HEADER VIRAL PROTEIN 03-NOV-06 2E1X TITLE NMR STRUCTURE OF THE HIV-2 NUCLEOCAPSID PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: GAG-POL POLYPROTEIN (PR160GAG-POL); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: NUCLEOCAPSID PROTEIN P7, RESIDUES 23-49; COMPND 5 SYNONYM: HIV-2 NUCLEOCAPSID PROTEIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS PEPTIDE HAS BEEN CHEMICALLY SYNTHESIZED. THIS SOURCE 4 SEQUENCE OCCURS NATURALLY IN HIV-2. KEYWDS NUCLEOCAPSID PROTEIN, HIV-2, RNA RECOGNITION, ZINC FINGER, VIRAL KEYWDS 2 PROTEIN EXPDTA SOLUTION NMR NUMMDL 12 AUTHOR T.MATSUI,Y.KODERA,E.MIYAUCHI,H.TANAKA,H.ENDOH,H.KOMATSU,T.TANAKA, AUTHOR 2 T.KOHNO,T.MAEDA REVDAT 3 09-MAR-22 2E1X 1 REMARK LINK REVDAT 2 24-FEB-09 2E1X 1 VERSN REVDAT 1 05-JUN-07 2E1X 0 JRNL AUTH T.MATSUI,Y.KODERA,E.MIYAUCHI,H.TANAKA,H.ENDOH,H.KOMATSU, JRNL AUTH 2 T.TANAKA,T.KOHNO,T.MAEDA JRNL TITL STRUCTURAL ROLE OF THE SECONDARY ACTIVE DOMAIN OF HIV-2 NCP8 JRNL TITL 2 IN MULTI-FUNCTIONALITY JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 358 673 2007 JRNL REFN ISSN 0006-291X JRNL PMID 17511966 JRNL DOI 10.1016/J.BBRC.2007.04.141 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XPLOR-NIH 2.9.9, XPLOR-NIH 2.9.9 REMARK 3 AUTHORS : C.D.SCHWIETERS,J.J.KUSZEWSKI,N.TJANDRA,G.M.CLORE REMARK 3 (XPLOR-NIH), C.D.SCHWIETERS,J.J.KUSZEWSKI, REMARK 3 N.TJANDRA,G.M.CLORE (XPLOR-NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2E1X COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-NOV-06. REMARK 100 THE DEPOSITION ID IS D_1000026123. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288 REMARK 210 PH : 5.8 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 5MM PROTEIN; 5.5MM ZNCL2; 90% REMARK 210 H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : DQF-COSY; 2D TOCSY; 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : DMX 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 : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 12 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: 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: 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 O VAL A 39 H CYS A 43 1.55 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 78.66 49.25 REMARK 500 1 LYS A 32 -43.51 -149.88 REMARK 500 1 HIS A 38 152.89 172.97 REMARK 500 1 VAL A 39 -164.24 -123.29 REMARK 500 1 CYS A 43 167.29 -48.68 REMARK 500 1 GLN A 47 -89.05 55.57 REMARK 500 1 ALA A 48 62.93 62.15 REMARK 500 2 GLN A 28 85.06 55.52 REMARK 500 2 CYS A 30 173.40 -54.73 REMARK 500 2 LYS A 32 -48.09 -146.10 REMARK 500 2 HIS A 38 167.01 173.49 REMARK 500 2 GLU A 45 53.76 -99.70 REMARK 500 2 GLN A 47 36.19 -171.90 REMARK 500 3 ALA A 24 155.07 59.05 REMARK 500 3 ARG A 26 124.84 58.14 REMARK 500 3 ARG A 27 25.12 43.90 REMARK 500 3 CYS A 30 154.61 -39.99 REMARK 500 3 LYS A 32 -37.99 -159.99 REMARK 500 3 HIS A 38 163.91 172.56 REMARK 500 3 GLU A 45 34.79 38.30 REMARK 500 4 ALA A 24 108.05 57.61 REMARK 500 4 ARG A 26 -120.09 -78.73 REMARK 500 4 GLN A 28 67.94 39.73 REMARK 500 4 LYS A 32 -36.97 -157.20 REMARK 500 4 HIS A 38 132.32 173.83 REMARK 500 4 VAL A 39 -152.43 -106.11 REMARK 500 4 CYS A 43 174.47 -48.50 REMARK 500 4 GLN A 47 41.70 39.34 REMARK 500 5 ARG A 26 -74.75 60.76 REMARK 500 5 ARG A 27 163.25 -47.50 REMARK 500 5 LYS A 32 -30.19 -140.39 REMARK 500 5 THR A 36 -158.01 -107.60 REMARK 500 5 HIS A 38 -178.04 177.72 REMARK 500 5 GLU A 45 68.65 -113.50 REMARK 500 5 GLN A 47 57.49 -176.63 REMARK 500 6 ARG A 26 154.02 65.93 REMARK 500 6 ARG A 27 -97.15 41.37 REMARK 500 6 GLN A 28 68.57 -173.75 REMARK 500 6 LYS A 32 -58.97 -124.49 REMARK 500 6 HIS A 38 144.28 176.68 REMARK 500 6 VAL A 39 -167.98 -116.92 REMARK 500 6 CYS A 43 144.50 -39.83 REMARK 500 6 ARG A 46 -117.55 -58.06 REMARK 500 6 GLN A 47 62.36 -67.53 REMARK 500 7 ALA A 24 98.37 49.52 REMARK 500 7 ARG A 27 -140.49 51.84 REMARK 500 7 LYS A 32 -35.40 -141.31 REMARK 500 7 HIS A 38 164.60 165.25 REMARK 500 7 GLN A 47 70.11 49.37 REMARK 500 8 ALA A 24 -54.57 169.93 REMARK 500 REMARK 500 THIS ENTRY HAS 87 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 23 0.19 SIDE CHAIN REMARK 500 1 ARG A 26 0.12 SIDE CHAIN REMARK 500 1 ARG A 27 0.30 SIDE CHAIN REMARK 500 1 ARG A 46 0.29 SIDE CHAIN REMARK 500 2 ARG A 23 0.20 SIDE CHAIN REMARK 500 2 ARG A 26 0.31 SIDE CHAIN REMARK 500 2 ARG A 27 0.26 SIDE CHAIN REMARK 500 2 ARG A 46 0.30 SIDE CHAIN REMARK 500 3 ARG A 23 0.29 SIDE CHAIN REMARK 500 3 ARG A 26 0.28 SIDE CHAIN REMARK 500 3 ARG A 27 0.24 SIDE CHAIN REMARK 500 3 ARG A 46 0.31 SIDE CHAIN REMARK 500 4 ARG A 23 0.32 SIDE CHAIN REMARK 500 4 ARG A 26 0.31 SIDE CHAIN REMARK 500 4 ARG A 27 0.12 SIDE CHAIN REMARK 500 4 ARG A 46 0.32 SIDE CHAIN REMARK 500 5 ARG A 23 0.28 SIDE CHAIN REMARK 500 5 ARG A 26 0.31 SIDE CHAIN REMARK 500 5 ARG A 27 0.12 SIDE CHAIN REMARK 500 5 ARG A 46 0.20 SIDE CHAIN REMARK 500 6 ARG A 26 0.14 SIDE CHAIN REMARK 500 6 ARG A 46 0.21 SIDE CHAIN REMARK 500 7 ARG A 23 0.30 SIDE CHAIN REMARK 500 7 ARG A 26 0.24 SIDE CHAIN REMARK 500 7 ARG A 27 0.13 SIDE CHAIN REMARK 500 7 ARG A 46 0.28 SIDE CHAIN REMARK 500 8 ARG A 23 0.32 SIDE CHAIN REMARK 500 8 ARG A 26 0.32 SIDE CHAIN REMARK 500 8 ARG A 46 0.32 SIDE CHAIN REMARK 500 9 ARG A 23 0.21 SIDE CHAIN REMARK 500 9 ARG A 26 0.31 SIDE CHAIN REMARK 500 9 ARG A 27 0.15 SIDE CHAIN REMARK 500 9 ARG A 46 0.32 SIDE CHAIN REMARK 500 10 ARG A 23 0.20 SIDE CHAIN REMARK 500 10 ARG A 26 0.17 SIDE CHAIN REMARK 500 10 ARG A 27 0.10 SIDE CHAIN REMARK 500 10 ARG A 46 0.28 SIDE CHAIN REMARK 500 11 ARG A 26 0.32 SIDE CHAIN REMARK 500 11 ARG A 27 0.29 SIDE CHAIN REMARK 500 11 ARG A 46 0.32 SIDE CHAIN REMARK 500 12 ARG A 23 0.26 SIDE CHAIN REMARK 500 12 ARG A 26 0.28 SIDE CHAIN REMARK 500 12 ARG A 27 0.17 SIDE CHAIN REMARK 500 12 ARG A 46 0.12 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 50 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 30 SG REMARK 620 2 CYS A 33 SG 83.3 REMARK 620 3 HIS A 38 NE2 122.8 123.7 REMARK 620 4 CYS A 43 SG 50.6 101.5 134.3 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 50 DBREF 2E1X 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 A 50 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ SSBOND 1 CYS A 30 CYS A 43 1555 1555 1.97 LINK SG CYS A 30 ZN ZN A 50 1555 1555 2.30 LINK SG CYS A 33 ZN ZN A 50 1555 1555 2.30 LINK NE2 HIS A 38 ZN ZN A 50 1555 1555 2.00 LINK SG CYS A 43 ZN ZN A 50 1555 1555 2.30 SITE 1 AC1 4 CYS A 30 CYS A 33 HIS A 38 CYS A 43 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