HEADER TRANSFERASE 30-JUN-06 2IWJ TITLE SOLUTION STRUCTURE OF THE ZN COMPLEX OF HIV-2 NCP(23-49) PEPTIDE, TITLE 2 ENCOMPASSING PROTEIN CCHC-LINKER, DISTAL CCHC ZN-BINDING MOTIF AND C- TITLE 3 TERMINAL TAIL. COMPND MOL_ID: 1; COMPND 2 MOLECULE: GAG-POL POLYPROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 405-431 OF NCP; COMPND 5 SYNONYM: NUCLEOCAPSID PROTEIN, PR160GAG-POL; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: FRAGMENT 23-49 OF NCP CORRESPONDS TO 405-431 OF THE COMPND 8 WHOLE HIV-2 GAG PROTEIN CONTAINS ONE ZN ION IN A CCHC ZN-BINDING COMPND 9 DOMAINS SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS TYPE 2; SOURCE 4 ORGANISM_COMMON: HIV-2; SOURCE 5 ORGANISM_TAXID: 11709 KEYWDS DNA-DIRECTED DNA POLYMERASE, RETROVIRUS ZINC FINGER-LIKE DOMAINS, KEYWDS 2 RNA-DIRECTED DNA POLYMERASE, POLYPROTEIN, RNA-BINDING, TRANSFERASE, KEYWDS 3 LIPOPROTEIN, VIRION PROTEIN, DNA INTEGRATION, ASPARTYL PROTEASE, KEYWDS 4 CAPSID MATURATION, DNA RECOMBINATION, NUCLEOTIDYLTRANSFERASE, KEYWDS 5 MULTIFUNCTIONAL ENZYME, ZINC, AIDS, MEMBRANE, PROTEASE, NUCLEASE, KEYWDS 6 MYRISTATE, HYDROLASE, MAGNESIUM, LENTIVIRUS, ZINC-FINGER, VIRAL KEYWDS 7 NUCLEOPROTEIN, NUCLEOCAPSID PROTEIN, CORE PROTEIN, ENDONUCLEASE, KEYWDS 8 METAL-BINDING EXPDTA SOLUTION NMR NUMMDL 30 AUTHOR P.AMODEO,M.A.CASTIGLIONE MORELLI,A.OSTUNI,P.CRISTINZIANO,A.BAVOSO REVDAT 4 14-JUN-23 2IWJ 1 LINK REVDAT 3 15-JAN-20 2IWJ 1 REMARK REVDAT 2 24-FEB-09 2IWJ 1 VERSN REVDAT 1 09-OCT-07 2IWJ 0 JRNL AUTH P.AMODEO,M.A.CASTIGLIONE MORELLI,A.OSTUNI,P.CRISTINZIANO, JRNL AUTH 2 A.BAVOSO JRNL TITL STRUCTURAL FEATURES OF THE C-TERMINAL ZINC FINGER DOMAIN OF JRNL TITL 2 THE HIV-2 NC PROTEIN (RESIDUES 23-49). JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON, REMARK 3 SEIBEL,SINGH,WEINER,KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SIMULATED ANNEALING FOLLOWED BY ENERGY REMARK 3 MINIMIZATION, BOTH PERFORMED WITH A GBSA IMPLICIT SOLVENT REMARK 3 APPROACH REMARK 4 REMARK 4 2IWJ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-JUN-06. REMARK 100 THE DEPOSITION ID IS D_1290029223. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298.0 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 130 REMARK 210 PRESSURE : 1.0 ATM REMARK 210 SAMPLE CONTENTS : 80% WATER/20% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY DQF-COSY TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : AMBER REMARK 210 METHOD USED : SIMULATED ANNEALING-ENERGY REMARK 210 MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 150 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 30 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY, FAVORABLE REMARK 210 ENERGY, THE LEAST RESTRAINT REMARK 210 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: 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 ARG A 23 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 ARG A 46 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 ARG A 27 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 3 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 5.0 DEGREES REMARK 500 4 ARG A 46 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 5 ARG A 46 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 6 ARG A 46 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 7 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 7 ARG A 46 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 8 ARG A 27 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 9 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 9 ARG A 27 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 10 ARG A 27 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 11 ARG A 46 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 12 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 12 ARG A 27 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 12 ARG A 46 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 13 ARG A 27 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 14 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 4.9 DEGREES REMARK 500 16 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 16 ARG A 27 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 16 ARG A 27 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 16 ARG A 46 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 17 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 17 ARG A 27 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 18 ARG A 27 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 18 ARG A 46 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 19 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 19 ARG A 27 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 21 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 21 ARG A 46 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 22 ARG A 27 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 22 ARG A 46 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 23 ARG A 46 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 24 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 24 ARG A 27 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 24 ARG A 46 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 25 ARG A 27 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 26 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 26 ARG A 27 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 27 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 28 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 28 ARG A 27 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 29 ARG A 27 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 30 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 30 ARG A 27 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 30 ARG A 46 NE - CZ - NH1 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 GLN A 28 -16.70 -145.73 REMARK 500 1 CYS A 30 17.24 43.65 REMARK 500 2 CYS A 30 14.19 53.85 REMARK 500 3 CYS A 30 23.19 45.07 REMARK 500 3 ALA A 48 -15.88 56.87 REMARK 500 4 ALA A 24 67.50 -156.52 REMARK 500 4 CYS A 30 15.01 45.33 REMARK 500 4 LYS A 42 -31.84 -130.24 REMARK 500 4 ARG A 46 55.77 -118.77 REMARK 500 5 CYS A 30 14.48 59.59 REMARK 500 7 CYS A 30 25.58 38.56 REMARK 500 7 LYS A 42 -32.78 -130.60 REMARK 500 7 GLN A 47 -5.36 -55.26 REMARK 500 8 CYS A 30 22.26 44.83 REMARK 500 8 LYS A 42 -31.65 -132.71 REMARK 500 9 CYS A 30 24.38 44.68 REMARK 500 9 LYS A 42 -35.20 -136.43 REMARK 500 9 ALA A 48 -11.59 55.84 REMARK 500 10 CYS A 30 15.39 48.77 REMARK 500 10 TRP A 31 0.15 -68.10 REMARK 500 11 ARG A 26 -36.04 58.41 REMARK 500 11 LYS A 42 -33.91 -130.84 REMARK 500 12 GLN A 28 -14.77 -140.24 REMARK 500 12 CYS A 30 25.50 41.84 REMARK 500 12 TRP A 31 0.21 -69.01 REMARK 500 12 LYS A 35 5.94 -65.60 REMARK 500 13 ALA A 24 75.59 22.08 REMARK 500 13 CYS A 30 19.13 44.82 REMARK 500 13 LYS A 42 -33.25 -131.58 REMARK 500 14 GLN A 28 -18.15 -147.05 REMARK 500 14 CYS A 30 13.83 43.12 REMARK 500 14 LYS A 42 -29.44 -144.73 REMARK 500 14 ARG A 46 30.51 -81.36 REMARK 500 15 CYS A 30 23.86 41.53 REMARK 500 15 LYS A 42 -30.79 -132.54 REMARK 500 16 CYS A 30 25.03 45.00 REMARK 500 16 CYS A 43 93.09 -10.56 REMARK 500 16 ALA A 48 -2.58 -141.53 REMARK 500 17 ARG A 26 -3.62 -59.55 REMARK 500 17 CYS A 30 24.83 40.22 REMARK 500 17 CYS A 43 78.88 8.71 REMARK 500 18 CYS A 30 23.55 41.07 REMARK 500 18 CYS A 43 81.21 1.15 REMARK 500 18 ALA A 48 42.42 -73.41 REMARK 500 19 GLN A 28 -20.30 -146.49 REMARK 500 19 CYS A 30 21.14 44.12 REMARK 500 19 LYS A 42 -44.16 -140.77 REMARK 500 19 CYS A 43 78.34 3.60 REMARK 500 19 GLU A 45 5.14 58.98 REMARK 500 20 GLN A 28 -19.78 -140.78 REMARK 500 REMARK 500 THIS ENTRY HAS 88 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 5 ARG A 27 0.09 SIDE CHAIN REMARK 500 9 ARG A 23 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 A1050 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 30 SG REMARK 620 2 CYS A 33 SG 120.1 REMARK 620 3 HIS A 38 NE2 108.3 101.7 REMARK 620 4 CYS A 43 SG 104.4 104.2 119.0 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 A1050 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NC8 RELATED DB: PDB REMARK 900 HIGH-RESOLUTION SOLUTION NMR STRUCTURE OF THE MINIMALACTIVE DOMAIN REMARK 900 OF THE HUMAN IMMUNODEFICIENCY VIRUS TYPE-2NUCLEOCAPSID PROTEIN, 15 REMARK 900 STRUCTURES REMARK 900 RELATED ID: 2CB7 RELATED DB: PDB REMARK 900 COMPUTATIONAL MODEL STRUCTURE OF HIV-2 POL POLYPROTEIN REMARK 900 RELATED ID: 7342 RELATED DB: BMRB REMARK 999 REMARK 999 SEQUENCE REMARK 999 CORRESPONDS TO RESIDUES 405-431 OF THE ENTRY DBREF 2IWJ A 23 49 UNP P18042 POL_HV2G1 405 431 SEQRES 1 A 27 ARG ALA PRO ARG ARG GLN GLY CYS TRP LYS CYS GLY LYS SEQRES 2 A 27 THR GLY HIS VAL MET ALA LYS CYS PRO GLU ARG GLN ALA SEQRES 3 A 27 GLY HET ZN A1050 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 1 ALA A 24 GLN A 28 5 5 HELIX 2 2 CYS A 43 ALA A 48 1 6 LINK SG CYS A 30 ZN ZN A1050 1555 1555 2.19 LINK SG CYS A 33 ZN ZN A1050 1555 1555 2.18 LINK NE2 HIS A 38 ZN ZN A1050 1555 1555 2.07 LINK SG CYS A 43 ZN ZN A1050 1555 1555 2.21 SITE 1 AC1 5 CYS A 30 CYS A 33 HIS A 38 CYS A 43 SITE 2 AC1 5 GLN A 47 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