HEADER TRANSCRIPTION 07-FEB-25 9IA7 TITLE NMR SOLUTION STRUCTURE OF RPRD2 CTD-INTERACTING DOMAIN AND PT4 RNAPII TITLE 2 CTD PEPTIDE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: REGULATION OF NUCLEAR PRE-MRNA DOMAIN-CONTAINING PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: LEHHHHHH = NON-CLEAVABLE EXPRESSION TAG M = INITIAL COMPND 6 METHIONINE S19-Q155 (Q5VT52) - WHOLE CONSTRUCT S19-T147 (Q5VT52) - COMPND 7 PDB FILE; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1; COMPND 10 CHAIN: B; COMPND 11 SYNONYM: RNA POLYMERASE II SUBUNIT B1,3'-5' EXORIBONUCLEASE,DNA- COMPND 12 DIRECTED RNA POLYMERASE II SUBUNIT A,DNA-DIRECTED RNA POLYMERASE III COMPND 13 LARGEST SUBUNIT,RNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1; COMPND 14 EC: 2.7.7.6,3.1.13.-,2.7.7.48; COMPND 15 ENGINEERED: YES; COMPND 16 OTHER_DETAILS: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1 C-TERMINAL COMPND 17 DOMAIN (UNIPROT: P24928), RESIDUES 1612 TO 1623 SEQUENCE: COMPND 18 SPSYSPTSPSYS (PHOSPHORYLATED ON THREONINE - SPSYSP(PTH)SPSYS) SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: RPRD2, KIAA0460, HSPC099; 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: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS RPRD2, CID, RNAPII CTD, COMPLEX, PROTEIN BINDING, THREONINE, KEYWDS 2 TRANSCRIPTION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR K.LINHARTOVA,K.KUBICEK,R.STEFL REVDAT 1 18-FEB-26 9IA7 0 JRNL AUTH K.LINHARTOVA,J.MACOSEK,K.KUBICEK,E.SMIRAKOVA,R.STEFL JRNL TITL RECOGNITION OF RNA POLYMERASE II C-TERMINAL DOMAIN BY RPRD2 JRNL REF TO BE PUBLISHED JRNL REFN 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 9IA7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-FEB-25. REMARK 100 THE DEPOSITION ID IS D_1292143797. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293.15 REMARK 210 PH : 8 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : 1 PA REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-100% 13C; U-100% 15N] REMARK 210 RPRD2 CID, 1.5 MM PT4 CTD, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-15N NOESY; 3D REMARK 210 CBCA(CO)NH; 3D HNCACB; 3D REMARK 210 HBHA(CO)NH; 3D CC(CO)NH REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 850 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III HD REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, NMRFAM-SPARKY, CYANA REMARK 210 METHOD USED : SIMULATED ANNEALING 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 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 MET A 15 REMARK 465 SER A 16 REMARK 465 ALA A 17 REMARK 465 SER A 18 REMARK 465 THR A 148 REMARK 465 PHE A 149 REMARK 465 LYS A 150 REMARK 465 THR A 151 REMARK 465 GLN A 152 REMARK 465 LYS A 153 REMARK 465 GLN A 154 REMARK 465 LEU A 155 REMARK 465 GLU 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 465 HIS A 162 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 HG1 THR A 37 OE1 GLU A 39 1.45 REMARK 500 OD2 ASP A 83 HH TYR B 151 1.45 REMARK 500 OD2 ASP A 129 HH TYR B 158 1.54 REMARK 500 O LYS A 30 HG SER A 33 1.55 REMARK 500 HG SER B 152 O2P TPO B 154 1.55 REMARK 500 HH TYR A 79 O TYR B 151 1.58 REMARK 500 O GLY A 43 HG SER A 46 1.60 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 THR A 35 9.41 -69.03 REMARK 500 1 ASN A 36 15.93 57.67 REMARK 500 1 ASN A 51 -61.89 -92.38 REMARK 500 1 LYS A 52 23.88 42.10 REMARK 500 1 LYS A 53 -34.53 -159.21 REMARK 500 1 SER A 69 -79.96 -67.89 REMARK 500 1 ASN A 87 -72.56 -64.21 REMARK 500 1 LYS A 89 -19.88 59.67 REMARK 500 1 LYS A 91 -8.33 -52.83 REMARK 500 1 ALA A 93 3.51 -160.58 REMARK 500 2 LYS A 52 27.71 42.53 REMARK 500 2 LYS A 53 -34.39 -156.59 REMARK 500 2 SER A 69 -85.22 -69.57 REMARK 500 2 ASN A 87 -79.23 -55.61 REMARK 500 2 LYS A 89 -1.78 47.81 REMARK 500 2 LYS A 91 -12.72 -47.33 REMARK 500 2 ALA A 93 6.19 -160.29 REMARK 500 2 VAL A 116 -17.89 -142.96 REMARK 500 2 SER B 150 -168.15 59.17 REMARK 500 2 PRO B 153 13.71 -68.79 REMARK 500 2 TPO B 154 -67.58 -127.06 REMARK 500 2 SER B 155 97.42 52.78 REMARK 500 2 PRO B 156 22.06 -59.11 REMARK 500 2 TYR B 158 -36.29 -156.76 REMARK 500 3 LYS A 52 3.98 48.73 REMARK 500 3 LYS A 53 -32.10 -148.12 REMARK 500 3 SER A 69 -82.34 -64.17 REMARK 500 3 ASN A 87 -84.91 -63.56 REMARK 500 3 LYS A 89 -7.76 56.76 REMARK 500 3 ALA A 93 -4.24 -145.03 REMARK 500 3 VAL A 116 -12.60 -141.94 REMARK 500 3 PRO B 156 15.15 -69.86 REMARK 500 4 THR A 35 1.99 -69.37 REMARK 500 4 LYS A 52 13.47 46.10 REMARK 500 4 LYS A 53 -27.20 -157.15 REMARK 500 4 SER A 69 -80.44 -55.83 REMARK 500 4 ASN A 87 -79.64 -57.04 REMARK 500 4 LYS A 89 -6.69 58.89 REMARK 500 4 LYS A 91 7.75 -53.19 REMARK 500 4 ALA A 93 10.93 -161.08 REMARK 500 4 VAL A 116 -11.34 -141.65 REMARK 500 4 SER B 155 146.37 58.65 REMARK 500 4 SER B 157 10.86 -69.19 REMARK 500 4 TYR B 158 -44.13 -161.14 REMARK 500 5 PHE A 31 -72.75 -57.46 REMARK 500 5 THR A 35 23.98 -65.34 REMARK 500 5 SER A 40 -22.47 -148.07 REMARK 500 5 LYS A 52 26.60 44.61 REMARK 500 5 LYS A 53 -33.57 -159.71 REMARK 500 5 SER A 69 -71.82 -55.60 REMARK 500 REMARK 500 THIS ENTRY HAS 198 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9HM8 RELATED DB: PDB REMARK 900 SAME RPRD2 CID WITH DIFFERENT CTD PEPTIDE REMARK 900 RELATED ID: 34979 RELATED DB: BMRB REMARK 900 NMR SOLUTION STRUCTURE OF RPRD2 CTD-INTERACTING DOMAIN AND PT4 REMARK 900 RNAPII CTD PEPTIDE. DBREF 9IA7 A 16 155 UNP Q5VT52 RPRD2_HUMAN 16 155 DBREF 9IA7 B 148 159 UNP P24928 RPB1_HUMAN 1612 1623 SEQADV 9IA7 MET A 15 UNP Q5VT52 INITIATING METHIONINE SEQADV 9IA7 GLU A 156 UNP Q5VT52 EXPRESSION TAG SEQADV 9IA7 HIS A 157 UNP Q5VT52 EXPRESSION TAG SEQADV 9IA7 HIS A 158 UNP Q5VT52 EXPRESSION TAG SEQADV 9IA7 HIS A 159 UNP Q5VT52 EXPRESSION TAG SEQADV 9IA7 HIS A 160 UNP Q5VT52 EXPRESSION TAG SEQADV 9IA7 HIS A 161 UNP Q5VT52 EXPRESSION TAG SEQADV 9IA7 HIS A 162 UNP Q5VT52 EXPRESSION TAG SEQRES 1 A 148 MET SER ALA SER SER ALA GLY ALA LEU GLU SER SER LEU SEQRES 2 A 148 ASP ARG LYS PHE GLN SER VAL THR ASN THR MET GLU SER SEQRES 3 A 148 ILE GLN GLY LEU SER SER TRP CYS ILE GLU ASN LYS LYS SEQRES 4 A 148 HIS HIS SER THR ILE VAL TYR HIS TRP MET LYS TRP LEU SEQRES 5 A 148 ARG ARG SER ALA TYR PRO HIS ARG LEU ASN LEU PHE TYR SEQRES 6 A 148 LEU ALA ASN ASP VAL ILE GLN ASN CYS LYS ARG LYS ASN SEQRES 7 A 148 ALA ILE ILE PHE ARG GLU SER PHE ALA ASP VAL LEU PRO SEQRES 8 A 148 GLU ALA ALA ALA LEU VAL LYS ASP PRO SER VAL SER LYS SEQRES 9 A 148 SER VAL GLU ARG ILE PHE LYS ILE TRP GLU ASP ARG ASN SEQRES 10 A 148 VAL TYR PRO GLU GLU MET ILE VAL ALA LEU ARG GLU ALA SEQRES 11 A 148 LEU SER THR THR PHE LYS THR GLN LYS GLN LEU GLU HIS SEQRES 12 A 148 HIS HIS HIS HIS HIS SEQRES 1 B 12 SER PRO SER TYR SER PRO TPO SER PRO SER TYR SER MODRES 9IA7 TPO B 154 THR MODIFIED RESIDUE HET TPO B 154 17 HETNAM TPO PHOSPHOTHREONINE HETSYN TPO PHOSPHONOTHREONINE FORMUL 2 TPO C4 H10 N O6 P HELIX 1 AA1 ALA A 20 SER A 33 1 14 HELIX 2 AA2 SER A 40 GLN A 42 5 3 HELIX 3 AA3 GLY A 43 LYS A 52 1 10 HELIX 4 AA4 HIS A 54 ARG A 68 1 15 HELIX 5 AA5 HIS A 73 LYS A 89 1 17 HELIX 6 AA6 ILE A 95 LYS A 112 1 18 HELIX 7 AA7 VAL A 116 ARG A 130 1 15 HELIX 8 AA8 PRO A 134 THR A 147 1 14 LINK C PRO B 153 N TPO B 154 1555 1555 1.34 LINK C TPO B 154 N SER B 155 1555 1555 1.34 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 MODEL 11 ENDMDL MODEL 12 ENDMDL MODEL 13 ENDMDL MODEL 14 ENDMDL MODEL 15 ENDMDL MODEL 16 ENDMDL MODEL 17 ENDMDL MODEL 18 ENDMDL MODEL 19 ENDMDL MODEL 20 ENDMDL CONECT 2182 2194 CONECT 2194 2182 2195 2205 CONECT 2195 2194 2196 2203 2206 CONECT 2196 2195 2197 2198 2207 CONECT 2197 2196 2208 2209 2210 CONECT 2198 2196 2199 CONECT 2199 2198 2200 2201 2202 CONECT 2200 2199 CONECT 2201 2199 CONECT 2202 2199 CONECT 2203 2195 2204 2211 CONECT 2204 2203 CONECT 2205 2194 CONECT 2206 2195 CONECT 2207 2196 CONECT 2208 2197 CONECT 2209 2197 CONECT 2210 2197 CONECT 2211 2203 MASTER 189 0 1 8 0 0 0 6 1147 2 19 13 END