1DPU - Header Asymmetric Unit

HEADER DNA BINDING PROTEIN 27-DEC-99 1DPU

TITLE SOLUTION STRUCTURE OF THE C-TERMINAL DOMAIN OF HUMAN RPA32 TITLE 2 COMPLEXED WITH UNG2(73-88)

COMPND MOL_ID: 1; COMPND 2 MOLECULE: REPLICATION PROTEIN A (RPA32) C-TERMINAL DOMAIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN (RESIDUES 172-270); COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: URACIL DNA GLYCOSYLASE (UNG2); COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: RESIDUES 73-88; COMPND 10 ENGINEERED: YES; COMPND 11 OTHER_DETAILS: CHEMICALLY SYNTHESIZED

SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 OTHER_DETAILS: THIS PEPTIDE SEQUENCE IS FOUND IN THE SOURCE 12 NUCLEAR [UNG2(73-88)] AND MITOCHONDRIAL [UNG1(64-79)] SOURCE 13 FORMS OF HUMAN URACIL-DNA GLYCOSYLASE

KEYWDS PROTEIN-PEPTIDE COMPLEX, DNA REPAIR, NMR, DNA BINDING KEYWDS 2 PROTEIN

EXPDTA SOLUTION NMR

NUMMDL 30

AUTHOR G.MER,A.M.EDWARDS,W.J.CHAZIN

REVDAT 2 24-FEB-09 1DPU 1 VERSN REVDAT 1 10-NOV-00 1DPU 0

JRNL AUTH G.MER,A.BOCHKAREV,R.GUPTA,E.BOCHKAREVA,L.FRAPPIER, JRNL AUTH 2 C.J.INGLES,A.M.EDWARDS,W.J.CHAZIN JRNL TITL STRUCTURAL BASIS FOR THE RECOGNITION OF DNA REPAIR JRNL TITL 2 PROTEINS UNG2, XPA, AND RAD52 BY REPLICATION JRNL TITL 3 FACTOR RPA. JRNL REF CELL(CAMBRIDGE,MASS.) V. 103 449 2000 JRNL REFN ISSN 0092-8674 JRNL PMID 11081631 JRNL DOI 10.1016/S0092-8674(00)00136-7

REMARK 1

REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DIANA 2.8 REMARK 3 AUTHORS : GUNTERT PROGRAM 2 : AMBER 4.1 AUTHORS 2 : REMARK 3 PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON, REMARK 3 SEIBEL,SINGH,WEINER,KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL

REMARK 4 REMARK 4 1DPU COMPLIES WITH FORMAT V. 3.15, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JAN-00. REMARK 100 THE RCSB ID CODE IS RCSB010272.

REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298.00 REMARK 210 PH : 7.00 REMARK 210 IONIC STRENGTH : 25MM PHOSPHATE, 50MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM RPA32(172-270) U- 15N, REMARK 210 13C; 1.2 MM UNG2(73- 88) NA; REMARK 210 25MM PHOSPHATE BUFFER NA; 50MM REMARK 210 NACL; 5 MM DTT NA REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, 3D_13C- SEPARATED_ REMARK 210 NOESY, 3D_15N- SEPARATED_ REMARK 210 NOESY, DQF- COSY, HNHA, HNHB, REMARK 210 HACAHB -COSY, FILTER-EDITED REMARK 210 NOESY, DOUBLE-HALF FILTERED REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ, 600 MHZ, 750 MHZ, REMARK 210 800 MHZ REMARK 210 SPECTROMETER MODEL : AMX, DRX, DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : MSI FELIX97 SOFTWARE USED 2 : REMARK 210 DIANA 2.8 SOFTWARE USED 3 : REMARK 210 AMBER 4.1 REMARK 210 METHOD USED : DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 30 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING DOUBLE- AND TRIPLE- REMARK 210 RESONANCE NMR SPECTROSCOPY ***

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 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 19 ARG B 88 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 21 ARG B 84 NE - CZ - NH2 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 GLU A 223 43.40 -73.55 REMARK 500 1 THR A 258 -96.89 -122.28 REMARK 500 1 ASP A 268 55.27 -176.07 REMARK 500 1 GLN B 75 -117.89 -148.54 REMARK 500 1 ARG B 76 49.53 -82.65 REMARK 500 2 CYS A 219 100.79 -27.67 REMARK 500 2 THR A 258 -90.51 -132.43 REMARK 500 2 ASP A 261 36.18 -80.98 REMARK 500 2 ASP A 268 141.86 167.18 REMARK 500 2 ALA A 269 -178.35 175.61 REMARK 500 2 ARG B 76 -58.58 71.63 REMARK 500 2 ASN B 77 -80.12 44.04 REMARK 500 3 PRO A 220 -171.27 -68.35 REMARK 500 3 PRO A 222 -117.96 -84.31 REMARK 500 3 THR A 258 -87.63 -125.10 REMARK 500 3 ASP A 268 40.46 -109.29 REMARK 500 3 ILE B 74 -109.82 46.27 REMARK 500 3 ALA B 87 -50.97 75.27 REMARK 500 4 ASN A 203 47.82 -80.51 REMARK 500 4 CYS A 219 111.15 -36.18 REMARK 500 4 THR A 258 -94.43 -120.28 REMARK 500 4 ILE B 74 -36.94 73.70 REMARK 500 5 LEU A 205 -139.48 -89.34 REMARK 500 5 CYS A 219 110.21 -29.31 REMARK 500 5 THR A 258 -82.09 -89.29 REMARK 500 5 ASP A 268 -49.78 -165.78 REMARK 500 5 ALA A 269 -72.87 64.79 REMARK 500 5 ARG B 76 -63.32 73.73 REMARK 500 5 ASN B 77 -71.67 62.81 REMARK 500 6 ASN A 203 62.96 64.69 REMARK 500 6 VAL A 207 -69.57 -26.66 REMARK 500 6 CYS A 219 106.49 -50.42 REMARK 500 6 HIS A 236 -32.56 -162.77 REMARK 500 6 THR A 258 -86.42 -144.03 REMARK 500 6 ASP A 262 46.48 -88.16 REMARK 500 6 ILE B 74 -69.87 62.43 REMARK 500 6 GLN B 75 -69.40 67.06 REMARK 500 7 ASN A 203 -40.15 178.04 REMARK 500 7 CYS A 219 101.36 -29.24 REMARK 500 7 THR A 258 -85.94 -94.54 REMARK 500 7 HIS A 263 88.56 -150.63 REMARK 500 7 THR A 267 -128.41 -81.80 REMARK 500 7 ASP A 268 -56.09 60.65 REMARK 500 7 GLN B 75 -148.22 54.49 REMARK 500 8 CYS A 219 107.63 -44.61 REMARK 500 8 THR A 258 -102.73 -104.20 REMARK 500 8 ASP A 261 2.42 -67.14 REMARK 500 9 HIS A 236 -28.66 -164.09 REMARK 500 9 THR A 258 -96.73 -123.29 REMARK 500 9 ASP A 268 57.23 -95.28 REMARK 500 9 GLN B 75 -46.85 69.50 REMARK 500 9 ASN B 77 -72.21 23.10 REMARK 500 9 ALA B 87 -66.33 67.87 REMARK 500 10 ASN A 203 28.92 92.95 REMARK 500 10 PRO A 222 -91.81 -74.98 REMARK 500 10 THR A 258 -75.34 -105.41 REMARK 500 10 LYS B 78 -54.62 69.96 REMARK 500 11 ASN A 203 -62.85 63.66 REMARK 500 11 VAL A 207 -64.87 -29.25 REMARK 500 11 PRO A 220 46.76 -90.15 REMARK 500 11 GLU A 223 44.54 -77.53 REMARK 500 11 THR A 258 -87.76 -111.77 REMARK 500 11 ALA B 86 -45.25 72.49 REMARK 500 11 ALA B 87 -54.69 74.30 REMARK 500 12 ASN A 203 -67.01 65.40 REMARK 500 12 VAL A 239 -58.10 -28.85 REMARK 500 12 THR A 258 -93.53 -113.04 REMARK 500 12 ASP A 260 164.06 77.82 REMARK 500 12 ASP A 262 -50.80 -148.05 REMARK 500 12 GLN B 75 -57.33 72.09 REMARK 500 12 ASN B 77 155.34 -48.05 REMARK 500 12 LYS B 78 -50.48 58.52 REMARK 500 13 PRO A 220 46.80 -78.83 REMARK 500 13 PRO A 222 -108.18 -79.63 REMARK 500 13 THR A 258 -89.30 -118.71 REMARK 500 13 THR A 267 -101.84 -70.90 REMARK 500 13 ASP A 268 -79.76 55.58 REMARK 500 13 GLN B 75 -49.80 64.88 REMARK 500 13 LYS B 78 -56.30 65.11 REMARK 500 14 VAL A 239 -57.68 -29.06 REMARK 500 14 THR A 258 -95.42 -111.91 REMARK 500 14 GLN B 75 -58.28 74.25 REMARK 500 14 ARG B 76 36.19 -75.75 REMARK 500 15 VAL A 207 -62.85 -29.82 REMARK 500 15 CYS A 219 109.62 -50.74 REMARK 500 15 THR A 258 -116.18 -146.71 REMARK 500 15 ASP A 268 73.07 -68.57 REMARK 500 16 CYS A 219 107.52 -55.80 REMARK 500 16 THR A 258 -100.63 -143.23 REMARK 500 16 GLN B 75 -66.15 65.02 REMARK 500 16 LYS B 78 26.37 49.66 REMARK 500 16 ALA B 79 -65.49 -154.08 REMARK 500 16 ALA B 87 -53.81 74.82 REMARK 500 17 ASN A 203 -26.15 64.16 REMARK 500 17 ARG A 221 64.08 60.03 REMARK 500 17 PRO A 222 -73.71 -69.67 REMARK 500 17 LYS A 235 61.48 -68.20 REMARK 500 17 HIS A 236 -32.91 -163.14 REMARK 500 17 THR A 258 -101.12 -118.83 REMARK 500 18 ASN A 203 88.84 -65.49 REMARK 500 18 CYS A 219 100.74 -27.51 REMARK 500 18 ARG A 221 109.66 -45.25 REMARK 500 18 THR A 258 -77.52 -97.97 REMARK 500 18 ASP A 261 20.61 -76.35 REMARK 500 18 ASP A 268 63.54 -111.74 REMARK 500 19 CYS A 219 101.64 -28.59 REMARK 500 19 THR A 258 -87.74 -96.29 REMARK 500 19 ILE B 74 -112.41 43.01 REMARK 500 19 ASN B 77 -72.03 -58.57 REMARK 500 20 PRO A 220 27.57 -62.63 REMARK 500 20 PRO A 222 -110.54 -80.93 REMARK 500 20 SER A 238 133.12 -38.83 REMARK 500 20 VAL A 239 -55.15 -28.08 REMARK 500 20 THR A 258 -92.92 -118.22 REMARK 500 20 LYS B 78 -52.29 58.85 REMARK 500 20 ALA B 86 46.50 -77.70 REMARK 500 20 ALA B 87 -30.78 67.06 REMARK 500 21 ASN A 203 -76.54 -150.11 REMARK 500 21 THR A 258 -96.69 -118.56 REMARK 500 21 ASP A 261 34.26 -79.60 REMARK 500 21 ILE B 74 88.59 -64.91 REMARK 500 21 ARG B 76 -90.98 -112.39 REMARK 500 21 ASN B 77 -61.06 69.59 REMARK 500 22 VAL A 207 -59.28 -28.74 REMARK 500 22 CYS A 219 109.53 -46.11 REMARK 500 22 THR A 258 -83.48 -149.43 REMARK 500 22 ASP A 260 143.65 82.81 REMARK 500 22 ASP A 261 27.16 -72.06 REMARK 500 22 ALA A 269 137.10 84.41 REMARK 500 22 ALA B 86 20.29 -78.60 REMARK 500 23 ASN A 203 -45.92 64.40 REMARK 500 23 PRO A 220 65.36 -66.31 REMARK 500 23 THR A 258 -79.28 -92.27 REMARK 500 23 LYS B 78 -64.51 68.47 REMARK 500 23 ALA B 86 -45.79 75.34 REMARK 500 24 ASN A 203 53.82 -151.64 REMARK 500 24 CYS A 219 106.97 -47.31 REMARK 500 24 THR A 258 -106.10 -128.63 REMARK 500 24 ASN B 77 -65.62 -21.56 REMARK 500 24 ALA B 86 -55.76 73.85 REMARK 500 25 ASN A 203 -89.02 -118.17 REMARK 500 25 THR A 258 -98.23 -111.99 REMARK 500 25 ASP A 268 -73.17 61.75 REMARK 500 25 ALA A 269 -56.80 -172.50 REMARK 500 25 GLN B 75 -125.51 -138.01 REMARK 500 25 ARG B 76 44.71 -76.80 REMARK 500 26 THR A 258 -80.66 -92.42 REMARK 500 26 ASP A 261 34.14 -73.41 REMARK 500 26 THR A 267 -77.25 -73.85 REMARK 500 26 ARG B 76 36.49 -77.49 REMARK 500 26 LEU B 85 52.30 32.16 REMARK 500 27 CYS A 219 103.55 -27.99 REMARK 500 27 THR A 258 -86.69 -94.05 REMARK 500 27 ASP A 262 -40.76 -145.03 REMARK 500 27 ASP A 268 43.58 -80.99 REMARK 500 27 ALA A 269 -58.34 -171.14 REMARK 500 27 LYS B 78 -55.61 69.15 REMARK 500 28 ASN A 203 -64.50 64.24 REMARK 500 28 THR A 258 -99.60 -116.71 REMARK 500 28 ASN B 77 -62.20 -25.41 REMARK 500 29 VAL A 207 -64.89 -27.01 REMARK 500 29 THR A 258 -89.04 -103.41 REMARK 500 29 ASN B 77 -107.75 47.99 REMARK 500 30 ASN A 203 -31.70 74.38 REMARK 500 30 LYS A 235 61.31 -70.00 REMARK 500 30 HIS A 236 -28.18 -162.82 REMARK 500 30 THR A 258 -89.97 -130.80 REMARK 500 30 ASP A 261 32.67 -77.18 REMARK 500 30 GLN B 75 97.34 -35.38 REMARK 500 30 ASN B 77 -78.62 -20.14 REMARK 500 30 ALA B 86 -59.62 69.49 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 4 TYR A 256 0.08 SIDE_CHAIN REMARK 500 7 TYR A 256 0.13 SIDE_CHAIN REMARK 500 8 ARG A 221 0.10 SIDE_CHAIN REMARK 500 8 TYR A 256 0.09 SIDE_CHAIN REMARK 500 9 ARG A 221 0.08 SIDE_CHAIN REMARK 500 9 TYR A 256 0.10 SIDE_CHAIN REMARK 500 10 ARG B 84 0.07 SIDE_CHAIN REMARK 500 11 TYR A 256 0.12 SIDE_CHAIN REMARK 500 12 ARG A 221 0.09 SIDE_CHAIN REMARK 500 14 TYR A 256 0.11 SIDE_CHAIN REMARK 500 18 TYR A 256 0.12 SIDE_CHAIN REMARK 500 20 ARG A 221 0.09 SIDE_CHAIN REMARK 500 20 TYR A 256 0.13 SIDE_CHAIN REMARK 500 22 ARG A 221 0.12 SIDE_CHAIN REMARK 500 23 ARG B 88 0.08 SIDE_CHAIN REMARK 500 26 ARG A 221 0.08 SIDE_CHAIN REMARK 500 26 TYR A 256 0.09 SIDE_CHAIN REMARK 500 29 HIS A 263 0.08 SIDE_CHAIN REMARK 500 30 TYR A 256 0.12 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL

DBREF 1DPU A 172 270 UNP P15927 RFA2_HUMAN 202 270 DBREF 1DPU B 73 88 UNP P13051 UNG_HUMAN 73 88

SEQRES 1 A 99 ALA ASN SER GLN PRO SER ALA GLY ARG ALA PRO ILE SER SEQRES 2 A 99 ASN PRO GLY MET SER GLU ALA GLY ASN PHE GLY GLY ASN SEQRES 3 A 99 SER PHE MET PRO ALA ASN GLY LEU THR VAL ALA GLN ASN SEQRES 4 A 99 GLN VAL LEU ASN LEU ILE LYS ALA CYS PRO ARG PRO GLU SEQRES 5 A 99 GLY LEU ASN PHE GLN ASP LEU LYS ASN GLN LEU LYS HIS SEQRES 6 A 99 MET SER VAL SER SER ILE LYS GLN ALA VAL ASP PHE LEU SEQRES 7 A 99 SER ASN GLU GLY HIS ILE TYR SER THR VAL ASP ASP ASP SEQRES 8 A 99 HIS PHE LYS SER THR ASP ALA GLU SEQRES 1 B 16 ARG ILE GLN ARG ASN LYS ALA ALA ALA LEU LEU ARG LEU SEQRES 2 B 16 ALA ALA ARG

HELIX 1 1 THR A 206 CYS A 219 1 14 HELIX 2 2 PHE A 227 LEU A 234 1 8 HELIX 3 3 SER A 238 GLU A 252 1 15 HELIX 4 4 ARG B 76 ALA B 87 1 12

SHEET 1 A 3 LEU A 225 ASN A 226 0 SHEET 2 A 3 HIS A 263 SER A 266 -1 O PHE A 264 N LEU A 225 SHEET 3 A 3 ILE A 255 SER A 257 -1 N TYR A 256 O LYS A 265

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