HEADER TRANSCRIPTION 17-JAN-12 2LO6 TITLE STRUCTURE OF NRD1 CID BOUND TO PHOSPHORYLATED RNAP II CTD COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN NRD1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CID DOMAIN RESIDUES 1-154; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: UNP RESIDUES 1556-1569; COMPND 10 SYNONYM: RNA POLYMERASE II SUBUNIT 1, RNA POLYMERASE II SUBUNIT B1, COMPND 11 DNA-DIRECTED RNA POLYMERASE III LARGEST SUBUNIT, RNA POLYMERASE II COMPND 12 SUBUNIT B220; COMPND 13 EC: 2.7.7.6; COMPND 14 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 STRAIN: ATCC 204508 / S288C; SOURCE 6 GENE: NRD1, YNL251C, N0868; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET22B; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE S288C; SOURCE 13 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 14 ORGANISM_TAXID: 559292 KEYWDS CTD-INTERACTING DOMAIN, CID, CARBOXY-TERMINAL DOMAIN, CTD, RNA- KEYWDS 2 PROCESSING, TRANSCIPTION TERMINATION, CIS-TRANS ISOMERIZATION OF KEYWDS 3 PROLINES, ESS1 ISOMERASE, PEPTIDE BINDING PROTEIN, TRANSCRIPTION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR K.KUBICEK,H.CERNA,J.PASULKA,P.HOLUB,D.HROSSOVA,F.LOEHR,C.HOFR, AUTHOR 2 S.VANACOVA,R.STEFL REVDAT 1 26-DEC-12 2LO6 0 JRNL AUTH K.KUBICEK,H.CERNA,P.HOLUB,J.PASULKA,D.HROSSOVA,F.LOEHR, JRNL AUTH 2 C.HOFR,S.VANACOVA,R.STEFL JRNL TITL SERINE PHOSPHORYLATION AND PROLINE ISOMERIZATION IN RNAP II JRNL TITL 2 CTD CONTROL RECRUITMENT OF NRD1. JRNL REF GENES DEV. V. 26 1891 2012 JRNL REFN ISSN 0890-9369 JRNL PMID 22892239 JRNL DOI 10.1101/GAD.192781.112 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER, CYANA REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, AND KOLLM (AMBER), GUNTERT, MUMENTHALER REMARK 3 AND WUTHRICH (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2LO6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JAN-12. REMARK 100 THE RCSB ID CODE IS RCSB102624. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 8 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2 MM [U-100% 13C; U-100% 15N] REMARK 210 NRD1 POLYPEPTIDE, 2.3 MM REMARK 210 PHOSPHOPEPTIDE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D CBCA(CO)NH; 3D HNCA; 3D REMARK 210 HNCACB; 3D HN(CO)CA; 3D HCCH- REMARK 210 TOCSY; 3D 1H-15N NOESY; 3D 1H-13C REMARK 210 NOESY ALIPHATIC; 3D FILTERED- REMARK 210 EDITED NOESY; 2D FILTERED- REMARK 210 FILTERED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, SPARKY, CYANA, CING REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST 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 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 GLU A 155 REMARK 465 HIS A 156 REMARK 465 HIS A 157 REMARK 465 HIS A 158 REMARK 465 HIS A 159 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 O ALA A 112 HG SER A 116 1.58 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 5 ARG A 74 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 7 ARG A 74 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 16 ARG A 74 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 18 ARG A 74 NE - CZ - NH1 ANGL. DEV. = 3.1 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 ASP A 6 -157.15 -72.95 REMARK 500 1 SER A 22 154.88 59.33 REMARK 500 1 ILE A 24 56.62 -116.26 REMARK 500 1 HIS A 39 -17.90 -153.11 REMARK 500 1 ILE A 40 75.91 47.75 REMARK 500 1 GLU A 43 -66.72 -120.22 REMARK 500 1 PRO A 58 -179.87 -55.77 REMARK 500 1 LYS A 90 101.58 54.85 REMARK 500 1 THR A 93 -161.80 53.86 REMARK 500 1 SER A 140 15.85 58.35 REMARK 500 1 ALA A 144 -36.71 -36.85 REMARK 500 1 ILE A 145 15.82 -65.53 REMARK 500 1 SER A 147 161.10 71.03 REMARK 500 1 PHE A 150 -85.80 -32.01 REMARK 500 1 PRO B 157 1.35 -61.40 REMARK 500 1 PRO B 164 -0.91 -57.02 REMARK 500 2 ASP A 5 19.01 52.39 REMARK 500 2 ASP A 6 -117.68 -105.57 REMARK 500 2 ILE A 24 50.71 -111.23 REMARK 500 2 HIS A 39 48.95 -145.65 REMARK 500 2 ILE A 40 79.05 -63.07 REMARK 500 2 ASP A 41 18.15 -153.36 REMARK 500 2 ILE A 42 36.88 -147.09 REMARK 500 2 PRO A 58 -177.47 -66.51 REMARK 500 2 SER A 84 24.45 49.45 REMARK 500 2 THR A 93 -151.72 50.62 REMARK 500 2 SER A 140 -2.20 63.28 REMARK 500 2 ILE A 145 29.39 -71.64 REMARK 500 2 SER A 147 22.59 46.87 REMARK 500 2 LYS A 148 -169.84 -125.02 REMARK 500 2 ASP A 153 -14.28 63.79 REMARK 500 2 SER B 161 148.48 -170.47 REMARK 500 3 GLN A 2 -25.07 -148.77 REMARK 500 3 GLN A 3 16.99 -149.30 REMARK 500 3 ASP A 4 9.17 58.82 REMARK 500 3 ASP A 5 15.60 -142.64 REMARK 500 3 ASP A 6 -151.32 -77.42 REMARK 500 3 LEU A 20 170.59 51.67 REMARK 500 3 LYS A 21 26.02 -141.10 REMARK 500 3 HIS A 39 -23.63 -152.30 REMARK 500 3 ILE A 40 74.96 46.51 REMARK 500 3 ASP A 41 20.57 -147.24 REMARK 500 3 ILE A 42 35.33 -147.45 REMARK 500 3 PRO A 58 -166.56 -74.76 REMARK 500 3 SER A 88 176.17 57.69 REMARK 500 3 ASN A 89 16.01 55.65 REMARK 500 3 THR A 93 -157.22 -152.76 REMARK 500 3 ILE A 145 22.03 -68.77 REMARK 500 3 SER A 147 23.76 49.39 REMARK 500 3 PHE A 150 -66.21 -29.96 REMARK 500 REMARK 500 THIS ENTRY HAS 286 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17173 RELATED DB: BMRB DBREF 2LO6 A 1 153 UNP P53617 NRD1_YEAST 1 153 DBREF 2LO6 B 155 168 UNP P04050 RPB1_YEAST 1556 1569 SEQADV 2LO6 LEU A 154 UNP P53617 EXPRESSION TAG SEQADV 2LO6 GLU A 155 UNP P53617 EXPRESSION TAG SEQADV 2LO6 HIS A 156 UNP P53617 EXPRESSION TAG SEQADV 2LO6 HIS A 157 UNP P53617 EXPRESSION TAG SEQADV 2LO6 HIS A 158 UNP P53617 EXPRESSION TAG SEQADV 2LO6 HIS A 159 UNP P53617 EXPRESSION TAG SEQADV 2LO6 HIS A 160 UNP P53617 EXPRESSION TAG SEQADV 2LO6 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 14 TYR SER PRO THR SEP PRO SER TYR SER PRO THR SEP PRO SEQRES 2 B 14 SER MODRES 2LO6 SEP B 159 SER PHOSPHOSERINE MODRES 2LO6 SEP B 166 SER PHOSPHOSERINE HET SEP B 159 14 HET SEP B 166 14 HETNAM SEP PHOSPHOSERINE HETSYN SEP PHOSPHONOSERINE FORMUL 2 SEP 2(C3 H8 N O6 P) HELIX 1 1 GLN A 2 ASP A 6 5 5 HELIX 2 2 PHE A 7 ASP A 19 1 13 HELIX 3 3 SER A 25 ASP A 38 1 14 HELIX 4 4 GLU A 43 CYS A 57 1 15 HELIX 5 5 PRO A 58 SER A 82 1 25 HELIX 6 6 GLY A 92 GLY A 102 1 11 HELIX 7 7 VAL A 104 LYS A 115 1 12 HELIX 8 8 ASN A 117 SER A 134 1 18 HELIX 9 9 LEU A 142 ARG A 146 5 5 HELIX 10 10 LYS A 148 ASP A 153 1 6 LINK C THR B 158 N SEP B 159 1555 1555 1.34 LINK C SEP B 159 N PRO B 160 1555 1555 1.34 LINK C THR B 165 N SEP B 166 1555 1555 1.34 LINK C SEP B 166 N PRO B 167 1555 1555 1.34 CISPEP 1 SEP B 159 PRO B 160 1 -10.62 CISPEP 2 SEP B 159 PRO B 160 2 -2.70 CISPEP 3 SEP B 159 PRO B 160 3 -4.94 CISPEP 4 SEP B 159 PRO B 160 4 -5.17 CISPEP 5 SEP B 159 PRO B 160 5 -8.38 CISPEP 6 SEP B 159 PRO B 160 6 -11.50 CISPEP 7 SEP B 159 PRO B 160 7 -5.46 CISPEP 8 SEP B 159 PRO B 160 8 -7.94 CISPEP 9 SEP B 159 PRO B 160 9 -10.46 CISPEP 10 SEP B 159 PRO B 160 10 -5.78 CISPEP 11 SEP B 159 PRO B 160 11 -7.08 CISPEP 12 SEP B 159 PRO B 160 12 -5.35 CISPEP 13 SEP B 159 PRO B 160 13 -6.07 CISPEP 14 SEP B 159 PRO B 160 14 -5.54 CISPEP 15 SEP B 159 PRO B 160 15 -5.20 CISPEP 16 SEP B 159 PRO B 160 16 -10.85 CISPEP 17 SEP B 159 PRO B 160 17 -4.30 CISPEP 18 SEP B 159 PRO B 160 18 -5.56 CISPEP 19 SEP B 159 PRO B 160 19 3.42 CISPEP 20 SEP B 159 PRO B 160 20 -3.31 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