10 20 30 40 50 60 70 80 2E1X - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER 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 SOURCE 4 SYNTHESIZED. THIS SEQUENCE OCCURS NATURALLY IN HIV-2.
KEYWDS NUCLEOCAPSID PROTEIN, HIV-2, RNA RECOGNITION, ZINC FINGER, KEYWDS 2 VIRAL PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 12
AUTHOR T.MATSUI,Y.KODERA,E.MIYAUCHI,H.TANAKA,H.ENDOH,H.KOMATSU, AUTHOR 2 T.TANAKA,T.KOHNO,T.MAEDA
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, JRNL AUTH 2 H.KOMATSU,T.TANAKA,T.KOHNO,T.MAEDA JRNL TITL STRUCTURAL ROLE OF THE SECONDARY ACTIVE DOMAIN OF JRNL TITL 2 HIV-2 NCP8 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 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XPLOR-NIH 2.9.9 REMARK 3 AUTHORS : C.D.SCHWIETERS,J.J.KUSZEWSKI,N.TJANDRA,G.M.CLORE 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 RCSB ID CODE IS RCSB026123.
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 : XPLOR-NIH 2.9.9 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 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 8 ARG A 26 135.47 64.14 REMARK 500 8 ARG A 27 -152.79 47.40 REMARK 500 8 HIS A 38 161.52 177.10 REMARK 500 8 ARG A 46 -158.12 -102.91 REMARK 500 8 ALA A 48 60.24 -69.61 REMARK 500 9 ARG A 26 -156.93 51.28 REMARK 500 9 ARG A 27 151.53 -43.71 REMARK 500 9 LYS A 32 13.26 -153.47 REMARK 500 9 HIS A 38 149.33 167.89 REMARK 500 9 VAL A 39 -161.27 -122.19 REMARK 500 9 GLU A 45 -42.14 -130.76 REMARK 500 9 ARG A 46 49.75 20.03 REMARK 500 9 GLN A 47 29.92 41.92 REMARK 500 10 ALA A 24 171.90 57.22 REMARK 500 10 GLN A 28 61.82 62.69 REMARK 500 10 LYS A 32 -62.79 -108.59 REMARK 500 10 HIS A 38 156.13 175.59 REMARK 500 10 VAL A 39 -166.73 -126.64 REMARK 500 10 PRO A 44 48.34 -82.39 REMARK 500 10 GLU A 45 -3.71 74.36 REMARK 500 10 ARG A 46 149.51 57.17 REMARK 500 10 GLN A 47 59.71 30.30 REMARK 500 10 ALA A 48 -52.85 -129.57 REMARK 500 11 ALA A 24 73.03 40.29 REMARK 500 11 ARG A 26 -100.51 50.44 REMARK 500 11 GLN A 28 56.99 32.73 REMARK 500 11 LYS A 32 -37.39 -144.37 REMARK 500 11 HIS A 38 153.09 177.25 REMARK 500 11 PRO A 44 41.17 -84.80 REMARK 500 11 GLU A 45 -22.45 78.77 REMARK 500 12 ALA A 24 147.71 177.82 REMARK 500 12 PRO A 25 46.03 -76.59 REMARK 500 12 ARG A 26 -79.79 59.32 REMARK 500 12 GLN A 28 108.19 70.14 REMARK 500 12 LYS A 32 1.64 -158.11 REMARK 500 12 HIS A 38 176.40 176.26 REMARK 500 12 GLN A 47 30.50 -176.13 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 1 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 CYS A 43 SG 50.6 101.5 REMARK 620 4 HIS A 38 NE2 122.8 123.7 134.3 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 ZN ZN A 50 SG CYS A 30 1555 1555 2.30 LINK ZN ZN A 50 SG CYS A 33 1555 1555 2.30 LINK ZN ZN A 50 SG CYS A 43 1555 1555 2.30 LINK ZN ZN A 50 NE2 HIS A 38 1555 1555 2.00
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