10 20 30 40 50 60 70 80 1HVN - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER VIRAL PROTEIN/DNA 08-DEC-92 1HVN
TITLE ZINC-AND SEQUENCE-DEPENDENT BINDING TO NUCLEIC ACIDS BY THE TITLE 2 N-TERMINAL ZINC FINGER DOMAIN OF THE HIV-1 NUCLEOCAPSID TITLE 3 PROTEIN: NMR STRUCTURE OF THE COMPLEX WITH THE PSI-SITE TITLE 4 ANALOG, D/ACGCC
COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(P*AP*CP*GP*CP*C)-3'); COMPND 3 CHAIN: D; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HIV-1 NUCLEOCAPSID ZINC FINGER; COMPND 7 CHAIN: E; COMPND 8 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 5 ORGANISM_TAXID: 11676
KEYWDS VIRAL PROTEIN/DNA
EXPDTA SOLUTION NMR
NUMMDL 15
AUTHOR T.L.SOUTH,M.F.SUMMERS
REVDAT 3 24-FEB-09 1HVN 1 VERSN REVDAT 2 01-APR-03 1HVN 1 JRNL REVDAT 1 31-JAN-94 1HVN 0
JRNL AUTH T.L.SOUTH,M.F.SUMMERS JRNL TITL ZINC- AND SEQUENCE-DEPENDENT BINDING TO NUCLEIC JRNL TITL 2 ACIDS BY THE N-TERMINAL ZINC FINGER OF THE HIV-1 JRNL TITL 3 NUCLEOCAPSID PROTEIN: NMR STRUCTURE OF THE COMPLEX JRNL TITL 4 WITH THE PSI-SITE ANALOG, DACGCC. JRNL REF PROTEIN SCI. V. 2 3 1993 JRNL REFN ISSN 0961-8368 JRNL PMID 8443588
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.F.SUMMERS,L.E.HENDERSON,M.R.CHANCE, REMARK 1 AUTH 2 J.W.BESS JUNIOR,T.L.SOUTH,P.R.BLAKE,I.SAGI, REMARK 1 AUTH 3 G.PEREZ-ALVARADO,R.C.SOWDER III,D.R.HARE,L.O.ARTHUR REMARK 1 TITL NUCLEOCAPSID ZINC FINGERS DETECTED IN REMARK 1 TITL 2 RETROVIRUSES: EXAFS STUDIES OF INTACT VIRUSES AND REMARK 1 TITL 3 THE SOLUTION-STATE STRUCTURE OF THE NUCLEOCAPSID REMARK 1 TITL 4 PROTEIN FROM HIV-1 REMARK 1 REF PROTEIN SCI. V. 1 563 1992 REMARK 1 REFN ISSN 0961-8368 REMARK 1 REFERENCE 2 REMARK 1 AUTH T.L.SOUTH,P.R.BLAKE,D.R.HARE,M.F.SUMMERS REMARK 1 TITL THE C-TERMINAL RETROVIRAL-TYPE ZINC FINGER DOMAIN REMARK 1 TITL 2 FROM THE HIV-1 NUCLEOCAPSID PROTEIN IS REMARK 1 TITL 3 STRUCTURALLY SIMILAR TO THE N-TERMINAL ZINC FINGER REMARK 1 TITL 4 DOMAIN REMARK 1 REF BIOCHEMISTRY V. 30 6342 1991 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 3 REMARK 1 AUTH T.L.SOUTH,P.R.BLAKE,R.SOWDER III,L.O.ARTHUR, REMARK 1 AUTH 2 L.E.HENDERSON,M.F.SUMMERS REMARK 1 TITL THE NUCLEOCAPSID PROTEIN ISOLATED FROM HIV-I REMARK 1 TITL 2 PARTICLES BINDS ZINC AND FORM RETROVIRAL-TYPE ZINC REMARK 1 TITL 3 FINGERS REMARK 1 REF BIOCHEMISTRY V. 29 7786 1990 REMARK 1 REFN ISSN 0006-2960
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1HVN COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : NULL REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 1 DA D 1 P DA D 1 OP3 -0.124 REMARK 500 2 DA D 1 P DA D 1 OP3 -0.124 REMARK 500 3 DA D 1 P DA D 1 OP3 -0.123 REMARK 500 4 DA D 1 P DA D 1 OP3 -0.123 REMARK 500 5 DA D 1 P DA D 1 OP3 -0.122 REMARK 500 6 DA D 1 P DA D 1 OP3 -0.123 REMARK 500 7 DA D 1 P DA D 1 OP3 -0.123 REMARK 500 8 DA D 1 P DA D 1 OP3 -0.123 REMARK 500 9 DA D 1 P DA D 1 OP3 -0.123 REMARK 500 10 DA D 1 P DA D 1 OP3 -0.123 REMARK 500 11 DA D 1 P DA D 1 OP3 -0.124 REMARK 500 12 DA D 1 P DA D 1 OP3 -0.123 REMARK 500 13 DA D 1 P DA D 1 OP3 -0.124 REMARK 500 14 DA D 1 P DA D 1 OP3 -0.122 REMARK 500 15 DA D 1 P DA D 1 OP3 -0.123 REMARK 500 REMARK 500 REMARK: NULL 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 DA D 1 C3' - O3' - P ANGL. DEV. = -11.9 DEGREES REMARK 500 1 DC D 2 C3' - O3' - P ANGL. DEV. = -12.0 DEGREES REMARK 500 1 DC D 4 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DG D 3 C3' - O3' - P ANGL. DEV. = -11.8 DEGREES REMARK 500 1 DC D 5 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DC D 4 C3' - O3' - P ANGL. DEV. = -11.2 DEGREES REMARK 500 2 DA D 1 C3' - O3' - P ANGL. DEV. = -11.9 DEGREES REMARK 500 2 DC D 2 C3' - O3' - P ANGL. DEV. = -12.0 DEGREES REMARK 500 2 DC D 4 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DG D 3 C3' - O3' - P ANGL. DEV. = -11.9 DEGREES REMARK 500 2 DC D 5 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DC D 4 C3' - O3' - P ANGL. DEV. = -11.3 DEGREES REMARK 500 3 DA D 1 C3' - O3' - P ANGL. DEV. = -11.9 DEGREES REMARK 500 3 DC D 2 C3' - O3' - P ANGL. DEV. = -12.0 DEGREES REMARK 500 3 DC D 4 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 3 DG D 3 C3' - O3' - P ANGL. DEV. = -11.9 DEGREES REMARK 500 3 DC D 5 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 3 DC D 4 C3' - O3' - P ANGL. DEV. = -11.2 DEGREES REMARK 500 4 DA D 1 C3' - O3' - P ANGL. DEV. = -11.9 DEGREES REMARK 500 4 DC D 2 C3' - O3' - P ANGL. DEV. = -12.0 DEGREES REMARK 500 4 DC D 4 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 4 DG D 3 C3' - O3' - P ANGL. DEV. = -11.9 DEGREES REMARK 500 4 DC D 5 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 4 DC D 4 C3' - O3' - P ANGL. DEV. = -11.2 DEGREES REMARK 500 5 DA D 1 C3' - O3' - P ANGL. DEV. = -11.9 DEGREES REMARK 500 5 DC D 2 C3' - O3' - P ANGL. DEV. = -12.0 DEGREES REMARK 500 5 DC D 4 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 5 DG D 3 C3' - O3' - P ANGL. DEV. = -11.9 DEGREES REMARK 500 5 DC D 5 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 5 DC D 4 C3' - O3' - P ANGL. DEV. = -11.2 DEGREES REMARK 500 6 DA D 1 C3' - O3' - P ANGL. DEV. = -11.9 DEGREES REMARK 500 6 DC D 2 C3' - O3' - P ANGL. DEV. = -12.1 DEGREES REMARK 500 6 DC D 4 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 6 DG D 3 C3' - O3' - P ANGL. DEV. = -11.9 DEGREES REMARK 500 6 DC D 5 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 6 DC D 4 C3' - O3' - P ANGL. DEV. = -11.2 DEGREES REMARK 500 7 DA D 1 C3' - O3' - P ANGL. DEV. = -11.9 DEGREES REMARK 500 7 DC D 2 C3' - O3' - P ANGL. DEV. = -12.0 DEGREES REMARK 500 7 DC D 4 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 7 DG D 3 C3' - O3' - P ANGL. DEV. = -11.9 DEGREES REMARK 500 7 DC D 5 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 7 DC D 4 C3' - O3' - P ANGL. DEV. = -11.2 DEGREES REMARK 500 8 DA D 1 C3' - O3' - P ANGL. DEV. = -11.9 DEGREES REMARK 500 8 DC D 2 C3' - O3' - P ANGL. DEV. = -12.0 DEGREES REMARK 500 8 DC D 4 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 8 DG D 3 C3' - O3' - P ANGL. DEV. = -11.9 DEGREES REMARK 500 8 DC D 5 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 8 DC D 4 C3' - O3' - P ANGL. DEV. = -11.2 DEGREES REMARK 500 9 DA D 1 C3' - O3' - P ANGL. DEV. = -11.9 DEGREES REMARK 500 9 DC D 2 C3' - O3' - P ANGL. DEV. = -12.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 91 ANGLE DEVIATIONS. 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 CYS E 16 -147.94 -65.21 REMARK 500 1 ARG E 17 -38.36 177.65 REMARK 500 2 CYS E 16 -117.70 -78.86 REMARK 500 2 ARG E 17 -73.09 170.71 REMARK 500 3 ARG E 17 29.48 -159.41 REMARK 500 4 ARG E 14 -8.73 -59.89 REMARK 500 7 CYS E 16 -72.00 -72.58 REMARK 500 7 ARG E 17 -54.86 78.30 REMARK 500 10 ARG E 14 -8.19 -59.99 REMARK 500 12 ARG E 14 -9.37 -59.61 REMARK 500 13 ARG E 14 -8.27 -59.68 REMARK 500 14 ARG E 17 28.26 -145.75 REMARK 500 15 ARG E 17 28.40 -148.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 1 CYS E 3 -13.76 REMARK 500 1 PHE E 4 -10.95 REMARK 500 1 ILE E 12 -13.16 REMARK 500 2 CYS E 3 -12.83 REMARK 500 2 HIS E 11 11.54 REMARK 500 2 ILE E 12 -14.39 REMARK 500 2 ARG E 17 10.45 REMARK 500 3 CYS E 3 -12.22 REMARK 500 3 PHE E 4 -10.09 REMARK 500 3 HIS E 11 13.01 REMARK 500 3 ILE E 12 -13.84 REMARK 500 4 CYS E 3 -11.75 REMARK 500 4 ILE E 12 -13.80 REMARK 500 5 CYS E 3 -10.93 REMARK 500 5 ILE E 12 -14.01 REMARK 500 6 CYS E 3 -11.92 REMARK 500 6 ILE E 12 -15.55 REMARK 500 7 CYS E 3 -11.22 REMARK 500 7 ILE E 12 -13.93 REMARK 500 7 CYS E 16 13.19 REMARK 500 8 VAL E 1 -12.01 REMARK 500 8 HIS E 11 11.73 REMARK 500 8 ILE E 12 -16.01 REMARK 500 9 CYS E 3 -11.10 REMARK 500 9 ILE E 12 -15.33 REMARK 500 10 CYS E 3 -12.07 REMARK 500 10 HIS E 11 12.37 REMARK 500 10 ILE E 12 -13.94 REMARK 500 11 CYS E 3 -13.08 REMARK 500 11 HIS E 11 10.80 REMARK 500 11 ILE E 12 -15.39 REMARK 500 12 CYS E 3 -13.40 REMARK 500 12 HIS E 11 11.02 REMARK 500 12 ILE E 12 -15.14 REMARK 500 13 CYS E 3 -14.24 REMARK 500 13 ASN E 5 -10.39 REMARK 500 13 HIS E 11 10.38 REMARK 500 13 ILE E 12 -14.70 REMARK 500 14 CYS E 3 -13.66 REMARK 500 14 ILE E 12 -12.78 REMARK 500 15 CYS E 3 -12.49 REMARK 500 15 HIS E 11 11.15 REMARK 500 15 ILE E 12 -15.38 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 E 19 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS E 6 SG REMARK 620 2 CYS E 3 SG 106.3 REMARK 620 3 HIS E 11 NE2 109.3 92.9 REMARK 620 4 CYS E 16 SG 108.9 115.0 122.7 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 E 19
DBREF 1HVN E 1 18 UNP Q70622 GAG_HV1LW 389 406 DBREF 1HVN D 1 5 PDB 1HVN 1HVN 1 5
SEQRES 1 D 5 DA DC DG DC DC SEQRES 1 E 18 VAL LYS CYS PHE ASN CYS GLY LYS GLU GLY HIS ILE ALA SEQRES 2 E 18 ARG ASN CYS ARG ALA
HET ZN E 19 1
HETNAM ZN ZINC ION
FORMUL 3 ZN ZN 2+
HELIX 1 1 ILE E 12 CYS E 16 5 5
LINK ZN ZN E 19 SG CYS E 6 1555 1555 2.30 LINK ZN ZN E 19 SG CYS E 3 1555 1555 2.31 LINK ZN ZN E 19 NE2 HIS E 11 1555 1555 2.02 LINK ZN ZN E 19 SG CYS E 16 1555 1555 2.30
SITE 1 AC1 4 CYS E 3 CYS E 6 HIS E 11 CYS E 16
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