HEADER VIRAL PROTEIN 25-APR-03 1P5A TITLE CONFORMATIONAL MAPPING OF THE N-TERMINAL PEPTIDE OF HIV-1 TITLE 2 GP41 IN LIPID DETERGENT AND AQUEOUS ENVIRONMENTS USING 13C- TITLE 3 ENHANCED FOURIER TRANSFORM INFRARED SPECTROSCOPY COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENVELOPE POLYPROTEIN GP160; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 519-541; COMPND 5 SYNONYM: N-TERMINAL FUSION PEPTIDE OF HIV-1 GP41; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: C-TERMINUS HAS BEEN AMIDATED SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE SEQUENCE OF THIS PEPTIDE OCCURS SOURCE 4 NATURALLY IN HUMAN IMMUNODEFICIENCY VIRUS GLYCOPROTEIN 41. KEYWDS HUMAN IMMUNODEFICIENCY VIRUS (HIV-1), VIRAL FUSION PEPTIDE, KEYWDS 2 GP41, VIRAL PROTEIN EXPDTA INFRARED SPECTROSCOPY NUMMDL 19 AUTHOR L.M.GORDON,P.W.MOBLEY,W.LEE,S.ESKANDARI,Y.N.KAZNESSIS, AUTHOR 2 M.A.SHERMAN,A.J.WARING REVDAT 3 24-FEB-09 1P5A 1 VERSN REVDAT 2 13-APR-04 1P5A 1 JRNL REVDAT 1 20-MAY-03 1P5A 0 JRNL AUTH L.M.GORDON,P.W.MOBLEY,W.LEE,S.ESKANDARI, JRNL AUTH 2 Y.N.KAZNESSIS,M.A.SHERMAN,A.J.WARING JRNL TITL CONFORMATIONAL MAPPING OF THE N-TERMINAL PEPTIDE JRNL TITL 2 OF HIV-1 GP41 IN LIPID DETERGENT AND AQUEOUS JRNL TITL 3 ENVIRONMENTS USING 13C-ENHANCED FOURIER TRANSFORM JRNL TITL 4 INFRARED SPECTROSCOPY. JRNL REF PROTEIN SCI. V. 13 1012 2004 JRNL REFN ISSN 0961-8368 JRNL PMID 15044732 JRNL DOI 10.1110/PS.03407704 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH L.M.GORDON,P.W.MOBLEY,R.PILPA,M.A.SHERMAN, REMARK 1 AUTH 2 A.J.WARING REMARK 1 TITL CONFORMATIONAL MAPPING OF THE N-TERMINAL PEPTIDE REMARK 1 TITL 2 OF HIV-1 GP41 IN MEMBRANE ENVIRONMENTS USING REMARK 1 TITL 3 13C-ENHANCED FOURIER TRANSFORM INFRARED REMARK 1 TITL 4 SPECTROSCOPY REMARK 1 REF BIOCHIM.BIOPHYS.ACTA V.1559 96 2002 REMARK 1 REFN ISSN 0006-3002 REMARK 1 DOI 10.1016/S0005-2736(01)00443-6 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 4 REMARK 4 1P5A COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-APR-03. REMARK 100 THE RCSB ID CODE IS RCSB019024. REMARK 250 REMARK 250 REMARK: THIS STRUCTURE WAS DETERMINED BY MEANS OF 13C-ENHANCED REMARK 250 FOURIER TRANSFORM INFRARED SPECTROSCOPY (FTIR). DATA SET REMARK 250 CONSISTS OF 19 CONFORMERS DERIVED FROM MOLECULAR DYNAMICS IN A REMARK 250 MODELED SDS MICELLE SURROUNDED BY WATER WITH PEPTIDE BACKBONE REMARK 250 CONSTRAINTS FROM FTIR. EXPERIMENTAL DETAILS EXPERIMENT TYPE : REMARK 250 INFRARED SPECTROSCOPY TEMPERATURE (KELVIN) : 298 PH : 7.4 IONIC REMARK 250 STRENGTH : 0.271 PRESSURE : AMBIENT SAMPLE CONTENTS : THIS REMARK 250 STRUCTURE WAS DETERMINED USING 13-C ISOTOPE ENHANCED FTIR REMARK 250 SPECTROSCOPY ON A FAMILY OF SELECTIVELY LABELED CHEMICALLY REMARK 250 SYNTHESIZED PEPTIDES. 13-C CARBONYL LABELS INCLUDED RESIDUES REMARK 250 519,521,523,524,525,526,527, 528,529,530,531,532,533,534,538, REMARK 250 539. EXPERIMENTS CONDUCTED : 13C-ISOTOPE ENHANCED FTIR REMARK 250 SPECTROMETER FIELD STRENGTH : NULL SPECTROMETER MODEL : RESEARCH REMARK 250 SERIES SPECTROMETER MANUFACTURER : MATTSON FTIR STRUCTURE REMARK 250 DETERMINATION. SOFTWARE USED : WINFIRST FTIR CURVE FITTING REMARK 250 SOFTWARE METHOD USED : MOLECULAR DYNAMICS CONFORMERS, NUMBER REMARK 250 CALCULATED : 20 CONFORMERS, NUMBER SUBMITTED : 19 CONFORMERS, REMARK 250 SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE COVALENT REMARK 250 GEOMETRY BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 250 REMARK: THE COORDINATES IN THIS ENTRY WERE GENERATED FROM 13-C REMARK 250 INDUCED SPECTRAL SHIFTS WHICH GIVE RESIDUE-SPECIFIC SECONDARY REMARK 250 STRUCTURE INFORMATION. PEPTIDE CONCENTRATION WAS 47 MICROMOLAR. REMARK 250 PEPTIDE/SDS RATIO WAS 1/200. FTIR SPECTRA WERE AVERAGED OVER 256 REMARK 250 SCANS AT A GAIN OF 4 AND A RESOLUTION OF 2 CM-1 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 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: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 1 PHE A 11 CG PHE A 11 CD1 0.091 REMARK 500 3 SER A 23 CA SER A 23 CB 0.093 REMARK 500 4 SER A 17 CA SER A 17 CB 0.095 REMARK 500 5 SER A 17 CA SER A 17 CB 0.113 REMARK 500 12 PHE A 8 CZ PHE A 8 CE2 0.122 REMARK 500 16 PHE A 11 CG PHE A 11 CD2 0.100 REMARK 500 18 PHE A 8 CG PHE A 8 CD2 0.095 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 PHE A 8 CB - CG - CD1 ANGL. DEV. = -7.4 DEGREES REMARK 500 1 MET A 19 CG - SD - CE ANGL. DEV. = -15.3 DEGREES REMARK 500 1 ARG A 22 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 ARG A 22 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 2 ARG A 22 NE - CZ - NH1 ANGL. DEV. = 7.0 DEGREES REMARK 500 2 ARG A 22 NE - CZ - NH2 ANGL. DEV. = -8.0 DEGREES REMARK 500 3 PHE A 8 CB - CG - CD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 3 PHE A 11 CB - CG - CD2 ANGL. DEV. = -6.5 DEGREES REMARK 500 3 PHE A 11 CB - CG - CD1 ANGL. DEV. = 5.1 DEGREES REMARK 500 3 ARG A 22 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 4 PHE A 11 CB - CG - CD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 4 LEU A 12 CB - CG - CD2 ANGL. DEV. = 10.4 DEGREES REMARK 500 4 ARG A 22 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 5 PHE A 11 CB - CG - CD1 ANGL. DEV. = -5.3 DEGREES REMARK 500 5 ARG A 22 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 6 ARG A 22 NE - CZ - NH1 ANGL. DEV. = 5.0 DEGREES REMARK 500 6 ARG A 22 NE - CZ - NH2 ANGL. DEV. = -5.8 DEGREES REMARK 500 7 ARG A 22 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 8 PHE A 11 CB - CG - CD2 ANGL. DEV. = -8.4 DEGREES REMARK 500 8 PHE A 11 CB - CG - CD1 ANGL. DEV. = 4.2 DEGREES REMARK 500 9 PHE A 11 CB - CG - CD2 ANGL. DEV. = -7.4 DEGREES REMARK 500 9 PHE A 11 CB - CG - CD1 ANGL. DEV. = 4.9 DEGREES REMARK 500 10 PHE A 11 CB - CG - CD2 ANGL. DEV. = -5.2 DEGREES REMARK 500 11 PHE A 11 CB - CG - CD1 ANGL. DEV. = -4.3 DEGREES REMARK 500 11 ARG A 22 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 11 ARG A 22 NE - CZ - NH2 ANGL. DEV. = -8.1 DEGREES REMARK 500 12 PHE A 11 CB - CG - CD2 ANGL. DEV. = 4.6 DEGREES REMARK 500 12 ARG A 22 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 12 ARG A 22 NE - CZ - NH2 ANGL. DEV. = -8.1 DEGREES REMARK 500 13 ARG A 22 NE - CZ - NH1 ANGL. DEV. = 7.1 DEGREES REMARK 500 13 SER A 23 N - CA - CB ANGL. DEV. = 11.2 DEGREES REMARK 500 14 ALA A 6 N - CA - CB ANGL. DEV. = -9.6 DEGREES REMARK 500 14 GLY A 20 N - CA - C ANGL. DEV. = -16.0 DEGREES REMARK 500 14 ARG A 22 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 15 ALA A 15 N - CA - CB ANGL. DEV. = 8.7 DEGREES REMARK 500 15 ARG A 22 NE - CZ - NH1 ANGL. DEV. = 6.7 DEGREES REMARK 500 16 ARG A 22 NE - CZ - NH2 ANGL. DEV. = -4.8 DEGREES REMARK 500 17 ARG A 22 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 17 ARG A 22 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 18 ARG A 22 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 19 PHE A 11 CB - CG - CD2 ANGL. DEV. = -7.6 DEGREES REMARK 500 19 ARG A 22 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 1 ALA A 15 -89.98 -91.29 REMARK 500 2 ALA A 14 -70.77 -73.60 REMARK 500 2 SER A 17 -141.56 -145.37 REMARK 500 2 MET A 19 -100.74 -91.25 REMARK 500 3 ARG A 22 -90.46 -65.84 REMARK 500 5 ARG A 22 -82.71 -97.21 REMARK 500 6 MET A 19 -64.87 -95.59 REMARK 500 6 ARG A 22 -79.87 -78.04 REMARK 500 7 LEU A 7 -71.32 -81.09 REMARK 500 7 MET A 19 -95.36 -103.44 REMARK 500 7 ARG A 22 -96.63 -83.95 REMARK 500 8 LEU A 12 -81.92 -57.90 REMARK 500 8 ALA A 15 -88.43 -62.66 REMARK 500 8 ARG A 22 -137.81 -94.70 REMARK 500 9 LEU A 7 -73.50 -73.33 REMARK 500 9 ARG A 22 -106.06 -81.08 REMARK 500 10 LEU A 7 -70.00 -61.71 REMARK 500 10 ARG A 22 -70.37 -93.28 REMARK 500 11 LEU A 7 -82.49 -63.86 REMARK 500 11 ALA A 14 -72.21 -53.37 REMARK 500 11 ARG A 22 -69.05 -100.09 REMARK 500 12 ALA A 15 -71.38 -65.27 REMARK 500 12 MET A 19 -74.98 -83.30 REMARK 500 15 MET A 19 -84.46 -98.21 REMARK 500 16 ARG A 22 -73.65 -84.12 REMARK 500 17 LEU A 7 -70.70 -70.35 REMARK 500 18 VAL A 2 -167.74 -104.46 REMARK 500 18 LEU A 7 -74.68 -77.53 REMARK 500 18 ARG A 22 -85.01 -79.58 REMARK 500 19 ALA A 15 -83.69 -60.57 REMARK 500 19 SER A 17 179.36 -57.47 REMARK 500 19 ARG A 22 -103.97 -100.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ALA A 15 GLY A 16 10 148.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 PHE A 11 0.07 SIDE_CHAIN REMARK 500 2 ARG A 22 0.18 SIDE_CHAIN REMARK 500 5 PHE A 11 0.08 SIDE_CHAIN REMARK 500 6 ARG A 22 0.08 SIDE_CHAIN REMARK 500 9 PHE A 8 0.09 SIDE_CHAIN REMARK 500 9 ARG A 22 0.12 SIDE_CHAIN REMARK 500 10 PHE A 11 0.11 SIDE_CHAIN REMARK 500 13 PHE A 11 0.09 SIDE_CHAIN REMARK 500 14 PHE A 8 0.07 SIDE_CHAIN REMARK 500 14 ARG A 22 0.07 SIDE_CHAIN REMARK 500 16 ARG A 22 0.12 SIDE_CHAIN REMARK 500 19 ARG A 22 0.08 SIDE_CHAIN 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 NH2 A 24 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ERF RELATED DB: PDB REMARK 900 CONFORMATIONAL MAPPING OF THE N-TERMINAL PEPTIDE OF HIV-1 REMARK 900 GP41 IN MEMBRANE ENVIRONMENTS USING 13C-ENHANCED FOURIER REMARK 900 TRANSFORM INFRARED SPECTROSCOPY DBREF 1P5A A 1 23 UNP P03377 ENV_HV1BR 517 539 SEQRES 1 A 24 ALA VAL GLY ILE GLY ALA LEU PHE LEU GLY PHE LEU GLY SEQRES 2 A 24 ALA ALA GLY SER THR MET GLY ALA ARG SER NH2 HET NH2 A 24 3 HETNAM NH2 AMINO GROUP FORMUL 1 NH2 H2 N HELIX 1 1 GLY A 3 PHE A 8 1 6 LINK C SER A 23 N NH2 A 24 1555 1555 1.32 SITE 1 AC1 1 SER A 23 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1