HEADER ANTIVIRAL PROTEIN 09-JUL-20 6XQJ TITLE STRUCTURE OF HIV-1 VPR IN COMPLEX WITH THE HUMAN NUCLEOTIDE EXCISION TITLE 2 REPAIR PROTEIN HHR23A COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN VPR,UV EXCISION REPAIR PROTEIN RAD23 HOMOLOG A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: R ORF PROTEIN,VIRAL PROTEIN R,HHR23A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 GROUP M SOURCE 3 SUBTYPE B (ISOLATE NY5), HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HIV-1, HUMAN; SOURCE 5 ORGANISM_TAXID: 11698, 9606; SOURCE 6 STRAIN: ISOLATE NY5; SOURCE 7 GENE: VPR, RAD23A; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS VPR, HHR23A, NER, ANTIVIRAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 55 AUTHOR I.-J.L.BYEON,G.CALERO,Y.WU,C.H.BYEON,A.M.GRONENBORN REVDAT 3 15-MAY-24 6XQJ 1 REMARK REVDAT 2 08-DEC-21 6XQJ 1 JRNL REVDAT 1 17-NOV-21 6XQJ 0 JRNL AUTH I.L.BYEON,G.CALERO,Y.WU,C.H.BYEON,J.JUNG,M.DELUCIA,X.ZHOU, JRNL AUTH 2 S.WEISS,J.AHN,C.HAO,J.SKOWRONSKI,A.M.GRONENBORN JRNL TITL STRUCTURE OF HIV-1 VPR IN COMPLEX WITH THE HUMAN NUCLEOTIDE JRNL TITL 2 EXCISION REPAIR PROTEIN HHR23A. JRNL REF NAT COMMUN V. 12 6864 2021 JRNL REFN ESSN 2041-1723 JRNL PMID 34824204 JRNL DOI 10.1038/S41467-021-27009-W REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH 2.48 REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6XQJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JUL-20. REMARK 100 THE DEPOSITION ID IS D_1000250025. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 298 REMARK 210 PH : 7.2; 7.5 REMARK 210 IONIC STRENGTH : 100; 100 REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 927 UM [U-100% 2H; U-100% 13C; U REMARK 210 -100% 15N] VPR-HHR23A COMPLEX, REMARK 210 25 MM SODIUM PHOSPHATE, 50 MM REMARK 210 SODIUM CHLORIDE, 2 MM DTT, 1 MM REMARK 210 TCEP, 0.1 MM ZNSO4, 0.1 MM EDTA, REMARK 210 0.02 % SODIUM AZIDE, 93% H2O/7% REMARK 210 D2O; 1100 UM [U-100% 13C; U-100% REMARK 210 15N] VPR-HHR23A COMPLEX, 25 MM REMARK 210 SODIUM PHOSPHATE, 50 MM SODIUM REMARK 210 CHLORIDE, 2 MM DTT, 1 MM TCEP, REMARK 210 0.1 MM ZNSO4, 0.1 MM EDTA, 0.02 % REMARK 210 SODIUM AZIDE, 93% H2O/7% D2O; REMARK 210 745 UM [U-100% 13C; U-100% 15N] REMARK 210 VPR-HHR23A COMPLEX, 25 MM SODIUM REMARK 210 PHOSPHATE, 50 MM SODIUM CHLORIDE, REMARK 210 2 MM DTT, 1 MM TCEP, 0.1 MM REMARK 210 ZNSO4, 0.1 MM EDTA, 0.02 % REMARK 210 SODIUM AZIDE, 93% H2O/7% D2O; REMARK 210 1110 UM [U-100% 15N] VPR-HHR23A REMARK 210 COMPLEX, 25 MM SODIUM PHOSPHATE, REMARK 210 50 MM SODIUM CHLORIDE, 2 MM DTT, REMARK 210 1 MM TCEP, 0.1 MM ZNSO4, 0.1 MM REMARK 210 EDTA, 0.02 % SODIUM AZIDE, 93% REMARK 210 H2O/7% D2O; 1000 UM [U-100% 15N] REMARK 210 VPR-HHR23A COMPLEX, 25 MM SODIUM REMARK 210 PHOSPHATE, 50 MM SODIUM CHLORIDE, REMARK 210 2 MM DTT, 1 MM TCEP, 0.1 MM REMARK 210 ZNSO4, 0.1 MM EDTA, 0.02 % REMARK 210 SODIUM AZIDE, 93% H2O/7% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D TROSY-HNCACB; 3D TROSY REMARK 210 -HNCOCACB; 3D HNCA; 3D HCCH- REMARK 210 TOCSY; 3D 1H-15N NOESY; 3D REMARK 210 SIMILTANEOUSLY 13C/15C-EDITED REMARK 210 NOESY (ALIPHATIC); 3D REMARK 210 SIMILTANEOUSLY 13C/15C-EDITED REMARK 210 NOESY (AROMATIC); 2D 1H-15N HSQC; REMARK 210 2D 1H-13C HSQC ALIPHATIC; 2D 1H- REMARK 210 13C HSQC AROMATIC; 3D HBHA(CO)NH; REMARK 210 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 800 MHZ; 700 MHZ; 600 REMARK 210 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 3.1, NMRPIPE 8.7, CCPNMR REMARK 210 ANALYSIS 2.3.1, TALOS+ REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 960 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 55 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST ENERGY STRUCTURES 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 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 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 1-55 REMARK 465 RES C SSSEQI REMARK 465 MET A 1 REMARK 465 GLU A 2 REMARK 465 GLN A 3 REMARK 465 ALA A 4 REMARK 465 PRO A 5 REMARK 465 GLU A 6 REMARK 465 ASP A 7 REMARK 465 GLN A 8 REMARK 465 GLY A 9 REMARK 465 PRO A 10 REMARK 465 GLN A 11 REMARK 465 ARG A 12 REMARK 465 GLY A 80 REMARK 465 GLY A 81 REMARK 465 SER A 82 REMARK 465 GLY A 83 REMARK 465 GLY A 84 REMARK 465 SER A 85 REMARK 465 ALA A 223 REMARK 465 THR A 224 REMARK 465 GLU A 225 REMARK 465 ALA A 226 REMARK 465 ALA A 227 REMARK 465 GLY A 228 REMARK 465 GLU A 229 REMARK 465 GLY A 289 REMARK 465 GLU A 290 REMARK 465 LEU A 291 REMARK 465 ALA A 292 REMARK 465 ASP A 293 REMARK 465 ILE A 294 REMARK 465 SER A 295 REMARK 465 ASP A 296 REMARK 465 VAL A 297 REMARK 465 GLU A 298 REMARK 465 GLY A 299 REMARK 465 GLU A 300 REMARK 465 VAL A 301 REMARK 465 GLY A 302 REMARK 465 ALA A 303 REMARK 465 ILE A 304 REMARK 465 GLY A 305 REMARK 465 GLU A 306 REMARK 465 GLU A 307 REMARK 465 ALA A 308 REMARK 465 PRO A 309 REMARK 465 GLN A 310 REMARK 465 MET A 311 REMARK 465 ASN A 312 REMARK 465 TYR A 313 REMARK 465 ASP A 361 REMARK 465 ASP A 362 REMARK 465 GLU A 363 REMARK 465 LEU A 364 REMARK 465 GLU A 365 REMARK 465 HIS A 366 REMARK 465 HIS A 367 REMARK 465 HIS A 368 REMARK 465 HIS A 369 REMARK 465 HIS A 370 REMARK 465 HIS A 371 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 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 TYR A 15 -15.56 -43.54 REMARK 500 1 ASN A 16 -73.78 -80.46 REMARK 500 1 THR A 53 152.85 -45.39 REMARK 500 1 ASN A 251 84.55 -162.98 REMARK 500 1 PRO A 252 -9.44 -49.67 REMARK 500 1 PRO A 256 -39.15 -36.51 REMARK 500 1 HIS A 276 56.25 -144.27 REMARK 500 1 GLN A 315 11.44 82.86 REMARK 500 1 ALA A 329 -17.30 -44.05 REMARK 500 1 PRO A 333 157.47 -49.58 REMARK 500 1 GLU A 345 33.42 72.21 REMARK 500 1 GLN A 358 49.38 -81.38 REMARK 500 1 ASN A 359 -144.10 86.41 REMARK 500 2 TYR A 15 -3.82 -51.26 REMARK 500 2 ASN A 16 -72.42 -76.48 REMARK 500 2 THR A 53 173.36 -49.93 REMARK 500 2 PRO A 252 -17.39 -40.98 REMARK 500 2 GLN A 315 31.50 34.10 REMARK 500 2 GLU A 322 -32.38 -38.96 REMARK 500 2 GLU A 345 54.82 75.71 REMARK 500 2 ASN A 359 124.37 151.33 REMARK 500 3 TYR A 15 -4.80 -50.40 REMARK 500 3 ASN A 16 -72.90 -74.60 REMARK 500 3 THR A 53 170.51 -48.56 REMARK 500 3 LEU A 64 -35.69 -39.97 REMARK 500 3 PHE A 234 -18.41 -48.10 REMARK 500 3 PRO A 252 -12.52 -45.27 REMARK 500 3 GLN A 315 10.39 -69.61 REMARK 500 3 GLU A 322 -25.94 -38.95 REMARK 500 3 LYS A 346 17.87 41.91 REMARK 500 3 ASN A 359 126.60 85.79 REMARK 500 4 TYR A 15 -3.19 -51.96 REMARK 500 4 ASN A 16 -72.88 -75.21 REMARK 500 4 THR A 53 154.05 -45.46 REMARK 500 4 PRO A 231 2.50 -67.42 REMARK 500 4 PRO A 252 -15.02 -43.52 REMARK 500 4 ASN A 266 64.94 -152.53 REMARK 500 4 HIS A 276 24.78 -141.36 REMARK 500 4 GLN A 315 39.90 26.71 REMARK 500 4 ALA A 343 -15.60 -48.55 REMARK 500 4 ASN A 347 99.51 -66.72 REMARK 500 4 GLN A 358 48.44 -71.93 REMARK 500 4 ASN A 359 -139.70 83.44 REMARK 500 5 TYR A 15 -1.37 -55.82 REMARK 500 5 ASN A 16 -72.58 -84.65 REMARK 500 5 ARG A 36 -17.74 -47.19 REMARK 500 5 PRO A 231 -5.86 -57.83 REMARK 500 5 PRO A 252 -12.14 -46.72 REMARK 500 5 PRO A 256 -30.30 -37.47 REMARK 500 5 HIS A 276 59.30 -146.66 REMARK 500 REMARK 500 THIS ENTRY HAS 602 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 33 ND1 REMARK 620 2 HIS A 71 NE2 108.6 REMARK 620 3 CYS A 76 SG 110.3 110.3 REMARK 620 4 HIS A 78 ND1 108.6 108.5 110.5 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30769 RELATED DB: BMRB REMARK 900 STRUCTURE OF HIV-1 VPR IN COMPLEX WITH THE HUMAN NUCLEOTIDE REMARK 900 EXCISION REPAIR PROTEIN HHR23A DBREF 6XQJ A 1 79 UNP P12520 VPR_HV1N5 1 79 DBREF 6XQJ A 223 363 UNP P54725 RD23A_HUMAN 223 363 SEQADV 6XQJ GLY A 80 UNP P12520 LINKER SEQADV 6XQJ GLY A 81 UNP P12520 LINKER SEQADV 6XQJ SER A 82 UNP P12520 LINKER SEQADV 6XQJ GLY A 83 UNP P12520 LINKER SEQADV 6XQJ GLY A 84 UNP P12520 LINKER SEQADV 6XQJ SER A 85 UNP P12520 LINKER SEQADV 6XQJ LEU A 364 UNP P54725 EXPRESSION TAG SEQADV 6XQJ GLU A 365 UNP P54725 EXPRESSION TAG SEQADV 6XQJ HIS A 366 UNP P54725 EXPRESSION TAG SEQADV 6XQJ HIS A 367 UNP P54725 EXPRESSION TAG SEQADV 6XQJ HIS A 368 UNP P54725 EXPRESSION TAG SEQADV 6XQJ HIS A 369 UNP P54725 EXPRESSION TAG SEQADV 6XQJ HIS A 370 UNP P54725 EXPRESSION TAG SEQADV 6XQJ HIS A 371 UNP P54725 EXPRESSION TAG SEQRES 1 A 234 MET GLU GLN ALA PRO GLU ASP GLN GLY PRO GLN ARG GLU SEQRES 2 A 234 PRO TYR ASN GLU TRP THR LEU GLU LEU LEU GLU GLU LEU SEQRES 3 A 234 LYS SER GLU ALA VAL ARG HIS PHE PRO ARG ILE TRP LEU SEQRES 4 A 234 HIS ASN LEU GLY GLN HIS ILE TYR GLU THR TYR GLY ASP SEQRES 5 A 234 THR TRP ALA GLY VAL GLU ALA ILE ILE ARG ILE LEU GLN SEQRES 6 A 234 GLN LEU LEU PHE ILE HIS PHE ARG ILE GLY CYS ARG HIS SEQRES 7 A 234 SER GLY GLY SER GLY GLY SER ALA THR GLU ALA ALA GLY SEQRES 8 A 234 GLU ASN PRO LEU GLU PHE LEU ARG ASP GLN PRO GLN PHE SEQRES 9 A 234 GLN ASN MET ARG GLN VAL ILE GLN GLN ASN PRO ALA LEU SEQRES 10 A 234 LEU PRO ALA LEU LEU GLN GLN LEU GLY GLN GLU ASN PRO SEQRES 11 A 234 GLN LEU LEU GLN GLN ILE SER ARG HIS GLN GLU GLN PHE SEQRES 12 A 234 ILE GLN MET LEU ASN GLU PRO PRO GLY GLU LEU ALA ASP SEQRES 13 A 234 ILE SER ASP VAL GLU GLY GLU VAL GLY ALA ILE GLY GLU SEQRES 14 A 234 GLU ALA PRO GLN MET ASN TYR ILE GLN VAL THR PRO GLN SEQRES 15 A 234 GLU LYS GLU ALA ILE GLU ARG LEU LYS ALA LEU GLY PHE SEQRES 16 A 234 PRO GLU SER LEU VAL ILE GLN ALA TYR PHE ALA CYS GLU SEQRES 17 A 234 LYS ASN GLU ASN LEU ALA ALA ASN PHE LEU LEU SER GLN SEQRES 18 A 234 ASN PHE ASP ASP GLU LEU GLU HIS HIS HIS HIS HIS HIS HET ZN A 401 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 AA1 GLU A 17 PHE A 34 1 18 HELIX 2 AA2 PRO A 35 GLY A 51 1 17 HELIX 3 AA3 THR A 53 GLY A 75 1 23 HELIX 4 AA4 LEU A 232 ASP A 237 5 6 HELIX 5 AA5 GLN A 238 GLN A 249 1 12 HELIX 6 AA6 ASN A 251 ALA A 253 5 3 HELIX 7 AA7 LEU A 254 ASN A 266 1 13 HELIX 8 AA8 ASN A 266 SER A 274 1 9 HELIX 9 AA9 HIS A 276 GLU A 286 1 11 HELIX 10 AB1 THR A 317 ALA A 329 1 13 HELIX 11 AB2 PRO A 333 CYS A 344 1 12 HELIX 12 AB3 ASN A 347 SER A 357 1 11 LINK ND1 HIS A 33 ZN ZN A 401 1555 1555 2.05 LINK NE2 HIS A 71 ZN ZN A 401 1555 1555 2.05 LINK SG CYS A 76 ZN ZN A 401 1555 1555 2.30 LINK ND1 HIS A 78 ZN ZN A 401 1555 1555 2.05 SITE 1 AC1 4 HIS A 33 HIS A 71 CYS A 76 HIS A 78 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