HEADER VIRAL PROTEIN 24-AUG-04 1X9V TITLE DIMERIC STRUCTURE OF THE C-TERMINAL DOMAIN OF VPR COMPND MOL_ID: 1; COMPND 2 MOLECULE: VPR PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN (RESIDUES 52-96); COMPND 5 SYNONYM: VIRAL PROTEIN R; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED BY SOLID SOURCE 4 PHASE. THE SEQUENCE OF THE PEPTIDE IS FOUND IN HUMAN SOURCE 5 IMMUNODEFICIENCY VIRUS TYPE 1 (HIV-1) KEYWDS ALPHA HELIX, ANTIPARALLEL HOMODIMER, LEUCINE-ZIPPER, VIRAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR S.BOURBIGOT,H.BELTZ,J.DENIS,N.MORELLET,B.P.ROQUES,Y.MELY,S.BOUAZIZ REVDAT 3 02-MAR-22 1X9V 1 REMARK REVDAT 2 24-FEB-09 1X9V 1 VERSN REVDAT 1 14-JUN-05 1X9V 0 JRNL AUTH S.BOURBIGOT,H.BELTZ,J.DENIS,N.MORELLET,B.P.ROQUES,Y.MELY, JRNL AUTH 2 S.BOUAZIZ JRNL TITL THE C-TERMINAL DOMAIN OF THE HIV-1 REGULATORY PROTEIN VPR JRNL TITL 2 ADOPTS AN ANTIPARALLEL DIMERIC STRUCTURE IN SOLUTION VIA ITS JRNL TITL 3 LEUCINE-ZIPPER-LIKE DOMAIN JRNL REF BIOCHEM.J. V. 387 333 2005 JRNL REFN ISSN 0264-6021 JRNL PMID 15571493 JRNL DOI 10.1042/BJ20041759 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 3.0, X-PLOR 3.851 REMARK 3 AUTHORS : BRUKER (XWINNMR), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON 573 NOE REMARK 3 -DERIVED DISTANCE CONSTRAINTS. REMARK 4 REMARK 4 1X9V COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-AUG-04. REMARK 100 THE DEPOSITION ID IS D_1000030121. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 3 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM VPR(52-96); 63% H2O, 7% D2O, REMARK 210 30% CD3CN REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D TOCSY; 2D NOESY; DQF-COSY; 2D REMARK 210 15N-HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 3.0, FELIX 98.0 REMARK 210 METHOD USED : RESTRAINED SIMULATED ANNEALING, REMARK 210 MOLECULAR DYNAMICS, ENERGY REMARK 210 MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY, STRUCTURES WITH THE REMARK 210 LEAST RESTRAINT VIOLATIONS 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 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 H2 ASP A 52 H THR A 53 1.33 REMARK 500 O ARG B 62 H GLN B 66 1.46 REMARK 500 O ARG A 62 H GLN A 66 1.46 REMARK 500 O TRP B 54 H VAL B 57 1.56 REMARK 500 O TRP A 54 H VAL A 57 1.56 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 53 -74.96 -47.50 REMARK 500 1 ARG A 77 35.61 -167.62 REMARK 500 1 ARG A 80 46.06 -90.91 REMARK 500 1 ILE A 84 71.50 46.85 REMARK 500 1 GLN A 86 75.24 -176.62 REMARK 500 1 THR A 89 38.90 38.26 REMARK 500 1 ARG A 90 -176.98 57.73 REMARK 500 1 ALA A 93 39.77 -99.26 REMARK 500 1 SER A 94 -160.85 53.64 REMARK 500 1 THR B 53 -74.98 -47.56 REMARK 500 1 ARG B 77 35.64 -167.65 REMARK 500 1 ARG B 80 45.92 -90.87 REMARK 500 1 ILE B 84 71.45 46.82 REMARK 500 1 GLN B 86 75.24 -176.61 REMARK 500 1 THR B 89 38.93 38.29 REMARK 500 1 ARG B 90 -176.96 57.63 REMARK 500 1 ALA B 93 39.81 -99.43 REMARK 500 1 SER B 94 -160.84 53.68 REMARK 500 2 ARG A 77 12.41 -140.39 REMARK 500 2 HIS A 78 145.77 67.72 REMARK 500 2 SER A 79 -145.46 -70.24 REMARK 500 2 ILE A 81 66.34 -69.62 REMARK 500 2 ILE A 83 -100.36 -72.08 REMARK 500 2 ILE A 84 -94.68 -134.16 REMARK 500 2 THR A 89 132.55 65.35 REMARK 500 2 ARG A 90 49.27 -85.69 REMARK 500 2 ASN A 91 85.32 -165.67 REMARK 500 2 ARG B 77 12.45 -140.44 REMARK 500 2 HIS B 78 145.69 67.79 REMARK 500 2 SER B 79 -145.47 -70.14 REMARK 500 2 ILE B 81 66.42 -69.55 REMARK 500 2 ILE B 83 -100.23 -72.08 REMARK 500 2 ILE B 84 -94.77 -134.25 REMARK 500 2 THR B 89 132.49 65.26 REMARK 500 2 ARG B 90 49.28 -85.64 REMARK 500 2 ASN B 91 85.39 -165.74 REMARK 500 3 ILE A 74 -34.69 -157.63 REMARK 500 3 ARG A 77 37.88 150.96 REMARK 500 3 ILE A 83 -86.17 -48.07 REMARK 500 3 ILE A 84 33.21 33.51 REMARK 500 3 GLN A 86 -168.92 44.15 REMARK 500 3 ARG A 88 54.69 -110.29 REMARK 500 3 THR A 89 -143.52 -133.94 REMARK 500 3 SER A 94 39.81 -155.35 REMARK 500 3 ILE B 74 -34.59 -157.62 REMARK 500 3 ARG B 77 37.79 151.03 REMARK 500 3 ILE B 83 -86.26 -48.07 REMARK 500 3 ILE B 84 33.23 33.55 REMARK 500 3 GLN B 86 -168.94 44.07 REMARK 500 3 ARG B 88 54.66 -110.31 REMARK 500 REMARK 500 THIS ENTRY HAS 156 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 62 0.16 SIDE CHAIN REMARK 500 1 ARG A 73 0.26 SIDE CHAIN REMARK 500 1 ARG A 77 0.16 SIDE CHAIN REMARK 500 1 ARG A 80 0.25 SIDE CHAIN REMARK 500 1 ARG A 87 0.24 SIDE CHAIN REMARK 500 1 ARG A 88 0.21 SIDE CHAIN REMARK 500 1 ARG A 90 0.26 SIDE CHAIN REMARK 500 1 ARG B 62 0.16 SIDE CHAIN REMARK 500 1 ARG B 73 0.26 SIDE CHAIN REMARK 500 1 ARG B 77 0.16 SIDE CHAIN REMARK 500 1 ARG B 80 0.26 SIDE CHAIN REMARK 500 1 ARG B 87 0.24 SIDE CHAIN REMARK 500 1 ARG B 88 0.21 SIDE CHAIN REMARK 500 1 ARG B 90 0.26 SIDE CHAIN REMARK 500 2 ARG A 73 0.29 SIDE CHAIN REMARK 500 2 ARG A 77 0.32 SIDE CHAIN REMARK 500 2 ARG A 80 0.16 SIDE CHAIN REMARK 500 2 ARG A 87 0.24 SIDE CHAIN REMARK 500 2 ARG A 88 0.31 SIDE CHAIN REMARK 500 2 ARG A 90 0.30 SIDE CHAIN REMARK 500 2 ARG B 73 0.29 SIDE CHAIN REMARK 500 2 ARG B 77 0.32 SIDE CHAIN REMARK 500 2 ARG B 80 0.16 SIDE CHAIN REMARK 500 2 ARG B 87 0.24 SIDE CHAIN REMARK 500 2 ARG B 88 0.31 SIDE CHAIN REMARK 500 2 ARG B 90 0.30 SIDE CHAIN REMARK 500 3 ARG A 62 0.27 SIDE CHAIN REMARK 500 3 ARG A 73 0.15 SIDE CHAIN REMARK 500 3 ARG A 77 0.21 SIDE CHAIN REMARK 500 3 ARG A 80 0.21 SIDE CHAIN REMARK 500 3 ARG A 87 0.17 SIDE CHAIN REMARK 500 3 ARG A 88 0.27 SIDE CHAIN REMARK 500 3 ARG A 90 0.30 SIDE CHAIN REMARK 500 3 ARG B 62 0.27 SIDE CHAIN REMARK 500 3 ARG B 73 0.15 SIDE CHAIN REMARK 500 3 ARG B 77 0.21 SIDE CHAIN REMARK 500 3 ARG B 80 0.21 SIDE CHAIN REMARK 500 3 ARG B 87 0.17 SIDE CHAIN REMARK 500 3 ARG B 88 0.27 SIDE CHAIN REMARK 500 3 ARG B 90 0.30 SIDE CHAIN REMARK 500 4 ARG A 62 0.32 SIDE CHAIN REMARK 500 4 ARG A 73 0.31 SIDE CHAIN REMARK 500 4 ARG A 77 0.27 SIDE CHAIN REMARK 500 4 ARG A 80 0.30 SIDE CHAIN REMARK 500 4 ARG A 87 0.29 SIDE CHAIN REMARK 500 4 ARG A 88 0.31 SIDE CHAIN REMARK 500 4 ARG A 90 0.32 SIDE CHAIN REMARK 500 4 ARG B 62 0.32 SIDE CHAIN REMARK 500 4 ARG B 73 0.31 SIDE CHAIN REMARK 500 4 ARG B 77 0.27 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 136 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1X9V A 52 96 UNP Q73369 Q73369_9HIV1 52 96 DBREF 1X9V B 52 96 UNP Q73369 Q73369_9HIV1 52 96 SEQRES 1 A 45 ASP THR TRP THR GLY VAL GLU ALA LEU ILE ARG ILE LEU SEQRES 2 A 45 GLN GLN LEU LEU PHE ILE HIS PHE ARG ILE GLY CYS ARG SEQRES 3 A 45 HIS SER ARG ILE GLY ILE ILE GLN GLN ARG ARG THR ARG SEQRES 4 A 45 ASN GLY ALA SER LYS SER SEQRES 1 B 45 ASP THR TRP THR GLY VAL GLU ALA LEU ILE ARG ILE LEU SEQRES 2 B 45 GLN GLN LEU LEU PHE ILE HIS PHE ARG ILE GLY CYS ARG SEQRES 3 B 45 HIS SER ARG ILE GLY ILE ILE GLN GLN ARG ARG THR ARG SEQRES 4 B 45 ASN GLY ALA SER LYS SER HELIX 1 1 TRP A 54 CYS A 76 1 23 HELIX 2 2 TRP B 54 CYS B 76 1 23 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