HEADER VIRAL PROTEIN/DNA 08-DEC-92 1HVO TITLE ZINC-AND SEQUENCE-DEPENDENT BINDING TO NUCLEIC ACIDS BY THE N-TERMINAL TITLE 2 ZINC FINGER DOMAIN OF THE HIV-1 NUCLEOCAPSID PROTEIN: NMR STRUCTURE TITLE 3 OF THE COMPLEX WITH THE PSI-SITE 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 DNA, ZINC FINGER DOMAIN, HIV-1 NUCLEOCAPSID PROTEIN, PSI-SITE ANALOG, KEYWDS 2 VIRAL PROTEIN-DNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR T.L.SOUTH,M.F.SUMMERS REVDAT 5 22-MAY-24 1HVO 1 REMARK REVDAT 4 23-FEB-22 1HVO 1 REMARK LINK REVDAT 3 24-FEB-09 1HVO 1 VERSN REVDAT 2 01-APR-03 1HVO 1 JRNL REVDAT 1 31-JAN-94 1HVO 0 JRNL AUTH T.L.SOUTH,M.F.SUMMERS JRNL TITL ZINC- AND SEQUENCE-DEPENDENT BINDING TO NUCLEIC ACIDS BY THE JRNL TITL 2 N-TERMINAL ZINC FINGER OF THE HIV-1 NUCLEOCAPSID PROTEIN: JRNL TITL 3 NMR STRUCTURE OF THE COMPLEX WITH THE PSI-SITE ANALOG, JRNL TITL 4 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,J.W.BESS JUNIOR, REMARK 1 AUTH 2 T.L.SOUTH,P.R.BLAKE,I.SAGI,G.PEREZ-ALVARADO,R.C.SOWDER III, REMARK 1 AUTH 3 D.R.HARE,L.O.ARTHUR REMARK 1 TITL NUCLEOCAPSID ZINC FINGERS DETECTED IN RETROVIRUSES: EXAFS REMARK 1 TITL 2 STUDIES OF INTACT VIRUSES AND THE SOLUTION-STATE STRUCTURE REMARK 1 TITL 3 OF THE NUCLEOCAPSID 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 FROM THE REMARK 1 TITL 2 HIV-1 NUCLEOCAPSID PROTEIN IS STRUCTURALLY SIMILAR TO THE REMARK 1 TITL 3 N-TERMINAL ZINC FINGER 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,L.O.ARTHUR,L.E.HENDERSON, REMARK 1 AUTH 2 M.F.SUMMERS REMARK 1 TITL THE NUCLEOCAPSID PROTEIN ISOLATED FROM HIV-I PARTICLES BINDS REMARK 1 TITL 2 ZINC AND FORM RETROVIRAL-TYPE ZINC 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 : DSPACE REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE INTERNAL CONFORMATION OF THE REMARK 3 OLIGODEOXYRIBONUCLEOTIDE, D(ACGCC), WAS HELD FIXED IN AN REMARK 3 IDEALIZED A-HELICAL CONFORMATION. THE A-HELIX STRUCTURE WAS REMARK 3 GENERATED WITH QUANTA. SIMULATED ANNEALING WAS PERFORMED IN A REMARK 3 MANNER THAT ALLOWED ATOMS OF THE ZINC FINGER ONLY TO MOVE DURING REMARK 3 REFINEMENT. REMARK 4 REMARK 4 1HVO 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_1000174052. 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 : SIMULATED ANNEALING 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: THE AVERAGE PAIRWISE RMDS'S FOR THE 40 DG/SA STRUCTURES REMARK 210 (C,CA,N ATOMS OF RESIDUES A1-L51) IS 0.42 (0.07) ANGSTROMS. THE REMARK 210 AVERAGE RMS DEVIATION FOR THE 40 DG/SA STRUCTURES RELATIVE TO REMARK 210 THE MEAN COORDINATES (C,CA,N ATOMS OF RESIDUES A1-L51) IS 0.29 REMARK 210 (0.07) ANGSTROMS. 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, E 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 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 -0.123 REMARK 500 2 DA D 1 P DA D 1 OP3 -0.123 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 -0.123 REMARK 500 6 DA D 1 P DA D 1 OP3 -0.123 REMARK 500 7 DA D 1 P DA D 1 OP3 -0.124 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 -0.123 REMARK 500 12 DA D 1 P DA D 1 OP3 -0.123 REMARK 500 13 DA D 1 P DA D 1 OP3 -0.123 REMARK 500 14 DA D 1 P DA D 1 OP3 -0.123 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 DG D 3 C3' - O3' - P ANGL. DEV. = -11.9 DEGREES REMARK 500 1 DC D 4 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DC D 4 C3' - O3' - P ANGL. DEV. = -11.2 DEGREES REMARK 500 1 DC D 5 O4' - C1' - N1 ANGL. DEV. = 2.0 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 DG D 3 C3' - O3' - P ANGL. DEV. = -11.8 DEGREES REMARK 500 2 DC D 4 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DC D 4 C3' - O3' - P ANGL. DEV. = -11.3 DEGREES REMARK 500 2 DC D 5 O4' - C1' - N1 ANGL. DEV. = 2.0 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 DG D 3 C3' - O3' - P ANGL. DEV. = -11.9 DEGREES REMARK 500 3 DC D 4 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 3 DC D 4 C3' - O3' - P ANGL. DEV. = -11.2 DEGREES REMARK 500 3 DC D 5 O4' - C1' - N1 ANGL. DEV. = 2.0 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 DG D 3 C3' - O3' - P ANGL. DEV. = -11.8 DEGREES REMARK 500 4 DC D 4 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 4 DC D 4 C3' - O3' - P ANGL. DEV. = -11.3 DEGREES REMARK 500 4 DC D 5 O4' - C1' - N1 ANGL. DEV. = 2.0 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 DG D 3 C3' - O3' - P ANGL. DEV. = -11.9 DEGREES REMARK 500 5 DC D 4 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 5 DC D 4 C3' - O3' - P ANGL. DEV. = -11.3 DEGREES REMARK 500 5 DC D 5 O4' - C1' - N1 ANGL. DEV. = 2.0 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 DG D 3 C3' - O3' - P ANGL. DEV. = -11.9 DEGREES REMARK 500 6 DC D 4 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 6 DC D 4 C3' - O3' - P ANGL. DEV. = -11.2 DEGREES REMARK 500 6 DC D 5 O4' - C1' - N1 ANGL. DEV. = 2.0 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 DG D 3 C3' - O3' - P ANGL. DEV. = -11.9 DEGREES REMARK 500 7 DC D 4 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 7 DC D 4 C3' - O3' - P ANGL. DEV. = -11.2 DEGREES REMARK 500 7 DC D 5 O4' - C1' - N1 ANGL. DEV. = 2.0 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 DG D 3 C3' - O3' - P ANGL. DEV. = -11.9 DEGREES REMARK 500 8 DC D 4 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 8 DC D 4 C3' - O3' - P ANGL. DEV. = -11.2 DEGREES REMARK 500 8 DC D 5 O4' - C1' - N1 ANGL. DEV. = 2.0 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 4 HIS E 11 -177.64 -172.76 REMARK 500 5 ASN E 15 43.92 -108.61 REMARK 500 8 HIS E 11 -177.48 -173.51 REMARK 500 10 CYS E 16 -94.47 -69.93 REMARK 500 10 ARG E 17 74.83 61.29 REMARK 500 14 HIS E 11 -175.68 -172.43 REMARK 500 15 ARG E 17 21.11 -142.10 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 ANGLE, 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 LYS E 2 -10.86 REMARK 500 1 CYS E 3 -11.55 REMARK 500 2 LYS E 2 -10.28 REMARK 500 2 ILE E 12 -10.81 REMARK 500 3 LYS E 2 -10.32 REMARK 500 4 VAL E 1 -10.23 REMARK 500 4 LYS E 2 -10.36 REMARK 500 5 CYS E 3 -10.33 REMARK 500 5 ARG E 14 10.78 REMARK 500 6 LYS E 2 -11.27 REMARK 500 7 CYS E 3 -11.68 REMARK 500 8 CYS E 3 -10.73 REMARK 500 9 CYS E 3 -10.72 REMARK 500 9 ASN E 5 -11.82 REMARK 500 10 CYS E 3 -11.48 REMARK 500 11 CYS E 3 -10.86 REMARK 500 11 ASN E 15 10.25 REMARK 500 12 CYS E 3 -12.76 REMARK 500 13 CYS E 3 -10.91 REMARK 500 14 LYS E 2 -10.57 REMARK 500 14 CYS E 3 -10.71 REMARK 500 14 ILE E 12 -10.19 REMARK 500 15 CYS E 3 -12.24 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 E 19 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS E 3 SG REMARK 620 2 CYS E 6 SG 106.7 REMARK 620 3 HIS E 11 NE2 92.8 99.6 REMARK 620 4 CYS E 16 SG 124.4 108.2 121.8 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 1HVO E 1 18 UNP Q70622 GAG_HV1LW 389 406 DBREF 1HVO D 1 5 PDB 1HVO 1HVO 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 SG CYS E 3 ZN ZN E 19 1555 1555 2.31 LINK SG CYS E 6 ZN ZN E 19 1555 1555 2.30 LINK NE2 HIS E 11 ZN ZN E 19 1555 1555 2.02 LINK SG CYS E 16 ZN ZN E 19 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 MODEL 1