HEADER VIRAL PROTEIN/DNA 03-JUL-98 1BJ6 TITLE 1H NMR OF (12-53) NCP7/D(ACGCC) COMPLEX, 10 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*AP*CP*GP*CP*C)-3'); COMPND 3 CHAIN: D; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: NUCLEOCAPSID PROTEIN 7; COMPND 7 CHAIN: A; COMPND 8 FRAGMENT: RESIDUES 12-53; COMPND 9 SYNONYM: (12-53)NCP7; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 5 ORGANISM_TAXID: 11676; SOURCE 6 STRAIN: MAL KEYWDS COMPLEX (NUCLEOCAPSID PROTEIN-DNA), NUCLEIC ACID, RETROVIRUS, VIRUS KEYWDS 2 MORPHOGENESIS, ZINC FINGER, VIRAL PROTEIN-DNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR H.DEMENE,N.MORELLET,V.TEILLEUX,T.HUYNH-DINH,H.DE ROCQUIGNY, AUTHOR 2 M.C.FOURNIE-ZALUSKI,B.P.ROQUES REVDAT 5 16-FEB-22 1BJ6 1 REMARK LINK REVDAT 4 24-FEB-09 1BJ6 1 VERSN REVDAT 3 01-APR-03 1BJ6 1 JRNL REVDAT 2 23-MAR-99 1BJ6 3 COMPND REMARK TITLE DBREF REVDAT 2 2 3 HEADER ATOM SOURCE SEQRES REVDAT 2 3 3 JRNL KEYWDS REVDAT 1 02-FEB-99 1BJ6 0 JRNL AUTH N.MORELLET,H.DEMENE,V.TEILLEUX,T.HUYNH-DINH,H.DE ROCQUIGNY, JRNL AUTH 2 M.C.FOURNIE-ZALUSKI,B.P.ROQUES JRNL TITL STRUCTURE OF THE COMPLEX BETWEEN THE HIV-1 NUCLEOCAPSID JRNL TITL 2 PROTEIN NCP7 AND THE SINGLE-STRANDED PENTANUCLEOTIDE JRNL TITL 3 D(ACGCC). JRNL REF J.MOL.BIOL. V. 283 419 1998 JRNL REFN ISSN 0022-2836 JRNL PMID 9769215 JRNL DOI 10.1006/JMBI.1998.2098 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DISCOVER REMARK 3 AUTHORS : BIOSYM REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE PROTEIN PART OF THE STRUCTURE WAS REMARK 3 FIRST GENERATED USING A RESTRAINTED DYNAMICAL ANNEALING REMARK 3 CALCULATION. THE D(ACGCC) NUCLEIC ACID UNDER A DNA CONFORMATION REMARK 3 WAS DOCKED APPROXIMATIVELY TO THE PROTEIN BASED ON THE 28 REMARK 3 INTERMOLECULAR NOES. THE DOCKED STRUCTURE WAS ENERGY-MINIMIZED REMARK 3 UNDER NOES RESTRAINTS. THIS INITIAL COMPLEXED STRUCTURE WAS THEN REMARK 3 USED FOR A SECOND SET OF SIMULATED ANNEALING CALCULATION. REMARK 4 REMARK 4 1BJ6 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000171818. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : LOW SALT CONDITIONS REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : WATER REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; TOCSY; DQF REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AMX600 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : BRUKER DISNMR DISNMR, BIOSYM/MSI REMARK 210 METHOD USED : DYNAMICAL SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST RESTRAINT VIOLATION AND REMARK 210 LOWEST TOTAL ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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: D, 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 DC D 2 N1 - C2 - O2 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DC D 4 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DA D 1 C4' - C3' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 2 DA D 1 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DC D 4 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 DC D 2 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 3 DC D 4 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 3 DC D 5 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 4 DA D 1 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 4 DC D 2 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 4 DC D 4 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 4 DC D 5 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 5 DC D 4 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 6 DC D 2 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 6 DC D 4 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 6 DC D 5 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 7 DA D 1 C4' - C3' - C2' ANGL. DEV. = -4.3 DEGREES REMARK 500 7 DA D 1 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 7 DC D 2 N1 - C2 - O2 ANGL. DEV. = 4.0 DEGREES REMARK 500 7 DC D 4 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 7 DC D 5 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 8 DA D 1 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 8 DC D 2 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 8 DC D 4 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 8 DC D 5 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 9 DA D 1 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 9 DC D 4 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 9 DC D 5 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 10 DA D 1 C4' - C3' - C2' ANGL. DEV. = -4.6 DEGREES REMARK 500 10 DA D 1 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 10 DC D 4 O4' - C1' - N1 ANGL. DEV. = 2.2 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 ASN A 17 -85.72 -143.86 REMARK 500 1 THR A 50 28.65 -161.23 REMARK 500 2 CYS A 15 117.55 -33.96 REMARK 500 2 ASN A 17 -88.64 -82.29 REMARK 500 2 THR A 50 40.68 -172.92 REMARK 500 2 GLU A 51 -81.19 -14.51 REMARK 500 3 LYS A 14 67.84 -163.23 REMARK 500 3 CYS A 15 111.70 -0.79 REMARK 500 3 ASN A 17 -64.58 -155.66 REMARK 500 3 HIS A 44 -161.19 -160.04 REMARK 500 3 THR A 50 37.32 -179.33 REMARK 500 3 GLU A 51 -78.97 -17.62 REMARK 500 3 ARG A 52 40.55 29.50 REMARK 500 4 ASN A 17 -77.67 -75.05 REMARK 500 4 LYS A 38 -76.43 -56.19 REMARK 500 4 THR A 50 29.80 -165.18 REMARK 500 4 ARG A 52 67.85 25.12 REMARK 500 5 VAL A 13 -57.21 -139.07 REMARK 500 5 LYS A 14 105.20 76.92 REMARK 500 5 PHE A 16 48.99 -79.62 REMARK 500 5 ASN A 17 -74.27 -151.54 REMARK 500 5 LYS A 38 -71.83 -56.15 REMARK 500 5 HIS A 44 -160.84 -103.60 REMARK 500 5 THR A 50 36.22 -177.15 REMARK 500 5 GLU A 51 -76.29 -22.36 REMARK 500 5 ARG A 52 74.27 56.40 REMARK 500 6 CYS A 15 121.74 -28.88 REMARK 500 6 PHE A 16 49.25 -83.92 REMARK 500 6 ASN A 17 -77.47 -152.33 REMARK 500 6 HIS A 44 -148.58 -97.03 REMARK 500 6 THR A 50 38.04 -160.90 REMARK 500 6 ARG A 52 -152.65 -66.60 REMARK 500 7 PHE A 16 39.21 -91.44 REMARK 500 7 ASN A 17 -75.41 -148.06 REMARK 500 7 THR A 50 25.47 -152.14 REMARK 500 7 GLU A 51 -120.10 -91.45 REMARK 500 7 ARG A 52 134.69 156.21 REMARK 500 8 ASN A 17 -80.14 -149.44 REMARK 500 8 THR A 50 36.70 -177.99 REMARK 500 8 GLU A 51 -80.12 -7.06 REMARK 500 9 CYS A 15 124.00 -34.95 REMARK 500 9 ASN A 17 -83.80 -154.88 REMARK 500 9 THR A 50 19.07 -141.97 REMARK 500 9 ARG A 52 85.87 -163.77 REMARK 500 10 CYS A 15 114.95 -21.44 REMARK 500 10 ASN A 17 -73.79 -151.95 REMARK 500 10 LYS A 38 -74.14 -57.14 REMARK 500 10 HIS A 44 -162.78 -116.76 REMARK 500 10 ARG A 52 79.12 -169.22 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 DG D 3 0.06 SIDE CHAIN REMARK 500 5 DC D 2 0.09 SIDE CHAIN REMARK 500 8 DC D 2 0.09 SIDE CHAIN REMARK 500 9 DC D 5 0.07 SIDE CHAIN REMARK 500 10 ARG A 52 0.09 SIDE CHAIN 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 54H ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 15 SG REMARK 620 2 CYS A 18 SG 114.9 REMARK 620 3 HIS A 23 NE2 105.4 109.4 REMARK 620 4 CYS A 28 SG 109.9 107.9 109.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 55H ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 36 SG REMARK 620 2 CYS A 39 SG 113.9 REMARK 620 3 HIS A 44 NE2 106.0 108.0 REMARK 620 4 CYS A 49 SG 106.8 112.4 109.4 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: ZNB REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: ZINC-BINDING SITES. REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 54H REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 55H DBREF 1BJ6 A 13 53 UNP Q74084 Q74084_9HIV1 390 430 DBREF 1BJ6 D 1 5 PDB 1BJ6 1BJ6 1 5 SEQRES 1 D 5 DA DC DG DC DC SEQRES 1 A 42 ASN VAL LYS CYS PHE ASN CYS GLY LYS GLU GLY HIS THR SEQRES 2 A 42 ALA ARG ASN CYS ARG ALA PRO ARG LYS LYS GLY CYS TRP SEQRES 3 A 42 LYS CYS GLY LYS GLU GLY HIS GLN MET LYS ASP CYS THR SEQRES 4 A 42 GLU ARG GLN HET ZN A 54H 1 HET ZN A 55H 1 HETNAM ZN ZINC ION FORMUL 3 ZN 2(ZN 2+) LINK SG CYS A 15 ZN ZN A 54H 1555 1555 2.31 LINK SG CYS A 18 ZN ZN A 54H 1555 1555 2.26 LINK NE2 HIS A 23 ZN ZN A 54H 1555 1555 2.04 LINK SG CYS A 28 ZN ZN A 54H 1555 1555 2.23 LINK SG CYS A 36 ZN ZN A 55H 1555 1555 2.30 LINK SG CYS A 39 ZN ZN A 55H 1555 1555 2.27 LINK NE2 HIS A 44 ZN ZN A 55H 1555 1555 2.03 LINK SG CYS A 49 ZN ZN A 55H 1555 1555 2.27 SITE 1 ZNB 7 CYS A 15 CYS A 18 HIS A 23 CYS A 28 SITE 2 ZNB 7 CYS A 36 CYS A 39 HIS A 44 SITE 1 AC1 4 CYS A 15 CYS A 18 HIS A 23 CYS A 28 SITE 1 AC2 4 CYS A 36 CYS A 39 HIS A 44 CYS A 49 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