HEADER VIRAL PROTEIN 22-AUG-14 4R61 TITLE CRYSTAL STRUCTURE OF A RATIONALLY DESIGNED SINGLE-CHAIN PROTEIN TITLE 2 MIMICKING A TRIMERIC GP41 N-TERMINAL HEPTAD-REPEAT REGION COMPND MOL_ID: 1; COMPND 2 MOLECULE: GP41-BASED CONSTRUCT COVNHR3-ABC; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_COMMON: HIV-1; SOURCE 4 ORGANISM_TAXID: 11676; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COILED-COIL, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.CAMARA-ARTIGAS,F.CONEJERO-LARA,S.CRESPILLO,S.CASARES REVDAT 4 20-SEP-23 4R61 1 REMARK REVDAT 3 14-JAN-15 4R61 1 JRNL REVDAT 2 24-DEC-14 4R61 1 JRNL REVDAT 1 10-DEC-14 4R61 0 JRNL AUTH S.CRESPILLO,A.CAMARA-ARTIGAS,S.CASARES,B.MOREL,E.S.COBOS, JRNL AUTH 2 P.L.MATEO,N.MOUZ,C.E.MARTIN,M.G.ROGER,R.EL HABIB,B.SU, JRNL AUTH 3 C.MOOG,F.CONEJERO-LARA JRNL TITL SINGLE-CHAIN PROTEIN MIMETICS OF THE N-TERMINAL JRNL TITL 2 HEPTAD-REPEAT REGION OF GP41 WITH POTENTIAL AS ANTI-HIV-1 JRNL TITL 3 DRUGS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 111 18207 2014 JRNL REFN ISSN 0027-8424 JRNL PMID 25489108 JRNL DOI 10.1073/PNAS.1413592112 REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.4_1496 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) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.910 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 3211 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.247 REMARK 3 FREE R VALUE : 0.289 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.540 REMARK 3 FREE R VALUE TEST SET COUNT : 314 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 17.8029 - 3.8990 0.98 2712 162 0.2165 0.2730 REMARK 3 2 3.8990 - 3.1000 0.95 2642 152 0.2922 0.3117 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.830 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 44.52 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 72.45 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.005 1147 REMARK 3 ANGLE : 0.586 1538 REMARK 3 CHIRALITY : 0.027 179 REMARK 3 PLANARITY : 0.002 201 REMARK 3 DIHEDRAL : 14.109 456 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 4R61 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-AUG-14. REMARK 100 THE DEPOSITION ID IS D_1000086943. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-FEB-14; 24-OCT-13 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : ESRF; ALBA REMARK 200 BEAMLINE : ID29; XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.96869; 0.97926 REMARK 200 MONOCHROMATOR : LIQUID NITROGEN-COOLED CHANNEL REMARK 200 -CUT SI(111); CHANNEL-CUT SI(111) REMARK 200 OPTICS : CYLINDRICAL GRAZING INCIDENCE REMARK 200 MIRROR; KB FOCUSING MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL; PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M; DECTRIS REMARK 200 PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.2.17 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3278 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 REMARK 200 RESOLUTION RANGE LOW (A) : 19.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 8.600 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 130.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.00 REMARK 200 R MERGE FOR SHELL (I) : 0.32700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 41.90 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2XRA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2 M SODIUM CHLORIDE, 0.1 M SODIUM REMARK 280 ACETATE TRIHYDRATE, PH 4.6, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 28.97800 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 16.73046 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 85.89033 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 28.97800 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 16.73046 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 85.89033 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 28.97800 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 16.73046 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 85.89033 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 28.97800 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 16.73046 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 85.89033 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 28.97800 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 16.73046 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 85.89033 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 28.97800 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 16.73046 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 85.89033 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 33.46091 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 171.78067 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 33.46091 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 171.78067 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 33.46091 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 171.78067 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 33.46091 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 171.78067 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 33.46091 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 171.78067 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 33.46091 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 171.78067 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 ARG A 3 REMARK 465 GLN A 4 REMARK 465 GLU A 5 REMARK 465 LEU A 6 REMARK 465 SER A 7 REMARK 465 LEU A 53 REMARK 465 GLY A 54 REMARK 465 LYS A 55 REMARK 465 GLY A 56 REMARK 465 ASN A 57 REMARK 465 GLY A 110 REMARK 465 LEU A 111 REMARK 465 ILE A 112 REMARK 465 ASP A 113 REMARK 465 GLY A 114 REMARK 465 PRO A 115 REMARK 465 LEU A 116 REMARK 465 LEU A 117 REMARK 465 SER A 118 REMARK 465 GLN A 162 REMARK 465 GLN A 163 REMARK 465 LEU A 164 REMARK 465 GLY A 165 REMARK 465 GLY A 166 REMARK 465 GLY A 167 REMARK 465 GLY A 168 REMARK 465 SER A 169 REMARK 465 HIS A 170 REMARK 465 HIS A 171 REMARK 465 HIS A 172 REMARK 465 HIS A 173 REMARK 465 HIS A 174 REMARK 465 HIS A 175 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 10 CG CD OE1 OE2 REMARK 470 GLN A 11 CG CD OE1 NE2 REMARK 470 LYS A 12 CG CD CE NZ REMARK 470 GLU A 102 CG CD OE1 OE2 REMARK 470 GLN A 108 CG CD OE1 NE2 REMARK 470 ARG A 109 CG CD NE CZ NH1 NH2 DBREF 4R61 A 1 175 PDB 4R61 4R61 1 175 SEQRES 1 A 175 MET ALA ARG GLN GLU LEU SER GLY ILE GLU GLN LYS GLN SEQRES 2 A 175 ASN ASN LEU LEU ARG GLN ILE GLU ALA GLN GLN HIS LEU SEQRES 3 A 175 LEU GLN LEU THR VAL SER LYS ILE LYS GLN LEU GLN ALA SEQRES 4 A 175 ARG ILE LEU ALA VAL GLU ARG TYR LEU LYS ASP GLN GLN SEQRES 5 A 175 LEU GLY LYS GLY ASN GLN PRO GLN GLN ASP LYS LEU TYR SEQRES 6 A 175 ARG GLU VAL ALA LEU ILE ARG ALA GLN LEU GLN LYS ILE SEQRES 7 A 175 GLU SER GLU THR LEU GLN LEU LEU HIS GLN GLN ALA GLU SEQRES 8 A 175 ILE GLU ARG GLU LEU ASN ASN GLN GLU GLN GLU ILE GLY SEQRES 9 A 175 SER LEU LYS GLN ARG GLY LEU ILE ASP GLY PRO LEU LEU SEQRES 10 A 175 SER GLY ILE ASP GLN ARG GLN ASN ASN LEU LYS ARG ALA SEQRES 11 A 175 ILE GLU ALA GLN LYS HIS LEU LEU GLN LEU THR VAL TRP SEQRES 12 A 175 GLY ILE LYS GLN LEU GLN ALA ARG ILE LEU ALA VAL GLU SEQRES 13 A 175 ARG TYR LEU LYS ASP GLN GLN LEU GLY GLY GLY GLY SER SEQRES 14 A 175 HIS HIS HIS HIS HIS HIS HELIX 1 1 ILE A 9 ASP A 50 1 42 HELIX 2 2 PRO A 59 SER A 105 1 47 HELIX 3 3 ILE A 120 LYS A 160 1 41 CRYST1 57.956 57.956 257.671 90.00 90.00 120.00 H 3 2 18 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 0.017255 0.009962 0.000000 0.00000 SCALE2 0.000000 0.019924 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003881 0.00000