HEADER VIRAL PROTEIN 14-MAY-98 1NC8 TITLE HIGH-RESOLUTION SOLUTION NMR STRUCTURE OF THE MINIMAL ACTIVE DOMAIN OF TITLE 2 THE HUMAN IMMUNODEFICIENCY VIRUS TYPE-2 NUCLEOCAPSID PROTEIN, 15 TITLE 3 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOCAPSID PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-29; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 2; SOURCE 3 ORGANISM_TAXID: 11709 KEYWDS NUCLEOCAPSID PROTEIN, HIV-2, RNA RECOGNITION, ZINC FINGER, VIRAL KEYWDS 2 PROTEIN EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR Y.KODERA,K.SATO,T.TSUKAHARA,H.KOMATSU,T.MAEDA,T.KOHNO REVDAT 4 06-NOV-24 1NC8 1 REMARK REVDAT 3 23-FEB-22 1NC8 1 REMARK LINK REVDAT 2 24-FEB-09 1NC8 1 VERSN REVDAT 1 25-MAY-99 1NC8 0 JRNL AUTH Y.KODERA,K.SATO,T.TSUKAHARA,H.KOMATSU,T.MAEDA,T.KOHNO JRNL TITL HIGH-RESOLUTION SOLUTION NMR STRUCTURE OF THE MINIMAL ACTIVE JRNL TITL 2 DOMAIN OF THE HUMAN IMMUNODEFICIENCY VIRUS TYPE-2 JRNL TITL 3 NUCLEOCAPSID PROTEIN. JRNL REF BIOCHEMISTRY V. 37 17704 1998 JRNL REFN ISSN 0006-2960 JRNL PMID 9922136 JRNL DOI 10.1021/BI981818O REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1NC8 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_1000175223. 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 : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; COSY; TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : DMX500 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR 3.1 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL 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: 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 HE1 HIS A 17 ZN ZN A 30 1.20 REMARK 500 NE2 HIS A 17 SG CYS A 22 2.02 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 3 76.23 44.62 REMARK 500 1 ASN A 11 -76.93 -41.00 REMARK 500 1 ALA A 24 -74.72 -74.86 REMARK 500 1 ARG A 27 85.69 -178.79 REMARK 500 2 ARG A 4 76.50 177.21 REMARK 500 2 CYS A 9 109.63 -41.78 REMARK 500 2 ASN A 11 -79.29 -38.91 REMARK 500 2 ALA A 24 -72.86 -81.00 REMARK 500 2 ARG A 27 105.88 174.81 REMARK 500 3 LYS A 5 -96.77 -96.08 REMARK 500 3 VAL A 6 176.86 49.02 REMARK 500 3 CYS A 9 98.88 -41.05 REMARK 500 3 ASN A 11 -79.12 -39.79 REMARK 500 3 ALA A 24 -77.20 -71.57 REMARK 500 3 ARG A 27 100.02 166.61 REMARK 500 4 GLN A 2 -140.92 -71.91 REMARK 500 4 CYS A 9 97.30 -48.43 REMARK 500 4 ALA A 24 -76.50 -87.37 REMARK 500 4 ARG A 27 95.45 169.46 REMARK 500 4 GLN A 28 15.89 59.91 REMARK 500 5 GLN A 3 72.21 65.32 REMARK 500 5 ARG A 4 85.88 -163.43 REMARK 500 5 CYS A 9 108.32 -43.00 REMARK 500 5 ALA A 24 -82.08 -72.96 REMARK 500 5 ARG A 27 95.93 164.17 REMARK 500 6 LYS A 5 96.61 55.09 REMARK 500 6 CYS A 9 98.90 -45.77 REMARK 500 6 ALA A 24 -77.91 -72.02 REMARK 500 6 ARG A 27 103.80 171.14 REMARK 500 7 GLN A 2 61.57 -113.57 REMARK 500 7 LYS A 5 -43.20 -142.19 REMARK 500 7 CYS A 9 93.89 -39.91 REMARK 500 7 ALA A 24 -80.05 -68.12 REMARK 500 7 ARG A 27 113.55 172.21 REMARK 500 8 GLN A 2 151.67 176.39 REMARK 500 8 LYS A 5 143.09 168.23 REMARK 500 8 VAL A 6 155.42 -43.07 REMARK 500 8 CYS A 9 101.55 -43.22 REMARK 500 8 ALA A 24 -80.82 -82.16 REMARK 500 8 ARG A 27 100.92 172.87 REMARK 500 9 VAL A 6 166.83 54.49 REMARK 500 9 ALA A 24 -93.91 -68.65 REMARK 500 9 ARG A 27 103.14 175.62 REMARK 500 10 CYS A 9 97.96 -34.50 REMARK 500 10 ALA A 24 -78.52 -65.37 REMARK 500 10 ARG A 27 111.44 178.31 REMARK 500 11 ARG A 4 159.03 64.92 REMARK 500 11 GLU A 15 137.13 -32.20 REMARK 500 11 CYS A 22 96.65 -54.94 REMARK 500 11 ALA A 24 -76.63 -74.42 REMARK 500 REMARK 500 THIS ENTRY HAS 74 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 4 0.32 SIDE CHAIN REMARK 500 1 ARG A 8 0.27 SIDE CHAIN REMARK 500 1 ARG A 20 0.28 SIDE CHAIN REMARK 500 1 ARG A 23 0.18 SIDE CHAIN REMARK 500 1 ARG A 26 0.31 SIDE CHAIN REMARK 500 1 ARG A 27 0.31 SIDE CHAIN REMARK 500 2 ARG A 4 0.23 SIDE CHAIN REMARK 500 2 ARG A 8 0.31 SIDE CHAIN REMARK 500 2 ARG A 20 0.20 SIDE CHAIN REMARK 500 2 ARG A 23 0.21 SIDE CHAIN REMARK 500 2 ARG A 26 0.31 SIDE CHAIN REMARK 500 2 ARG A 27 0.18 SIDE CHAIN REMARK 500 3 ARG A 8 0.27 SIDE CHAIN REMARK 500 3 ARG A 20 0.18 SIDE CHAIN REMARK 500 3 ARG A 26 0.28 SIDE CHAIN REMARK 500 3 ARG A 27 0.25 SIDE CHAIN REMARK 500 4 ARG A 4 0.20 SIDE CHAIN REMARK 500 4 ARG A 8 0.27 SIDE CHAIN REMARK 500 4 ARG A 20 0.20 SIDE CHAIN REMARK 500 4 ARG A 26 0.32 SIDE CHAIN REMARK 500 4 ARG A 27 0.15 SIDE CHAIN REMARK 500 5 ARG A 8 0.28 SIDE CHAIN REMARK 500 5 ARG A 20 0.29 SIDE CHAIN REMARK 500 5 ARG A 23 0.24 SIDE CHAIN REMARK 500 5 ARG A 27 0.09 SIDE CHAIN REMARK 500 6 ARG A 4 0.25 SIDE CHAIN REMARK 500 6 ARG A 8 0.31 SIDE CHAIN REMARK 500 6 ARG A 20 0.18 SIDE CHAIN REMARK 500 6 ARG A 23 0.27 SIDE CHAIN REMARK 500 6 ARG A 27 0.22 SIDE CHAIN REMARK 500 7 ARG A 4 0.20 SIDE CHAIN REMARK 500 7 ARG A 8 0.29 SIDE CHAIN REMARK 500 7 ARG A 20 0.21 SIDE CHAIN REMARK 500 7 ARG A 23 0.31 SIDE CHAIN REMARK 500 7 ARG A 26 0.11 SIDE CHAIN REMARK 500 7 ARG A 27 0.22 SIDE CHAIN REMARK 500 8 ARG A 4 0.11 SIDE CHAIN REMARK 500 8 ARG A 8 0.21 SIDE CHAIN REMARK 500 8 ARG A 20 0.22 SIDE CHAIN REMARK 500 8 ARG A 23 0.27 SIDE CHAIN REMARK 500 8 ARG A 27 0.32 SIDE CHAIN REMARK 500 9 ARG A 4 0.30 SIDE CHAIN REMARK 500 9 ARG A 8 0.23 SIDE CHAIN REMARK 500 9 ARG A 20 0.22 SIDE CHAIN REMARK 500 9 ARG A 23 0.32 SIDE CHAIN REMARK 500 9 ARG A 26 0.12 SIDE CHAIN REMARK 500 9 ARG A 27 0.32 SIDE CHAIN REMARK 500 10 ARG A 4 0.27 SIDE CHAIN REMARK 500 10 ARG A 8 0.32 SIDE CHAIN REMARK 500 10 ARG A 20 0.30 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 81 PLANE DEVIATIONS. 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 30 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 9 SG REMARK 620 2 CYS A 12 SG 86.9 REMARK 620 3 HIS A 17 CE1 96.3 174.7 REMARK 620 4 HIS A 17 NE2 69.3 144.0 41.3 REMARK 620 5 CYS A 22 SG 68.4 91.2 93.9 55.5 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: ZNB REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: CCHC ZINC FINGER. REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 30 DBREF 1NC8 A 1 29 UNP P18042 POL_HV2G1 384 412 SEQRES 1 A 29 ALA GLN GLN ARG LYS VAL ILE ARG CYS TRP ASN CYS GLY SEQRES 2 A 29 LYS GLU GLY HIS SER ALA ARG GLN CYS ARG ALA PRO ARG SEQRES 3 A 29 ARG GLN GLY HET ZN A 30 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 1 ALA A 19 GLN A 21 5 3 SSBOND 1 CYS A 9 CYS A 22 1555 1555 2.59 LINK SG CYS A 9 ZN ZN A 30 1555 1555 2.30 LINK SG CYS A 12 ZN ZN A 30 1555 1555 2.30 LINK CE1 HIS A 17 ZN ZN A 30 1555 1555 1.72 LINK NE2 HIS A 17 ZN ZN A 30 1555 1555 2.00 LINK SG CYS A 22 ZN ZN A 30 1555 1555 2.30 SITE 1 ZNB 14 CYS A 9 TRP A 10 ASN A 11 CYS A 12 SITE 2 ZNB 14 GLY A 13 LYS A 14 GLU A 15 GLY A 16 SITE 3 ZNB 14 HIS A 17 SER A 18 ALA A 19 ARG A 20 SITE 4 ZNB 14 GLN A 21 CYS A 22 SITE 1 AC1 5 CYS A 9 CYS A 12 LYS A 14 HIS A 17 SITE 2 AC1 5 CYS A 22 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