HEADER VIRAL PROTEIN 22-MAY-07 2JPR
TITLE JOINT REFINEMENT OF THE HIV-1 CA-NTD IN COMPLEX WITH THE ASSEMBLY
TITLE 2 INHIBITOR CAP-1
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: GAG-POL POLYPROTEIN;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: SEQUENCE DATABASE RESIDUES, 133-277;
COMPND 5 SYNONYM: PR160GAG-POL;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (NEW YORK-5
SOURCE 3 ISOLATE);
SOURCE 4 ORGANISM_TAXID: 11698;
SOURCE 5 GENE: GAG-POL;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PLN4-3
KEYWDS CAP-1, CAPSID, HIV-1, ASSEMBLY INHIBITOR, VIRAL PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR B.N.KELLY,S.KYERE,I.KINDE,C.TANG,B.R.HOWARD,H.ROBINSON,W.I.SUNDQUIST,
AUTHOR 2 M.F.SUMMERS,C.P.HILL
REVDAT 4 29-MAY-24 2JPR 1 REMARK
REVDAT 3 09-MAR-22 2JPR 1 REMARK
REVDAT 2 24-FEB-09 2JPR 1 VERSN
REVDAT 1 09-OCT-07 2JPR 0
JRNL AUTH B.N.KELLY,S.KYERE,I.KINDE,C.TANG,B.R.HOWARD,H.ROBINSON,
JRNL AUTH 2 W.I.SUNDQUIST,M.F.SUMMERS,C.P.HILL
JRNL TITL STRUCTURE OF THE ANTIVIRAL ASSEMBLY INHIBITOR CAP-1 COMPLEX
JRNL TITL 2 WITH THE HIV-1 CA PROTEIN
JRNL REF J.MOL.BIOL. V. 373 355 2007
JRNL REFN ISSN 0022-2836
JRNL PMID 17826792
JRNL DOI 10.1016/J.JMB.2007.07.070
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : AMBER 9.0
REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG,
REMARK 3 DUKE, LUO, AND KOLL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS:
REMARK 3 THE STRUCTURE OF THE "BOUND" CONFORMATION OF THE HIV-1 CAPSID
REMARK 3 PROTEIN (IN THE
REMARK 3 PRESENCE OF THE LIGAND) WAS OBTAINED FROM THE CRYSTAL. THE
REMARK 3 COMPLEX WAS
REMARK 3 CALCULATED USING NMR DISTANCE RESTRAINTS IN REFERENCE TO THE BOUND
REMARK 3 CONFORMATION OF THE CAPSID PROTEIN. REFINEMENT WAS PERFORMED
REMARK 3 USING SIMULATED
REMARK 3 MOLECULAR DYNAMICS IN AMBER 9.0.
REMARK 4
REMARK 4 2JPR COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-MAY-07.
REMARK 100 THE DEPOSITION ID IS D_1000100135.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 308
REMARK 210 PH : 7.0
REMARK 210 IONIC STRENGTH : 25
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 100-700 UM [U-15N] SODIUM
REMARK 210 PHOSPHATE, 100% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ
REMARK 210 SPECTROMETER MODEL : AMX
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NMRVIEW, NMRPIPE
REMARK 210 METHOD USED : MOLECULAR DYNAMICS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 20
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20
REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES
REMARK 210 SUBMITTED
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: 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 TYR A 145 C TYR A 145 OXT 0.648
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 7 ARG A 100 0.08 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2PXR RELATED DB: PDB
REMARK 900 HIV-1 CA146 IN THE PRESENCE OF CAP-1
REMARK 900 RELATED ID: 2PWM RELATED DB: PDB
REMARK 900 HIV-1 CA146 A92E REAL CELL
REMARK 900 RELATED ID: 2PWO RELATED DB: PDB
REMARK 900 HIV-1 CA146 A92E PSUEDO CELL
DBREF 2JPR A 1 145 UNP P12497 POL_HV1N5 133 277
SEQRES 1 A 145 PRO ILE VAL GLN ASN LEU GLN GLY GLN MET VAL HIS GLN
SEQRES 2 A 145 ALA ILE SER PRO ARG THR LEU ASN ALA TRP VAL LYS VAL
SEQRES 3 A 145 VAL GLU GLU LYS ALA PHE SER PRO GLU VAL ILE PRO MET
SEQRES 4 A 145 PHE SER ALA LEU SER GLU GLY ALA THR PRO GLN ASP LEU
SEQRES 5 A 145 ASN THR MET LEU ASN THR VAL GLY GLY HIS GLN ALA ALA
SEQRES 6 A 145 MET GLN MET LEU LYS GLU THR ILE ASN GLU GLU ALA ALA
SEQRES 7 A 145 GLU TRP ASP ARG LEU HIS PRO VAL HIS ALA GLY PRO ILE
SEQRES 8 A 145 ALA PRO GLY GLN MET ARG GLU PRO ARG GLY SER ASP ILE
SEQRES 9 A 145 ALA GLY THR THR SER THR LEU GLN GLU GLN ILE GLY TRP
SEQRES 10 A 145 MET THR HIS ASN PRO PRO ILE PRO VAL GLY GLU ILE TYR
SEQRES 11 A 145 LYS ARG TRP ILE ILE LEU GLY LEU ASN LYS ILE VAL ARG
SEQRES 12 A 145 MET TYR
HET JPR A 146 50
HETNAM JPR 1-(3-CHLORO-4-METHYLPHENYL)-3-{2-[({5-[(DIMETHYLAMINO)
HETNAM 2 JPR METHYL]-2-FURYL}METHYL)THIO]ETHYL}UREA
FORMUL 2 JPR C18 H24 CL N3 O2 S
HELIX 1 1 SER A 16 ALA A 31 1 16
HELIX 2 2 GLU A 35 LEU A 43 1 9
HELIX 3 3 THR A 48 THR A 58 1 11
HELIX 4 4 HIS A 62 HIS A 84 1 23
HELIX 5 5 ARG A 100 ALA A 105 1 6
HELIX 6 6 THR A 110 THR A 119 1 10
HELIX 7 7 PRO A 125 TYR A 145 1 21
SHEET 1 A 2 ILE A 2 GLN A 4 0
SHEET 2 A 2 MET A 10 HIS A 12 -1 O VAL A 11 N VAL A 3
CISPEP 1 ASN A 121 PRO A 122 1 -6.59
CISPEP 2 ASN A 121 PRO A 122 2 -6.77
CISPEP 3 ASN A 121 PRO A 122 3 -6.61
CISPEP 4 ASN A 121 PRO A 122 4 -6.64
CISPEP 5 ASN A 121 PRO A 122 5 -6.60
CISPEP 6 ASN A 121 PRO A 122 6 -6.66
CISPEP 7 ASN A 121 PRO A 122 7 -6.58
CISPEP 8 ASN A 121 PRO A 122 8 -6.68
CISPEP 9 ASN A 121 PRO A 122 9 -6.68
CISPEP 10 ASN A 121 PRO A 122 10 -6.64
CISPEP 11 ASN A 121 PRO A 122 11 -6.62
CISPEP 12 ASN A 121 PRO A 122 12 -6.62
CISPEP 13 ASN A 121 PRO A 122 13 -6.62
CISPEP 14 ASN A 121 PRO A 122 14 -6.64
CISPEP 15 ASN A 121 PRO A 122 15 -6.68
CISPEP 16 ASN A 121 PRO A 122 16 -6.60
CISPEP 17 ASN A 121 PRO A 122 17 -6.64
CISPEP 18 ASN A 121 PRO A 122 18 -6.65
CISPEP 19 ASN A 121 PRO A 122 19 -6.65
CISPEP 20 ASN A 121 PRO A 122 20 -6.69
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