMARK 500 2 ILE A 119 129.67 63.34 REMARK 500 2 MET A 121 21.79 -75.12 REMARK 500 2 SER A 141 24.12 -156.53 REMARK 500 2 VAL A 150 33.99 35.86 REMARK 500 2 ILE A 167 38.59 -82.51 REMARK 500 2 ARG A 177 29.77 49.27 REMARK 500 3 TYR A 19 122.91 -38.23 REMARK 500 3 ASP A 20 104.71 -47.88 REMARK 500 3 SER A 21 -2.49 -142.43 REMARK 500 3 THR A 22 24.05 -148.10 REMARK 500 3 LYS A 29 35.59 -82.44 REMARK 500 3 TYR A 31 55.89 -144.77 REMARK 500 3 ASN A 43 38.59 -79.11 REMARK 500 3 ASN A 66 43.46 -78.39 REMARK 500 3 ALA A 93 81.18 54.73 REMARK 500 3 PRO A 106 171.02 -57.75 REMARK 500 3 ILE A 119 140.96 62.57 REMARK 500 3 MET A 121 36.34 -80.08 REMARK 500 3 HIS A 122 -36.95 -135.65 REMARK 500 3 SER A 132 -20.45 -143.24 REMARK 500 3 VAL A 133 33.50 -140.16 REMARK 500 3 SER A 134 22.62 -72.81 REMARK 500 3 TRP A 137 44.64 -75.73 REMARK 500 3 THR A 140 22.34 -140.01 REMARK 500 3 PRO A 144 20.25 -62.77 REMARK 500 3 ILE A 149 42.84 -86.39 REMARK 500 3 VAL A 150 24.71 -141.14 REMARK 500 3 ILE A 157 29.58 -77.59 REMARK 500 4 PRO A 16 -174.40 -69.29 REMARK 500 REMARK 500 THIS ENTRY HAS 293 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19232 RELATED DB: BMRB DBREF 2M88 A 1 185 UNP P53617 NRD1_YEAST 307 491 SEQADV 2M88 MET A 0 UNP P53617 INITIATING METHIONINE SEQADV 2M88 LEU A 186 UNP P53617 EXPRESSION TAG SEQADV 2M88 GLU A 187 UNP P53617 EXPRESSION TAG SEQADV 2M88 HIS A 188 UNP P53617 EXPRESSION TAG SEQADV 2M88 HIS A 189 UNP P53617 EXPRESSION TAG SEQADV 2M88 HIS A 190 UNP P53617 EXPRESSION TAG SEQADV 2M88 HIS A 191 UNP P53617 EXPRESSION TAG SEQADV 2M88 HIS A 192 UNP P53617 EXPRESSION TAG SEQADV 2M88 HIS A 193 UNP P53617 EXPRESSION TAG SEQRES 1 A 194 MET PRO ASP GLU LEU ASN VAL SER ASN ASN PRO HIS TYR SEQRES 2 A 194 ARG PRO LYS PRO VAL SER TYR ASP SER THR LEU PRO PRO SEQRES 3 A 194 ASP HIS ILE LYS VAL TYR SER ARG THR LEU PHE ILE GLY SEQRES 4 A 194 GLY VAL PRO LEU ASN MET LYS GLU TRP ASP LEU ALA ASN SEQRES 5 A 194 VAL LEU LYS PRO PHE ALA GLU VAL GLN SER VAL ILE LEU SEQRES 6 A 194 ASN ASN SER ARG LYS HIS ALA PHE VAL LYS VAL TYR SER SEQRES 7 A 194 ARG HIS GLU ALA GLU ASN VAL LEU GLN ASN PHE ASN LYS SEQRES 8 A 194 ASP GLY ALA LEU PRO LEU ARG THR ARG TRP GLY VAL GLY SEQRES 9 A 194 PHE GLY PRO ARG ASP CYS CYS ASP TYR GLN HIS GLY TYR SEQRES 10 A 194 SER ILE ILE PRO MET HIS ARG LEU THR ASP ALA ASP LYS SEQRES 11 A 194 LYS TRP SER VAL SER ALA GLN TRP GLY GLY THR SER GLY SEQRES 12 A 194 GLN PRO LEU VAL THR GLY ILE VAL PHE GLU GLU PRO ASP SEQRES 13 A 194 ILE ILE VAL GLY GLU GLY VAL SER SER LYS ALA ILE SER SEQRES 14 A 194 GLN LYS MET PRO THR ASP SER GLY ARG ASN GLY PRO ARG SEQRES 15 A 194 SER GLY LYS PRO LEU GLU HIS HIS HIS HIS HIS HIS HELIX 1 1 LYS A 45 ALA A 50 1 6 HELIX 2 2 SER A 77 ASP A 91 1 15 HELIX 3 3 ASP A 111 GLY A 115 5 5 HELIX 4 4 ILE A 119 MET A 121 5 3 HELIX 5 5 HIS A 122 SER A 132 1 11 HELIX 6 6 GLN A 143 GLY A 148 5 6 SHEET 1 A 4 VAL A 59 ASN A 65 0 SHEET 2 A 4 HIS A 70 VAL A 75 -1 O LYS A 74 N GLN A 60 SHEET 3 A 4 THR A 34 GLY A 38 -1 N ILE A 37 O ALA A 71 SHEET 4 A 4 ARG A 97 GLY A 101 -1 O ARG A 99 N PHE A 36 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