HEADER VIRAL PROTEIN 09-DEC-99 1DLB TITLE HELICAL INTERACTIONS IN THE HIV-1 GP41 CORE REVEALS STRUCTURAL BASIS TITLE 2 FOR THE INHIBITORY ACTIVITY OF GP41 PEPTIDES COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIV-1 ENVELOPE GLYCOPROTEIN GP41; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1 - 34 AND 41 - 68 CONNECTED BY A SIX-RESIDUE COMPND 5 LINKER (SER-GLY-GLY-ARG- GLY-GLY); COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 OTHER_DETAILS: RECOMBINANT GP41 WITH LINKER (SER-GLY-GLY- ARG-GLY- SOURCE 7 GLY) BETWEEN TWO FRAGMENTS KEYWDS GP41, HIV-1, MEMBRANE FUSION, HIV-1 INHIBITION, VIRUS/VIRAL PROTEIN, KEYWDS 2 VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR W.SHU,J.LIU,H.JI,L.RADING,S.JIANG,M.LU REVDAT 8 07-FEB-24 1DLB 1 REMARK REVDAT 7 03-NOV-21 1DLB 1 SEQADV REVDAT 6 09-AUG-17 1DLB 1 SOURCE REMARK REVDAT 5 13-JUL-11 1DLB 1 VERSN REVDAT 4 24-FEB-09 1DLB 1 VERSN REVDAT 3 01-APR-03 1DLB 1 JRNL REVDAT 2 02-APR-00 1DLB 1 JRNL REVDAT 1 15-DEC-99 1DLB 0 JRNL AUTH W.SHU,J.LIU,H.JI,L.RADIGEN,S.JIANG,M.LU JRNL TITL HELICAL INTERACTIONS IN THE HIV-1 GP41 CORE REVEAL JRNL TITL 2 STRUCTURAL BASIS FOR THE INHIBITORY ACTIVITY OF GP41 JRNL TITL 3 PEPTIDES. JRNL REF BIOCHEMISTRY V. 39 1634 2000 JRNL REFN ISSN 0006-2960 JRNL PMID 10677212 JRNL DOI 10.1021/BI9921687 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.5 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 4167 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 12.000 REMARK 3 FREE R VALUE TEST SET COUNT : 499 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.011 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 596 REMARK 3 BIN R VALUE (WORKING SET) : 0.2640 REMARK 3 BIN FREE R VALUE : 0.3410 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 13.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 90 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.036 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 509 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 77 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.88000 REMARK 3 B22 (A**2) : -0.88000 REMARK 3 B33 (A**2) : 1.77000 REMARK 3 B12 (A**2) : 1.15000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.23 REMARK 3 ESD FROM SIGMAA (A) : 0.19 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.31 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.29 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 0.800 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 14.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.560 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.140 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.950 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.490 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.440 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 109.5 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1DLB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-DEC-99. REMARK 100 THE DEPOSITION ID IS D_1000010181. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-MAR-99 REMARK 200 TEMPERATURE (KELVIN) : 293.0 REMARK 200 PH : 4.6 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4167 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, AMMONIUM SULPHATE, SODIUM REMARK 280 ACETATE, PH 4.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293.0K 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 26.19100 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 15.12138 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 20.16067 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 26.19100 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 15.12138 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 20.16067 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 26.19100 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 15.12138 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 20.16067 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 30.24276 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 40.32133 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 30.24276 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 40.32133 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 30.24276 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 40.32133 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 6420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -61.0 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 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 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 100 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 102 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 IN THE STRUCTURE, SEQUENCE 1 - 34 IS FROM GP41 RESIDUES REMARK 400 546 - 579 (IN GP160 NUMBERING SYSTEM), 35 - 40 IS AN REMARK 400 ARTIFICIAL LINKER SGGRGG AND 41 - 68 IS GP41 RESIDUES REMARK 400 628 - 655. 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 SER A 1 REMARK 465 GLY A 36 REMARK 465 GLY A 37 REMARK 465 GLU A 67 REMARK 465 LYS A 68 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 ARG A 34 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 38 CG CD NE CZ NH1 NH2 DBREF 1DLB A 1 34 UNP P04578 ENV_HV1H2 546 579 DBREF 1DLB A 41 68 UNP P04578 ENV_HV1H2 628 655 SEQADV 1DLB SER A 35 UNP P04578 SEE REMARK 999 SEQADV 1DLB GLY A 36 UNP P04578 SEE REMARK 999 SEQADV 1DLB GLY A 37 UNP P04578 SEE REMARK 999 SEQADV 1DLB ARG A 38 UNP P04578 SEE REMARK 999 SEQADV 1DLB GLY A 39 UNP P04578 SEE REMARK 999 SEQADV 1DLB GLY A 40 UNP P04578 SEE REMARK 999 SEQADV 1DLB LEU A 65 UNP P04578 GLN 652 ENGINEERED MUTATION SEQRES 1 A 68 SER GLY ILE VAL GLN GLN GLN ASN ASN LEU LEU ARG ALA SEQRES 2 A 68 ILE GLU ALA GLN GLN HIS LEU LEU GLN LEU THR VAL TRP SEQRES 3 A 68 GLY ILE LYS GLN LEU GLN ALA ARG SER GLY GLY ARG GLY SEQRES 4 A 68 GLY TRP MET GLU TRP ASP ARG GLU ILE ASN ASN TYR THR SEQRES 5 A 68 SER LEU ILE HIS SER LEU ILE GLU GLU SER GLN ASN LEU SEQRES 6 A 68 GLN GLU LYS FORMUL 2 HOH *77(H2 O) HELIX 1 1 GLY A 2 SER A 35 1 34 HELIX 2 2 TRP A 41 GLN A 66 1 26 CRYST1 52.382 52.382 60.482 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 0.019091 0.011022 0.000000 0.00000 SCALE2 0.000000 0.022044 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016534 0.00000