HEADER VIRAL PROTEIN/VIRAL PROTEIN INHIBITOR 15-FEB-13 4J93 TITLE CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF HIV-1 CAPSID IN COMPLEX TITLE 2 WITH INHIBITOR BI-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GAG PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN,UNP RESIDUES 133-278; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 GENE: GAG; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS STRUCTURAL PROTEIN CAPSID, VIRAL PROTEIN, VIRAL PROTEIN-VIRAL PROTEIN KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.T.LEMKE REVDAT 4 28-FEB-24 4J93 1 REMARK REVDAT 3 09-OCT-13 4J93 1 JRNL REVDAT 2 17-JUL-13 4J93 1 JRNL REVDAT 1 10-JUL-13 4J93 0 JRNL AUTH L.LAMORTE,S.TITOLO,C.T.LEMKE,N.GOUDREAU,J.F.MERCIER, JRNL AUTH 2 E.WARDROP,V.B.SHAH,U.K.VON SCHWEDLER,C.LANGELIER,S.S.BANIK, JRNL AUTH 3 C.AIKEN,W.I.SUNDQUIST,S.W.MASON JRNL TITL DISCOVERY OF NOVEL SMALL-MOLECULE HIV-1 REPLICATION JRNL TITL 2 INHIBITORS THAT STABILIZE CAPSID COMPLEXES. JRNL REF ANTIMICROB.AGENTS CHEMOTHER. V. 57 4622 2013 JRNL REFN ISSN 0066-4804 JRNL PMID 23817385 JRNL DOI 10.1128/AAC.00985-13 REMARK 2 REMARK 2 RESOLUTION. 1.74 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7_650) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.74 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.74 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 3 NUMBER OF REFLECTIONS : 14785 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.170 REMARK 3 FREE R VALUE TEST SET COUNT : 1503 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 29.7454 - 3.8510 1.00 1374 161 0.1731 0.2089 REMARK 3 2 3.8510 - 3.0577 0.99 1293 145 0.1818 0.2182 REMARK 3 3 3.0577 - 2.6715 0.98 1248 139 0.1950 0.2350 REMARK 3 4 2.6715 - 2.4273 0.98 1248 139 0.1926 0.2418 REMARK 3 5 2.4273 - 2.2534 0.97 1229 141 0.1852 0.2281 REMARK 3 6 2.2534 - 2.1206 0.96 1222 129 0.1850 0.2137 REMARK 3 7 2.1206 - 2.0144 0.95 1189 137 0.2041 0.2748 REMARK 3 8 2.0144 - 1.9267 0.94 1180 133 0.2122 0.2704 REMARK 3 9 1.9267 - 1.8526 0.93 1146 128 0.2413 0.2899 REMARK 3 10 1.8526 - 1.7887 0.90 1140 139 0.3038 0.3584 REMARK 3 11 1.7887 - 1.7400 0.81 1013 112 0.4130 0.4215 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.72 REMARK 3 K_SOL : 0.39 REMARK 3 B_SOL : 60.01 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.080 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.58720 REMARK 3 B22 (A**2) : 2.04940 REMARK 3 B33 (A**2) : -4.63660 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.003 1231 REMARK 3 ANGLE : 0.789 1680 REMARK 3 CHIRALITY : 0.050 177 REMARK 3 PLANARITY : 0.004 217 REMARK 3 DIHEDRAL : 17.004 449 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4J93 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-FEB-13. REMARK 100 THE DEPOSITION ID IS D_1000077750. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : OSMIC HIRES2 REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15051 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.740 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 8.200 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.74 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.2 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 0.44500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22.5 % PEG8000, 0.1 M TAPS PH 9.0 AND REMARK 280 0.1 M NAOAC, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 284K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 20.38950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.63950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.24700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.63950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.38950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.24700 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 ALA A 31 77.54 41.91 REMARK 500 HIS A 87 89.51 -67.77 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 0OE A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1JR A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4E91 RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX WITH AN UNRELATED INHIBITOR REMARK 900 RELATED ID: 4E92 RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX WITH AN UNRELATED INHIBITOR DBREF 4J93 A 1 146 UNP Q79791 Q79791_9HIV1 133 278 SEQRES 1 A 146 PRO ILE VAL GLN ASN LEU GLN GLY GLN MET VAL HIS GLN SEQRES 2 A 146 ALA ILE SER PRO ARG THR LEU ASN ALA TRP VAL LYS VAL SEQRES 3 A 146 VAL GLU GLU LYS ALA PHE SER PRO GLU VAL ILE PRO MET SEQRES 4 A 146 PHE SER ALA LEU SER GLU GLY ALA THR PRO GLN ASP LEU SEQRES 5 A 146 ASN THR MET LEU ASN THR VAL GLY GLY HIS GLN ALA ALA SEQRES 6 A 146 MET GLN MET LEU LYS GLU THR ILE ASN GLU GLU ALA ALA SEQRES 7 A 146 GLU TRP ASP ARG LEU HIS PRO VAL HIS ALA GLY PRO ILE SEQRES 8 A 146 ALA PRO GLY GLN MET ARG GLU PRO ARG GLY SER ASP ILE SEQRES 9 A 146 ALA GLY THR THR SER THR LEU GLN GLU GLN ILE GLY TRP SEQRES 10 A 146 MET THR HIS ASN PRO PRO ILE PRO VAL GLY GLU ILE TYR SEQRES 11 A 146 LYS ARG TRP ILE ILE LEU GLY LEU ASN LYS ILE VAL ARG SEQRES 12 A 146 MET TYR SER HET 0OE A 201 38 HET 1JR A 202 21 HETNAM 0OE 4-{2-[5-(3-CHLOROPHENYL)-1H-PYRAZOL-4-YL]-1-[3-(1H- HETNAM 2 0OE IMIDAZOL-1-YL)PROPYL]-1H-BENZIMIDAZOL-5-YL}BENZOIC HETNAM 3 0OE ACID HETNAM 1JR (4S)-3-PHENYL-4-(PYRIDIN-3-YL)-4,5-DIHYDROPYRROLO[3,4- HETNAM 2 1JR C]PYRAZOL-6(2H)-ONE FORMUL 2 0OE C29 H23 CL N6 O2 FORMUL 3 1JR C16 H12 N4 O FORMUL 4 HOH *148(H2 O) HELIX 1 1 SER A 16 ALA A 31 1 16 HELIX 2 2 GLU A 35 SER A 44 1 10 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 HIS A 120 1 11 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 0 1.17 SITE 1 AC1 20 ARG A 18 MET A 68 TRP A 80 MET A 96 SITE 2 AC1 20 TRP A 117 HIS A 120 PRO A 122 ILE A 124 SITE 3 AC1 20 PRO A 125 ARG A 132 ARG A 143 MET A 144 SITE 4 AC1 20 TYR A 145 HOH A 302 HOH A 339 HOH A 356 SITE 5 AC1 20 HOH A 358 HOH A 359 HOH A 379 HOH A 415 SITE 1 AC2 11 ASN A 53 LEU A 56 ASN A 57 MET A 66 SITE 2 AC2 11 LYS A 70 ALA A 105 GLY A 106 THR A 107 SITE 3 AC2 11 TYR A 130 HOH A 431 HOH A 444 CRYST1 40.779 42.494 83.279 90.00 90.00 90.00 P 21 21 21 4 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 0.024522 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023533 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012008 0.00000