HEADER VIRAL PROTEIN 28-JAN-13 2M3Z TITLE NMR SOLUTION STRUCTURE OF HIV-1 NUCLEOCAPSID PROTEIN IN COMPLEX WITH TITLE 2 AN INHIBITOR DISPLAYING A 2 INHIBITORS:1 NC STOICHIOMETRY COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOCAPSID PROTEIN P7; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1; SOURCE 3 ORGANISM_COMMON: HIV-1; SOURCE 4 ORGANISM_TAXID: 11698; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET-11A KEYWDS HIV-1 NC, VIRAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR N.GOUDREAU,O.HUCKE REVDAT 4 14-JUN-23 2M3Z 1 REMARK LINK REVDAT 3 29-MAY-13 2M3Z 1 JRNL REVDAT 2 27-MAR-13 2M3Z 1 JRNL REVDAT 1 27-FEB-13 2M3Z 0 JRNL AUTH N.GOUDREAU,O.HUCKE,A.M.FAUCHER,C.GRAND-MAITRE,O.LEPAGE, JRNL AUTH 2 P.R.BONNEAU,S.W.MASON,S.TITOLO JRNL TITL DISCOVERY AND STRUCTURAL CHARACTERIZATION OF A NEW INHIBITOR JRNL TITL 2 SERIES OF HIV-1 NUCLEOCAPSID FUNCTION: NMR SOLUTION JRNL TITL 3 STRUCTURE DETERMINATION OF A TERNARY COMPLEX INVOLVING A 2:1 JRNL TITL 4 INHIBITOR/NC STOICHIOMETRY. JRNL REF J.MOL.BIOL. V. 425 1982 2013 JRNL REFN ISSN 0022-2836 JRNL PMID 23485336 JRNL DOI 10.1016/J.JMB.2013.02.022 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 8.0, AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN (AMBER), CASE, DARDEN, REMARK 3 CHEATHAM, III, SIMMERLING, WANG, DUKE, LUO, ... REMARK 3 AND KOLLMAN (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2M3Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-JAN-13. REMARK 100 THE DEPOSITION ID IS D_1000103179. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0.025 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 250 UM [U-100% 13C; U-100% 15N] REMARK 210 PROTEIN, 500 UM INHIBITOR, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCA; 3D HNCACB; 2D DQF-COSY; REMARK 210 2D 1H-1H NOESY; 2D 1H-15N HSQC; REMARK 210 3D CBCA(CO)NH; 3D HCCH-TOCSY; 3D REMARK 210 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE 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 : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 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: 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 9 -44.05 -143.21 REMARK 500 1 ARG A 10 99.34 -53.59 REMARK 500 1 LYS A 11 -59.98 66.12 REMARK 500 2 GLN A 9 -60.36 -108.95 REMARK 500 2 LYS A 11 -69.38 67.88 REMARK 500 3 GLN A 9 -38.09 -141.14 REMARK 500 3 LYS A 11 -19.87 65.54 REMARK 500 3 CYS A 49 43.35 -77.40 REMARK 500 4 ASN A 8 17.79 -66.73 REMARK 500 4 LYS A 11 -44.56 70.58 REMARK 500 4 THR A 50 -72.12 -87.74 REMARK 500 4 GLN A 53 -148.35 -86.33 REMARK 500 4 ALA A 54 27.26 -77.28 REMARK 500 5 GLN A 2 160.53 78.39 REMARK 500 5 ASN A 8 -40.97 66.30 REMARK 500 5 GLN A 9 -41.22 -139.28 REMARK 500 5 LYS A 11 -32.76 68.24 REMARK 500 5 THR A 50 -81.77 -139.41 REMARK 500 6 PHE A 6 -162.13 -79.09 REMARK 500 6 ASN A 8 8.43 -66.74 REMARK 500 6 ARG A 10 -71.31 -140.90 REMARK 500 7 ASN A 8 47.68 -76.64 REMARK 500 7 LYS A 11 -43.48 70.54 REMARK 500 7 THR A 50 -52.88 -139.99 REMARK 500 8 ARG A 7 34.20 -75.98 REMARK 500 8 ASN A 8 6.54 -69.41 REMARK 500 8 LYS A 11 -50.15 72.44 REMARK 500 9 ASN A 8 -25.44 -148.87 REMARK 500 9 GLN A 9 -37.07 -136.32 REMARK 500 9 LYS A 11 -34.78 66.83 REMARK 500 10 GLN A 9 -56.17 -147.32 REMARK 500 10 LYS A 11 -41.07 69.28 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 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 15 SG REMARK 620 2 CYS A 18 SG 112.1 REMARK 620 3 HIS A 23 NE2 98.6 101.6 REMARK 620 4 CYS A 28 SG 117.8 120.0 101.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 102 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 36 SG REMARK 620 2 CYS A 39 SG 109.2 REMARK 620 3 HIS A 44 NE2 100.4 105.1 REMARK 620 4 CYS A 49 SG 117.5 116.1 106.4 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 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1HF A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1HF A 104 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1A1T RELATED DB: PDB REMARK 900 HIV-1 NC COMPLEX WITH RNA STEM LOOP REMARK 900 RELATED ID: 1F6U RELATED DB: PDB REMARK 900 HIV-1 NC COMPLEX WITH RNA STEM LOOP REMARK 900 RELATED ID: 18980 RELATED DB: BMRB DBREF 2M3Z A 1 55 UNP P12497 POL_HV1N5 378 432 SEQRES 1 A 55 ILE GLN LYS GLY ASN PHE ARG ASN GLN ARG LYS THR VAL SEQRES 2 A 55 LYS CYS PHE ASN CYS GLY LYS GLU GLY HIS ILE ALA LYS SEQRES 3 A 55 ASN CYS ARG ALA PRO ARG LYS LYS GLY CYS TRP LYS CYS SEQRES 4 A 55 GLY LYS GLU GLY HIS GLN MET LYS ASP CYS THR GLU ARG SEQRES 5 A 55 GLN ALA ASN HET ZN A 101 1 HET ZN A 102 1 HET 1HF A 103 37 HET 1HF A 104 37 HETNAM ZN ZINC ION HETNAM 1HF (3E)-3-{(2Z)-[(5Z)-5-(FURAN-2-YLMETHYLIDENE)-4-OXO-1,3- HETNAM 2 1HF THIAZOLIDIN-2-YLIDENE]HYDRAZINYLIDENE}-2-OXO-2,3- HETNAM 3 1HF DIHYDRO-1H-INDOLE-5-SULFONIC ACID FORMUL 2 ZN 2(ZN 2+) FORMUL 4 1HF 2(C16 H10 N4 O6 S2) LINK SG CYS A 15 ZN ZN A 101 1555 1555 2.38 LINK SG CYS A 18 ZN ZN A 101 1555 1555 2.39 LINK NE2 HIS A 23 ZN ZN A 101 1555 1555 2.27 LINK SG CYS A 28 ZN ZN A 101 1555 1555 2.40 LINK SG CYS A 36 ZN ZN A 102 1555 1555 2.38 LINK SG CYS A 39 ZN ZN A 102 1555 1555 2.37 LINK NE2 HIS A 44 ZN ZN A 102 1555 1555 2.29 LINK SG CYS A 49 ZN ZN A 102 1555 1555 2.40 SITE 1 AC1 4 CYS A 15 CYS A 18 HIS A 23 CYS A 28 SITE 1 AC2 4 CYS A 36 CYS A 39 HIS A 44 CYS A 49 SITE 1 AC3 14 LYS A 3 ASN A 8 GLN A 9 VAL A 13 SITE 2 AC3 14 LYS A 14 CYS A 15 PHE A 16 ILE A 24 SITE 3 AC3 14 ALA A 25 LYS A 26 ARG A 32 TRP A 37 SITE 4 AC3 14 MET A 46 1HF A 104 SITE 1 AC4 9 ARG A 32 LYS A 33 GLY A 35 CYS A 36 SITE 2 AC4 9 TRP A 37 GLN A 45 MET A 46 LYS A 47 SITE 3 AC4 9 1HF A 103 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