HEADER VIRAL PROTEIN 01-JUN-16 5KA5 TITLE HIV-1 GP41 VARIANT V549E RESISTANCE MUTATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSMEMBRANE GLYCOPROTEIN GP41; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 543-582 AND 625-661 LINKED VIA GGRGG; COMPND 5 SYNONYM: GLYCOPROTEIN 41; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1; SOURCE 3 ORGANISM_COMMON: HIV-1; SOURCE 4 ORGANISM_TAXID: 11676; SOURCE 5 STRAIN: ISOLATE HXB2; SOURCE 6 GENE: ENV; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: RP3098; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: P4 KEYWDS HIV-1, MEMBRANE FUSION, 5-HELIX, C-PEPTIDE, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.BHARDWAJ,M.D.KHASNIS,K.HALKIDIS,M.J.ROOT REVDAT 5 27-SEP-23 5KA5 1 REMARK REVDAT 4 25-DEC-19 5KA5 1 REMARK REVDAT 3 13-SEP-17 5KA5 1 REMARK REVDAT 2 18-JAN-17 5KA5 1 JRNL REVDAT 1 14-DEC-16 5KA5 0 JRNL AUTH M.D.KHASNIS,K.HALKIDIS,A.BHARDWAJ,M.J.ROOT JRNL TITL RECEPTOR ACTIVATION OF HIV-1 ENV LEADS TO ASYMMETRIC JRNL TITL 2 EXPOSURE OF THE GP41 TRIMER. JRNL REF PLOS PATHOG. V. 12 06098 2016 JRNL REFN ESSN 1553-7374 JRNL PMID 27992602 JRNL DOI 10.1371/JOURNAL.PPAT.1006098 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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 : TWIN_LSQ_F REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 3 NUMBER OF REFLECTIONS : 12745 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.500 REMARK 3 FREE R VALUE TEST SET COUNT : 1292 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 13.9889 - 3.7256 0.90 1328 138 0.1467 0.2200 REMARK 3 2 3.7256 - 2.9664 0.90 1327 142 0.1606 0.1791 REMARK 3 3 2.9664 - 2.5941 0.88 1295 153 0.1865 0.2471 REMARK 3 4 2.5941 - 2.3582 0.87 1268 150 0.2160 0.2332 REMARK 3 5 2.3582 - 2.1898 0.87 1304 146 0.2302 0.2405 REMARK 3 6 2.1898 - 2.0611 0.85 1223 142 0.2528 0.2833 REMARK 3 7 2.0611 - 1.9582 0.85 1228 140 0.2759 0.2748 REMARK 3 8 1.9582 - 1.8732 0.84 1245 144 0.2951 0.3227 REMARK 3 9 1.8732 - 1.8012 0.81 1198 137 0.3105 0.3320 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) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.250 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) : 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 : 0.002 655 REMARK 3 ANGLE : 0.321 882 REMARK 3 CHIRALITY : 0.028 96 REMARK 3 PLANARITY : 0.001 116 REMARK 3 DIHEDRAL : 16.595 392 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 542 THROUGH 624 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.1095 -11.1729 -5.5117 REMARK 3 T TENSOR REMARK 3 T11: 0.1958 T22: 0.2445 REMARK 3 T33: 0.2607 T12: 0.0140 REMARK 3 T13: -0.0011 T23: -0.0244 REMARK 3 L TENSOR REMARK 3 L11: 0.3305 L22: 0.6636 REMARK 3 L33: 7.7584 L12: 0.0790 REMARK 3 L13: -0.2409 L23: 0.7659 REMARK 3 S TENSOR REMARK 3 S11: -0.0179 S12: 0.0184 S13: 0.0331 REMARK 3 S21: 0.0048 S22: -0.0922 S23: 0.0255 REMARK 3 S31: 0.0957 S32: -0.3325 S33: 0.0619 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 625 THROUGH 663 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.2055 -1.8871 -3.6067 REMARK 3 T TENSOR REMARK 3 T11: 0.2773 T22: 0.2052 REMARK 3 T33: 0.2459 T12: 0.0387 REMARK 3 T13: -0.0654 T23: -0.0171 REMARK 3 L TENSOR REMARK 3 L11: 2.6851 L22: 0.3858 REMARK 3 L33: 5.3694 L12: 1.0014 REMARK 3 L13: 3.7244 L23: 1.3806 REMARK 3 S TENSOR REMARK 3 S11: -0.2770 S12: -0.0132 S13: 0.2069 REMARK 3 S21: -0.0466 S22: -0.0969 S23: 0.0655 REMARK 3 S31: -0.4064 S32: -0.1201 S33: 0.1363 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 5KA5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1000221884. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.03320 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL CRYO-COOLED REMARK 200 SI(111) REMARK 200 OPTICS : ADJUSTABLE FOCUS K-B PAIR SI REMARK 200 PLUS PT, RH COATINGS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13238 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 18.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.59700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1AIK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3M SODIUM CHLORIDE, 0.1M SODIUM REMARK 280 ACETATE SAMPLE CONCENTRATION: 6 MG/ML, PH 4.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 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 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+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 1.000000 0.000000 0.000000 20.35800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 11.75370 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 38.50700 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 20.35800 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 11.75370 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 38.50700 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 20.35800 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 11.75370 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 38.50700 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 23.50739 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 77.01400 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 23.50739 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 77.01400 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 23.50739 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 77.01400 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -57.0 KCAL/MOL 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 20.35800 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 -35.26109 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 40.71600 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 701 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 720 LIES ON A SPECIAL POSITION. 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 ILE A 617 REMARK 465 LEU A 618 REMARK 465 ALA A 619 REMARK 465 GLY A 620 REMARK 465 GLY A 621 REMARK 465 ARG A 622 REMARK 465 HIS A 664 REMARK 465 HIS A 665 REMARK 465 HIS A 666 REMARK 465 HIS A 667 REMARK 465 HIS A 668 REMARK 465 HIS A 669 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5KA6 RELATED DB: PDB DBREF 5KA5 A 543 619 UNP P04578 ENV_HV1H2 543 582 DBREF 5KA5 A 625 661 UNP P04578 ENV_HV1H2 625 661 SEQADV 5KA5 MET A 542 UNP P04578 INITIATING METHIONINE SEQADV 5KA5 GLU A 549 UNP P04578 VAL 549 ENGINEERED MUTATION SEQADV 5KA5 GLY A 620 UNP P04578 LINKER SEQADV 5KA5 GLY A 621 UNP P04578 LINKER SEQADV 5KA5 ARG A 622 UNP P04578 LINKER SEQADV 5KA5 GLY A 623 UNP P04578 LINKER SEQADV 5KA5 GLY A 624 UNP P04578 LINKER SEQADV 5KA5 GLY A 662 UNP P04578 EXPRESSION TAG SEQADV 5KA5 GLY A 663 UNP P04578 EXPRESSION TAG SEQADV 5KA5 HIS A 664 UNP P04578 EXPRESSION TAG SEQADV 5KA5 HIS A 665 UNP P04578 EXPRESSION TAG SEQADV 5KA5 HIS A 666 UNP P04578 EXPRESSION TAG SEQADV 5KA5 HIS A 667 UNP P04578 EXPRESSION TAG SEQADV 5KA5 HIS A 668 UNP P04578 EXPRESSION TAG SEQADV 5KA5 HIS A 669 UNP P04578 EXPRESSION TAG SEQRES 1 A 91 MET GLN LEU LEU SER GLY ILE GLU GLN GLN GLN ASN ASN SEQRES 2 A 91 LEU LEU ARG ALA ILE GLU ALA GLN GLN HIS LEU LEU GLN SEQRES 3 A 91 LEU THR VAL TRP GLY ILE LYS GLN LEU GLN ALA ARG ILE SEQRES 4 A 91 LEU ALA GLY GLY ARG GLY GLY HIS THR THR TRP MET GLU SEQRES 5 A 91 TRP ASP ARG GLU ILE ASN ASN TYR THR SER LEU ILE HIS SEQRES 6 A 91 SER LEU ILE GLU GLU SER GLN ASN GLN GLN GLU LYS ASN SEQRES 7 A 91 GLU GLN GLU LEU LEU GLY GLY HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *32(H2 O) HELIX 1 AA1 MET A 542 ALA A 578 1 37 HELIX 2 AA2 GLY A 624 LEU A 661 1 38 CRYST1 40.716 40.716 115.521 90.00 90.00 120.00 H 3 9 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 0.024560 0.014180 0.000000 0.00000 SCALE2 0.000000 0.028360 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008656 0.00000