HEADER VIRAL PROTEIN 18-JUN-01 1JEK TITLE VISNA TM CORE STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENV POLYPROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: COAT POLYPROTEIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: ENV POLYPROTEIN; COMPND 8 CHAIN: B; COMPND 9 SYNONYM: COAT POLYPROTEIN; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE SOURCE 4 OF THE PEPTIDE IS NATURALLY FOUND IN VISNA VIRUS.; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 OTHER_DETAILS: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE SOURCE 8 OF THE PEPTIDE IS NATURALLY FOUND IN VISNA VIRUS. KEYWDS ENVELOPE GLYCOPROTEIN, RETROVIRUS, HIV, SIV, GP41, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR V.N.MALASHKEVICH,M.SINGH,P.S.KIM REVDAT 5 16-AUG-23 1JEK 1 REMARK LINK REVDAT 4 16-NOV-11 1JEK 1 HETATM REVDAT 3 13-JUL-11 1JEK 1 VERSN REVDAT 2 24-FEB-09 1JEK 1 VERSN REVDAT 1 25-JUL-01 1JEK 0 JRNL AUTH V.N.MALASHKEVICH,M.SINGH,P.S.KIM JRNL TITL THE TRIMER-OF-HAIRPINS MOTIF IN MEMBRANE FUSION: VISNA JRNL TITL 2 VIRUS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 98 8502 2001 JRNL REFN ISSN 0027-8424 JRNL PMID 11447278 JRNL DOI 10.1073/PNAS.151254798 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH V.N.MALASHKEVICH,D.C.CHAN,C.T.CHUTKOWSKI,P.S.KIM REMARK 1 TITL CRYSTAL STRUCTURE OF THE SIMIAN IMMUNODEFICIENCY VIRUS (SIV) REMARK 1 TITL 2 GP41 CORE: CONSERVED HELICAL INTERACTIONS UNDERLIE THE BROAD REMARK 1 TITL 3 INHIBITORY ACTIVITY OF GP41 PEPTIDES REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 95 9134 1998 REMARK 1 REFN ISSN 0027-8424 REMARK 1 DOI 10.1073/PNAS.95.16.9134 REMARK 1 REFERENCE 2 REMARK 1 AUTH D.C.CHAN,D.FASS,J.M.BERGER,P.S.KIM REMARK 1 TITL CORE STRUCTURE OF GP41 FROM THE HIV ENVELOPE GLYCOPROTEIN REMARK 1 REF CELL(CAMBRIDGE,MASS.) V. 89 263 1997 REMARK 1 REFN ISSN 0092-8674 REMARK 1 DOI 10.1016/S0092-8674(00)80205-6 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 9.96 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 914104.100 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.9 REMARK 3 NUMBER OF REFLECTIONS : 15369 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) : 0.213 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1559 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.59 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 72.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1723 REMARK 3 BIN R VALUE (WORKING SET) : 0.3190 REMARK 3 BIN FREE R VALUE : 0.3630 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 202 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.026 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 598 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 142 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.82000 REMARK 3 B22 (A**2) : 6.82000 REMARK 3 B33 (A**2) : -13.64000 REMARK 3 B12 (A**2) : 3.16000 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) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 0.21 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) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.22 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 13.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.990 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) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.45 REMARK 3 BSOL : 94.78 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 : ION.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1JEK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-JUN-01. REMARK 100 THE DEPOSITION ID IS D_1000013684. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-DEC-98 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.28 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 : 16300 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.1 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : 0.06600 REMARK 200 FOR THE DATA SET : 13.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.52 REMARK 200 COMPLETENESS FOR SHELL (%) : 64.7 REMARK 200 DATA REDUNDANCY IN SHELL : 1.50 REMARK 200 R MERGE FOR SHELL (I) : 0.13800 REMARK 200 R SYM FOR SHELL (I) : 0.13800 REMARK 200 FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 2SIV REMARK 200 REMARK 200 REMARK: POLYSERINE MODEL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% TERT-BUTANOL, 0.1M TRIS-HCL, PH REMARK 280 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 2 1 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 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 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 300 REMARK: TRIMER IS FORMED AROUND THE CRYSTALLOGRAPHIC 3-FOLD AXIS 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 13060 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -103.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 26.27400 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 45.50790 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -26.27400 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 45.50790 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 1 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 4 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 40 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 46 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 42 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE2 GLU B 632 O HOH A 107 3565 2.12 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 ACE A 545 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACE B 627 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NH2 A 586 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NH2 B 662 DBREF 1JEK A 546 585 UNP P35954 ENV_VILVK 693 732 DBREF 1JEK B 628 661 UNP P35954 ENV_VILVK 775 808 SEQRES 1 A 42 ACE GLN SER LEU ALA ASN ALA THR ALA ALA GLN GLN GLU SEQRES 2 A 42 VAL LEU GLU ALA SER TYR ALA MET VAL GLN HIS ILE ALA SEQRES 3 A 42 LYS GLY ILE ARG ILE LEU GLU ALA ARG VAL ALA ARG VAL SEQRES 4 A 42 GLU ALA NH2 SEQRES 1 B 36 ACE TRP GLN GLN TRP GLU GLU GLU ILE GLU GLN HIS GLU SEQRES 2 B 36 GLY ASN LEU SER LEU LEU LEU ARG GLU ALA ALA LEU GLN SEQRES 3 B 36 VAL HIS ILE ALA GLN ARG ASP ALA ARG NH2 HET ACE A 545 3 HET NH2 A 586 1 HET ACE B 627 3 HET NH2 B 662 1 HETNAM ACE ACETYL GROUP HETNAM NH2 AMINO GROUP FORMUL 1 ACE 2(C2 H4 O) FORMUL 1 NH2 2(H2 N) FORMUL 3 HOH *142(H2 O) HELIX 1 1 GLN A 546 ALA A 585 1 40 HELIX 2 2 TRP B 628 ARG B 661 1 34 LINK C ACE A 545 N GLN A 546 1555 1555 1.33 LINK C ALA A 585 N NH2 A 586 1555 1555 1.32 LINK C ACE B 627 N TRP B 628 1555 1555 1.32 LINK C ARG B 661 N NH2 B 662 1555 1555 1.32 SITE 1 AC1 2 ALA A 549 HOH B 66 SITE 1 AC2 3 GLN B 629 TRP B 631 HOH B 47 SITE 1 AC3 2 ALA A 585 HOH B 12 SITE 1 AC4 2 ALA B 660 ARG B 661 CRYST1 52.548 52.548 61.686 90.00 90.00 120.00 P 3 2 1 6 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 0.019030 0.010987 0.000000 0.00000 SCALE2 0.000000 0.021974 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016211 0.00000 HETATM 1 C ACE A 545 0.940 25.074 40.150 1.00 23.60 C HETATM 2 O ACE A 545 1.196 25.331 38.982 1.00 23.29 O HETATM 3 CH3 ACE A 545 0.608 26.198 41.093 1.00 25.98 C