HEADER VIRAL PROTEIN 10-APR-00 1ESK TITLE SOLUTION STRUCTURE OF NCP7 FROM HIV-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GAG POLYPROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 12-53; COMPND 5 SYNONYM: NUCLEOCAPSID PROTEIN NCP7; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE PROTEIN WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE SOURCE 4 IS NATURALLY FOUND IN HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (HIV-1). KEYWDS (12-53)NCP7, HIV-1, PROTEIN, VIRAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 9 AUTHOR N.MORELLET,H.DEMENE,V.TEILLEUX,T.HUYNH-DINH,H.DE ROCQUIGNY,M.- AUTHOR 2 C.FOURNIE-ZALUSKI,B.P.ROQUES REVDAT 3 16-FEB-22 1ESK 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1ESK 1 VERSN REVDAT 1 26-APR-00 1ESK 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 SOLUTION STRUCTURE OF (12-53)NCP7 OF HIV-1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH N.MORELLET,H.DE ROQUIGNY,Y.MELY,N.JULLIAN,H.DEMENE, REMARK 1 AUTH 2 M.OTTMANN,D.GERARD,J.L.DARLIX,M.C.FOURNIE-ZALUSKI,B.P.ROQUES REMARK 1 TITL CONFORMATIONAL BEHAVIOUR OF THE ACTIVE AND INACTIVE FORMS OF REMARK 1 TITL 2 THE NUCLEOCAPSID NCP7 OF HIV-1 STUDIED BY 1H NMR. REMARK 1 REF J.MOL.BIOL. V. 235 287 1994 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 2 REMARK 1 AUTH N.MORELLET,H.DEMENE,V.TEILLEUX,T.HUYNH-DINH,H.DE ROQUIGNY, REMARK 1 AUTH 2 M.C.FOURNIE-ZALUSKI,B.P.ROQUES REMARK 1 TITL STRUCTURE OF THE COMPLEX BETWEEN THE HIV-1 NUCLEOCAPSID REMARK 1 TITL 2 PROTEIN AND THE SINGLE-STRANDED PENTANUCLEOTIDE D(ACGCC). REMARK 1 REF J.MOL.BIOL. V. 283 419 1998 REMARK 1 REFN ISSN 0022-2836 REMARK 1 DOI 10.1006/JMBI.1998.2098 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : UXNMR 940501, DISCOVER REMARK 3 AUTHORS : BRUKER (UXNMR), MSI (DISCOVER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF REMARK 3 444 NOE-DERIVED DISTANCE CONSTRAINTS REMARK 4 REMARK 4 1ESK COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-APR-00. REMARK 100 THE DEPOSITION ID IS D_1000010857. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : N.A. REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2MM (12-53)NCP7, 90%H2O, 10% REMARK 210 D2O, PH 6.0 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 9 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY,STRUCTURES REMARK 210 WITH FAVORABLE NON-BOND ENERGY, REMARK 210 STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS,STRUCTURES REMARK 210 WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR TECHNIQUES. 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 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 PRO A 31 C - N - CD ANGL. DEV. = -15.2 DEGREES REMARK 500 3 PRO A 31 C - N - CD ANGL. DEV. = -14.5 DEGREES REMARK 500 7 CYS A 15 CB - CA - C ANGL. DEV. = 7.3 DEGREES REMARK 500 8 PRO A 31 C - N - CD ANGL. DEV. = -15.0 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 -83.58 -54.39 REMARK 500 1 ARG A 29 56.40 -111.20 REMARK 500 1 PRO A 31 164.95 40.77 REMARK 500 1 LYS A 38 -60.13 -121.43 REMARK 500 1 HIS A 44 168.23 151.89 REMARK 500 2 PRO A 31 178.63 32.76 REMARK 500 3 VAL A 13 135.04 -35.98 REMARK 500 3 ASN A 17 -84.46 -57.68 REMARK 500 3 ARG A 29 55.76 -114.28 REMARK 500 3 PRO A 31 173.00 40.37 REMARK 500 3 HIS A 44 163.97 149.81 REMARK 500 4 GLU A 21 171.33 55.52 REMARK 500 4 PRO A 31 176.03 31.76 REMARK 500 5 CYS A 18 -43.39 -131.63 REMARK 500 5 GLU A 21 171.55 74.91 REMARK 500 5 PRO A 31 170.47 34.41 REMARK 500 5 LYS A 38 -60.93 -101.42 REMARK 500 5 HIS A 44 165.22 146.95 REMARK 500 6 PRO A 31 174.59 33.84 REMARK 500 6 LYS A 38 -62.59 -103.17 REMARK 500 6 HIS A 44 162.22 153.75 REMARK 500 6 ARG A 52 46.08 -88.07 REMARK 500 7 VAL A 13 135.03 -35.72 REMARK 500 7 PRO A 31 176.58 32.99 REMARK 500 7 LYS A 38 -63.87 -106.46 REMARK 500 7 HIS A 44 160.19 151.29 REMARK 500 7 ARG A 52 36.86 -154.15 REMARK 500 8 ASN A 17 -80.27 -52.26 REMARK 500 8 ARG A 29 58.43 -110.25 REMARK 500 8 PRO A 31 165.49 40.18 REMARK 500 8 THR A 50 -75.69 -96.15 REMARK 500 8 GLU A 51 32.86 -167.65 REMARK 500 9 VAL A 13 135.28 -36.94 REMARK 500 9 CYS A 18 -35.63 -136.26 REMARK 500 9 GLU A 21 167.65 64.55 REMARK 500 9 PRO A 31 169.80 36.47 REMARK 500 9 GLU A 42 -4.14 -145.97 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 ARG A 52 0.08 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 54 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 15 SG REMARK 620 2 CYS A 18 SG 112.7 REMARK 620 3 HIS A 23 NE2 105.2 109.4 REMARK 620 4 CYS A 28 SG 109.0 110.5 109.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 55 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 36 SG REMARK 620 2 CYS A 39 SG 112.4 REMARK 620 3 HIS A 44 NE2 108.6 109.9 REMARK 620 4 CYS A 49 SG 106.5 113.3 105.7 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 54 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 55 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BJ6 RELATED DB: PDB DBREF 1ESK A 12 53 UNP P04585 POL_HV1H2 388 429 SEQADV 1ESK ASN A 12 UNP P04585 ILE 388 CONFLICT 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 54 1 HET ZN A 55 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) LINK SG CYS A 15 ZN ZN A 54 1555 1555 2.25 LINK SG CYS A 18 ZN ZN A 54 1555 1555 2.22 LINK NE2 HIS A 23 ZN ZN A 54 1555 1555 2.00 LINK SG CYS A 28 ZN ZN A 54 1555 1555 2.24 LINK SG CYS A 36 ZN ZN A 55 1555 1555 2.25 LINK SG CYS A 39 ZN ZN A 55 1555 1555 2.23 LINK NE2 HIS A 44 ZN ZN A 55 1555 1555 2.03 LINK SG CYS A 49 ZN ZN A 55 1555 1555 2.19 SITE 1 AC1 4 CYS A 15 CYS A 18 HIS A 23 CYS A 28 SITE 1 AC2 5 CYS A 36 CYS A 39 HIS A 44 CYS A 49 SITE 2 AC2 5 GLU A 51 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