HEADER TRANSCRIPTION 17-APR-18 6GC3 TITLE STRUCTURE OF NRD1 CID - SEN1 NIM COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN NRD1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HELICASE SEN1; COMPND 7 CHAIN: B; COMPND 8 SYNONYM: TRNA-SPLICING ENDONUCLEASE POSITIVE EFFECTOR; COMPND 9 EC: 3.6.4.-; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE S288C; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 559292; SOURCE 5 GENE: NRD1, YNL251C, N0868; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE S288C; SOURCE 11 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 12 ORGANISM_TAXID: 559292 KEYWDS CTD-INTERACTING DOMAIN, TRANSCRIPTION TERMINATION, HELICASE, KEYWDS 2 TRANSCRIPTION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR O.JASNOVIDOVA,K.KUBICEK,R.STEFL REVDAT 2 14-JUN-23 6GC3 1 REMARK REVDAT 1 05-FEB-20 6GC3 0 JRNL AUTH O.JASNOVIDOVA,K.KUBICEK,R.STEFL JRNL TITL STRUCTURE OF NRD1 CID - SEN1 NIM COMPLEX JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 16 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 6GC3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-APR-18. REMARK 100 THE DEPOSITION ID IS D_1200005898. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 8.0 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1.0 MM [U-99% 13C; U-99% 15N] REMARK 210 CTD-INTERACTING DOMAIN OF NRD1, 1.5 MM ASP-ASP-ASP-GLU-ASP-ASP- REMARK 210 TYR-THR-PRO-SER-ILE-SER, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCACB; HCCCONH; 3D 1H-15N REMARK 210 NOESY; 3D 1H-13C NOESY ALIPHATIC; REMARK 210 3D 1H-13C NOESY AROMATIC; 3D REMARK 210 HBHA(CO)NH; 4D HCCH TOCSY; F1- REMARK 210 13C/15N-FILTERED NOESY-[13C,1H]- REMARK 210 HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 950 MHZ; 850 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 3.97, SPARKY, TOPSPIN REMARK 210 METHOD USED : MOLECULAR DYNAMICS 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8710 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 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 HIS A 160 REMARK 465 HIS A 161 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 HG SER A 22 OD1 ASP B 2056 1.52 REMARK 500 OD2 ASP A 6 HH TYR A 35 1.52 REMARK 500 OD2 ASP A 132 HH TYR A 141 1.52 REMARK 500 HG SER A 25 OD2 ASP B 2054 1.54 REMARK 500 O ILE A 29 HG1 THR A 33 1.56 REMARK 500 O ALA A 12 HG SER A 16 1.57 REMARK 500 O LYS A 21 HG SER A 60 1.57 REMARK 500 O LYS A 62 HG SER A 65 1.59 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 3 TYR A 67 CB - CG - CD1 ANGL. DEV. = -3.6 DEGREES REMARK 500 9 TYR A 67 CB - CG - CD1 ANGL. DEV. = -3.8 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 GLN A 2 -136.42 -136.17 REMARK 500 1 GLN A 3 45.25 -75.96 REMARK 500 1 SER A 25 83.03 -162.22 REMARK 500 1 PRO A 58 172.77 -59.70 REMARK 500 1 GLN A 138 32.67 -73.39 REMARK 500 1 LYS A 139 46.80 -78.35 REMARK 500 1 TYR A 141 45.21 -72.47 REMARK 500 1 HIS A 158 28.64 -159.17 REMARK 500 1 ASP B2054 -173.30 61.80 REMARK 500 1 GLU B2055 68.10 -66.14 REMARK 500 2 SER A 22 -26.05 -141.73 REMARK 500 2 SER A 25 99.10 -166.03 REMARK 500 2 SER A 88 -2.72 -148.52 REMARK 500 2 ASN A 89 32.02 -147.96 REMARK 500 2 VAL A 104 -7.60 -143.58 REMARK 500 2 GLN A 138 31.88 -73.07 REMARK 500 2 TYR A 141 27.52 -67.23 REMARK 500 2 SER A 147 72.12 61.87 REMARK 500 2 HIS A 158 40.43 -79.59 REMARK 500 2 ASP B2054 89.31 -166.47 REMARK 500 2 ASP B2056 16.15 -66.10 REMARK 500 2 ASP B2057 65.71 -153.04 REMARK 500 3 GLN A 2 -28.04 -152.16 REMARK 500 3 GLN A 3 24.41 -157.01 REMARK 500 3 ASP A 4 29.58 -75.31 REMARK 500 3 ASP A 5 18.55 57.85 REMARK 500 3 SER A 25 79.84 -159.09 REMARK 500 3 ASN A 85 26.58 -156.55 REMARK 500 3 GLN A 138 17.13 -66.50 REMARK 500 3 ASP B2053 31.51 -80.62 REMARK 500 3 ASP B2056 16.67 48.12 REMARK 500 4 GLN A 3 28.20 -143.87 REMARK 500 4 ASP A 4 16.37 58.38 REMARK 500 4 SER A 25 97.40 -165.67 REMARK 500 4 SER A 86 -9.58 62.26 REMARK 500 4 SER A 87 175.69 58.69 REMARK 500 4 LYS A 90 134.59 67.72 REMARK 500 4 TYR A 141 35.72 -73.24 REMARK 500 4 GLU A 155 8.99 51.53 REMARK 500 4 HIS A 158 40.92 -91.37 REMARK 500 4 ASP B2056 -6.66 -57.96 REMARK 500 4 THR B2059 55.38 34.33 REMARK 500 5 SER A 25 81.46 -158.29 REMARK 500 5 HIS A 39 88.99 -151.52 REMARK 500 5 PRO A 58 -179.51 -58.79 REMARK 500 5 ASN A 83 16.61 -151.94 REMARK 500 5 SER A 88 -157.62 -81.84 REMARK 500 5 TYR A 141 -72.94 -66.36 REMARK 500 5 HIS A 157 19.78 -161.83 REMARK 500 5 ASP B2054 -158.50 -140.10 REMARK 500 REMARK 500 THIS ENTRY HAS 184 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34260 RELATED DB: BMRB REMARK 900 STRUCTURE OF NRD1 CID - SEN1 NIM COMPLEX DBREF 6GC3 A 1 153 UNP P53617 NRD1_YEAST 1 153 DBREF 6GC3 B 2052 2063 UNP Q00416 SEN1_YEAST 2052 2063 SEQADV 6GC3 LEU A 154 UNP P53617 EXPRESSION TAG SEQADV 6GC3 GLU A 155 UNP P53617 EXPRESSION TAG SEQADV 6GC3 HIS A 156 UNP P53617 EXPRESSION TAG SEQADV 6GC3 HIS A 157 UNP P53617 EXPRESSION TAG SEQADV 6GC3 HIS A 158 UNP P53617 EXPRESSION TAG SEQADV 6GC3 HIS A 159 UNP P53617 EXPRESSION TAG SEQADV 6GC3 HIS A 160 UNP P53617 EXPRESSION TAG SEQADV 6GC3 HIS A 161 UNP P53617 EXPRESSION TAG SEQRES 1 A 161 MET GLN GLN ASP ASP ASP PHE GLN ASN PHE VAL ALA THR SEQRES 2 A 161 LEU GLU SER PHE LYS ASP LEU LYS SER GLY ILE SER GLY SEQRES 3 A 161 SER ARG ILE LYS LYS LEU THR THR TYR ALA LEU ASP HIS SEQRES 4 A 161 ILE ASP ILE GLU SER LYS ILE ILE SER LEU ILE ILE ASP SEQRES 5 A 161 TYR SER ARG LEU CYS PRO ASP SER HIS LYS LEU GLY SER SEQRES 6 A 161 LEU TYR ILE ILE ASP SER ILE GLY ARG ALA TYR LEU ASP SEQRES 7 A 161 GLU THR ARG SER ASN SER ASN SER SER SER ASN LYS PRO SEQRES 8 A 161 GLY THR CYS ALA HIS ALA ILE ASN THR LEU GLY GLU VAL SEQRES 9 A 161 ILE GLN GLU LEU LEU SER ASP ALA ILE ALA LYS SER ASN SEQRES 10 A 161 GLN ASP HIS LYS GLU LYS ILE ARG MET LEU LEU ASP ILE SEQRES 11 A 161 TRP ASP ARG SER GLY LEU PHE GLN LYS SER TYR LEU ASN SEQRES 12 A 161 ALA ILE ARG SER LYS CYS PHE ALA MET ASP LEU GLU HIS SEQRES 13 A 161 HIS HIS HIS HIS HIS SEQRES 1 B 12 ASP ASP ASP GLU ASP ASP TYR THR PRO SER ILE SER HELIX 1 AA1 ASP A 6 LEU A 20 1 15 HELIX 2 AA2 SER A 25 HIS A 39 1 15 HELIX 3 AA3 ILE A 42 CYS A 57 1 16 HELIX 4 AA4 PRO A 58 ASN A 83 1 26 HELIX 5 AA5 SER A 84 SER A 87 5 4 HELIX 6 AA6 THR A 93 SER A 116 1 24 HELIX 7 AA7 ASN A 117 GLY A 135 1 19 HELIX 8 AA8 LEU A 142 SER A 147 1 6 HELIX 9 AA9 SER A 147 ASP A 153 1 7 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