HEADER CHAPERONE 22-DEC-17 6FD7 TITLE NMR STRUCTURE OF THE FIRST TPR DOMAIN OF THE HUMAN RPAP3 PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA POLYMERASE II-ASSOCIATED PROTEIN 3; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: RPAP3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS TPR HSP CHAPERONE, CHAPERONE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.QUINTERNET,M.E.CHAGOT,X.MANIVAL REVDAT 5 19-JUN-24 6FD7 1 REMARK REVDAT 4 14-JUN-23 6FD7 1 REMARK REVDAT 3 08-MAY-19 6FD7 1 REMARK REVDAT 2 12-SEP-18 6FD7 1 JRNL REVDAT 1 01-AUG-18 6FD7 0 JRNL AUTH J.HENRI,M.E.CHAGOT,M.BOURGUET,Y.ABEL,G.TERRAL,C.MAURIZY, JRNL AUTH 2 C.AIGUEPERSE,F.GEORGESCAULD,F.VANDERMOERE,R.SAINT-FORT, JRNL AUTH 3 I.BEHM-ANSMANT,B.CHARPENTIER,B.PRADET-BALADE,C.VERHEGGEN, JRNL AUTH 4 E.BERTRAND,P.MEYER,S.CIANFERANI,X.MANIVAL,M.QUINTERNET JRNL TITL DEEP STRUCTURAL ANALYSIS OF RPAP3 AND PIH1D1, TWO COMPONENTS JRNL TITL 2 OF THE HSP90 CO-CHAPERONE R2TP COMPLEX. JRNL REF STRUCTURE V. 26 1196 2018 JRNL REFN ISSN 1878-4186 JRNL PMID 30033218 JRNL DOI 10.1016/J.STR.2018.06.002 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.E.CHAGOT,C.JACQUEMIN,C.BRANLANT,B.CHARPENTIER,X.MANIVAL, REMARK 1 AUTH 2 M.QUINTERNET REMARK 1 TITL (1)H, (15)N AND (13)C RESONANCE ASSIGNMENTS OF THE TWO TPR REMARK 1 TITL 2 DOMAINS FROM THE HUMAN RPAP3 PROTEIN. REMARK 1 REF BIOMOL NMR ASSIGN V. 9 99 2015 REMARK 1 REFN ESSN 1874-270X REMARK 1 PMID 24668569 REMARK 1 DOI 10.1007/S12104-014-9552-4 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 6FD7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1200008099. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.4 REMARK 210 IONIC STRENGTH : 150 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1 MM [U-13C; U-15N] RPAP3-TPR1, REMARK 210 10 MM SODIUM PHOSPHATE, 150 MM REMARK 210 SODIUM CHLORIDE, 0.5 MM TCEP, 95% REMARK 210 H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 3D 1H-15N NOESY; REMARK 210 3D 1H-13C NOESY; 3D HNCA; 3D REMARK 210 HNCO; 3D HNCACB; 3D HCCH-TOCSY; REMARK 210 3D HNHA; 3D HCCH-COSY; 2D 1H-15N REMARK 210 HSQC; 2D 1H-13C HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, CARA, CYANA, TALOS REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 RESTRAINT ENERGIES 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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: 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 ARG A 173 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 ARG A 179 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 ARG A 198 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 ARG A 207 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 ARG A 242 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 ARG A 173 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 ARG A 207 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 ARG A 211 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 ARG A 242 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 3 ARG A 173 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 3 ARG A 242 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 5 ARG A 198 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 5 ARG A 206 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 5 ARG A 226 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 5 ARG A 242 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 6 ARG A 179 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 6 ARG A 207 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 6 ARG A 211 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 6 ARG A 242 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 7 ARG A 206 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 7 ARG A 207 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 7 ARG A 242 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 8 ARG A 179 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 8 ARG A 206 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 8 ARG A 242 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 9 ARG A 207 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 9 ARG A 226 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 9 ARG A 242 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 10 ARG A 179 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 10 ARG A 206 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 10 ARG A 207 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 10 ARG A 211 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 11 ARG A 207 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 11 ARG A 242 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 12 ARG A 173 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 12 ARG A 179 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 12 ARG A 206 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 12 ARG A 226 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 12 ARG A 242 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 13 ARG A 173 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 13 ARG A 207 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 14 ARG A 173 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 15 ARG A 179 NE - CZ - NH1 ANGL. DEV. = 5.2 DEGREES REMARK 500 15 ARG A 198 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 15 ARG A 207 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 15 ARG A 211 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 16 ARG A 179 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 16 ARG A 206 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 16 ARG A 207 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 17 ARG A 173 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 64 ANGLE DEVIATIONS. 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 163 79.05 -163.77 REMARK 500 1 LYS A 182 53.57 -98.82 REMARK 500 1 LYS A 216 50.52 -92.57 REMARK 500 1 PRO A 232 -4.29 -53.60 REMARK 500 2 ASP A 163 81.08 -163.49 REMARK 500 2 LYS A 182 56.38 -100.38 REMARK 500 2 LYS A 216 48.81 -85.23 REMARK 500 2 PRO A 232 -4.52 -58.71 REMARK 500 2 SER A 254 87.51 -68.94 REMARK 500 3 ASP A 163 79.58 -161.74 REMARK 500 3 LYS A 182 58.27 -103.40 REMARK 500 3 LYS A 216 49.09 -87.31 REMARK 500 4 ASP A 163 73.96 -152.81 REMARK 500 4 LYS A 182 59.13 -102.79 REMARK 500 4 LYS A 216 46.64 -86.97 REMARK 500 4 PRO A 232 -5.48 -58.89 REMARK 500 4 ASN A 234 108.67 -52.15 REMARK 500 5 LYS A 148 59.07 -91.30 REMARK 500 5 ASP A 163 75.43 -153.15 REMARK 500 5 PRO A 164 3.77 -65.75 REMARK 500 5 LYS A 182 55.85 -100.60 REMARK 500 5 LYS A 216 46.65 -87.28 REMARK 500 5 PRO A 232 -8.18 -58.56 REMARK 500 5 ASN A 253 14.23 58.11 REMARK 500 6 ASP A 163 77.69 -164.18 REMARK 500 6 LYS A 216 45.53 -98.47 REMARK 500 6 PRO A 232 -9.19 -58.10 REMARK 500 6 ASN A 253 -28.11 62.49 REMARK 500 6 SER A 254 40.31 -76.15 REMARK 500 7 LYS A 148 59.69 -91.59 REMARK 500 7 ASP A 163 79.19 -151.78 REMARK 500 7 LYS A 182 55.04 -104.32 REMARK 500 7 LYS A 216 49.15 -95.73 REMARK 500 7 SER A 254 27.69 -74.42 REMARK 500 8 ASP A 163 74.09 -157.13 REMARK 500 8 LYS A 182 56.27 -103.24 REMARK 500 8 LYS A 216 47.91 -85.06 REMARK 500 9 ASP A 163 73.99 -151.31 REMARK 500 9 PRO A 164 3.27 -65.13 REMARK 500 9 LYS A 182 53.89 -107.67 REMARK 500 9 LYS A 216 49.21 -82.28 REMARK 500 9 PRO A 232 -8.47 -57.89 REMARK 500 9 ASN A 253 11.14 56.63 REMARK 500 10 ASP A 163 80.48 -160.55 REMARK 500 10 LYS A 182 59.14 -97.78 REMARK 500 10 LYS A 216 48.26 -86.06 REMARK 500 10 PRO A 232 -7.17 -58.12 REMARK 500 11 LYS A 148 59.41 -93.78 REMARK 500 11 ASP A 163 77.70 -157.27 REMARK 500 11 PRO A 164 3.19 -67.49 REMARK 500 REMARK 500 THIS ENTRY HAS 98 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 226 0.08 SIDE CHAIN REMARK 500 2 ARG A 206 0.10 SIDE CHAIN REMARK 500 2 ARG A 226 0.09 SIDE CHAIN REMARK 500 4 ARG A 226 0.08 SIDE CHAIN REMARK 500 9 ARG A 206 0.09 SIDE CHAIN REMARK 500 10 ARG A 206 0.09 SIDE CHAIN REMARK 500 11 ARG A 226 0.07 SIDE CHAIN REMARK 500 12 TYR A 177 0.09 SIDE CHAIN REMARK 500 13 ARG A 206 0.08 SIDE CHAIN REMARK 500 13 ARG A 211 0.09 SIDE CHAIN REMARK 500 15 TYR A 165 0.07 SIDE CHAIN REMARK 500 16 ARG A 242 0.09 SIDE CHAIN REMARK 500 17 ARG A 206 0.08 SIDE CHAIN REMARK 500 19 TYR A 224 0.07 SIDE CHAIN REMARK 500 20 ARG A 206 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19758 RELATED DB: BMRB DBREF 6FD7 A 133 255 UNP Q9H6T3 RPAP3_HUMAN 133 255 SEQADV 6FD7 GLY A 129 UNP Q9H6T3 EXPRESSION TAG SEQADV 6FD7 PRO A 130 UNP Q9H6T3 EXPRESSION TAG SEQADV 6FD7 HIS A 131 UNP Q9H6T3 EXPRESSION TAG SEQADV 6FD7 MET A 132 UNP Q9H6T3 EXPRESSION TAG SEQRES 1 A 127 GLY PRO HIS MET ALA LEU VAL LEU LYS GLU LYS GLY ASN SEQRES 2 A 127 LYS TYR PHE LYS GLN GLY LYS TYR ASP GLU ALA ILE ASP SEQRES 3 A 127 CYS TYR THR LYS GLY MET ASP ALA ASP PRO TYR ASN PRO SEQRES 4 A 127 VAL LEU PRO THR ASN ARG ALA SER ALA TYR PHE ARG LEU SEQRES 5 A 127 LYS LYS PHE ALA VAL ALA GLU SER ASP CYS ASN LEU ALA SEQRES 6 A 127 VAL ALA LEU ASN ARG SER TYR THR LYS ALA TYR SER ARG SEQRES 7 A 127 ARG GLY ALA ALA ARG PHE ALA LEU GLN LYS LEU GLU GLU SEQRES 8 A 127 ALA LYS LYS ASP TYR GLU ARG VAL LEU GLU LEU GLU PRO SEQRES 9 A 127 ASN ASN PHE GLU ALA THR ASN GLU LEU ARG LYS ILE SER SEQRES 10 A 127 GLN ALA LEU ALA SER LYS GLU ASN SER TYR HELIX 1 AA1 PRO A 130 GLY A 147 1 18 HELIX 2 AA2 LYS A 148 ASP A 163 1 16 HELIX 3 AA3 PRO A 167 LEU A 180 1 14 HELIX 4 AA4 LYS A 182 ASN A 197 1 16 HELIX 5 AA5 TYR A 200 LEU A 214 1 15 HELIX 6 AA6 LYS A 216 GLU A 231 1 16 HELIX 7 AA7 ASN A 234 GLU A 252 1 19 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