HEADER VIRAL PROTEIN 31-MAY-01 1JAU TITLE NMR SOLUTION STRUCTURE OF THE TRP-RICH PEPTIDE OF HIV GP41 BOUND TO TITLE 2 DPC MICELLES COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSMEMBRANE GLYCOPROTEIN (GP41); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 665-683; COMPND 5 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 HUMAN IMMUNODEFICIENCY VIRUS SOURCE 5 (HIV). KEYWDS AMPHIPATHIC ALPHA HELIX, VIRAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 40 AUTHOR D.J.SCHIBLI,R.C.MONTELARO,H.J.VOGEL REVDAT 3 23-FEB-22 1JAU 1 REMARK LINK REVDAT 2 24-FEB-09 1JAU 1 VERSN REVDAT 1 17-OCT-01 1JAU 0 JRNL AUTH D.J.SCHIBLI,R.C.MONTELARO,H.J.VOGEL JRNL TITL THE MEMBRANE-PROXIMAL TRYPTOPHAN-RICH REGION OF THE HIV JRNL TITL 2 GLYCOPROTEIN, GP41, FORMS A WELL-DEFINED HELIX IN JRNL TITL 3 DODECYLPHOSPHOCHOLINE MICELLES. JRNL REF BIOCHEMISTRY V. 40 9570 2001 JRNL REFN ISSN 0006-2960 JRNL PMID 11583156 JRNL DOI 10.1021/BI010640U REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.6, CNS 1.0 REMARK 3 AUTHORS : BRUKER (XWINNMR), A.T.BRUNGER, P.D.ADAMS, REMARK 3 G.M.CLORE, W.L.DELANO, P.GROS, R.W.GROSSE- REMARK 3 KUNSTLEVE, J.-S.JIANG, J.KUSZEWSKI, M.NILGES, REMARK 3 N.S.PANNU, R.J.READ, L.M.RICE, T.SIMONSON, REMARK 3 G.L.WARREN (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 STRUCTURES WERE INITIALLY GENERATED USING CNS. AMBIGUOUS AND REMARK 3 UNASSIGNED NOE CONSTRAINTS REMARK 3 WERE THEN USED IN CONJUCTION WITH MATRIX RELAXATION ANALYSIS USING REMARK 3 THE PROGRAM ARIA. REMARK 4 REMARK 4 1JAU COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUN-01. REMARK 100 THE DEPOSITION ID IS D_1000013566. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310 REMARK 210 PH : 3.51 REMARK 210 IONIC STRENGTH : 200 MM DPC-D38 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.6 MM SYNTHETIC GP41 PEPTIDE, REMARK 210 200 MM PERDEUTERATED REMARK 210 DODECYLPHOSPHOCHOLINE; 1.6 MM REMARK 210 SYNTHETIC GP41 PEPTIDE, 200 MM REMARK 210 REMARK 210 PERDEUTERATED DODECYLPHOSPHOCHOLIN REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 1.8, NMRVIEW 4.1.3, CNS REMARK 210 1.0, ARIA 1.0 REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED REMARK 210 ANNEALING, MOLECULAR DYNAMICS, REMARK 210 MATRIX RELAXATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 40 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR TECHNIQUES. REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 LYS A 19 O - C - N ANGL. DEV. = -27.2 DEGREES REMARK 500 3 LYS A 19 O - C - N ANGL. DEV. = -10.1 DEGREES REMARK 500 4 LYS A 19 O - C - N ANGL. DEV. = -38.4 DEGREES REMARK 500 5 LYS A 19 O - C - N ANGL. DEV. = -42.4 DEGREES REMARK 500 6 LYS A 19 O - C - N ANGL. DEV. = -22.9 DEGREES REMARK 500 7 LYS A 19 O - C - N ANGL. DEV. = -11.8 DEGREES REMARK 500 9 LYS A 19 O - C - N ANGL. DEV. = -56.6 DEGREES REMARK 500 10 LYS A 19 O - C - N ANGL. DEV. = -38.2 DEGREES REMARK 500 11 LYS A 19 O - C - N ANGL. DEV. = -20.2 DEGREES REMARK 500 12 LYS A 19 O - C - N ANGL. DEV. = -13.5 DEGREES REMARK 500 13 LYS A 19 O - C - N ANGL. DEV. = -20.3 DEGREES REMARK 500 15 LYS A 19 O - C - N ANGL. DEV. = -46.8 DEGREES REMARK 500 16 LYS A 19 O - C - N ANGL. DEV. = -47.0 DEGREES REMARK 500 19 LYS A 19 O - C - N ANGL. DEV. = -33.1 DEGREES REMARK 500 20 LYS A 19 O - C - N ANGL. DEV. = -11.8 DEGREES REMARK 500 21 LYS A 19 O - C - N ANGL. DEV. = -52.3 DEGREES REMARK 500 23 LYS A 19 O - C - N ANGL. DEV. = -9.7 DEGREES REMARK 500 25 LYS A 19 O - C - N ANGL. DEV. = -28.8 DEGREES REMARK 500 27 LYS A 19 O - C - N ANGL. DEV. = -11.4 DEGREES REMARK 500 30 LYS A 19 O - C - N ANGL. DEV. = -9.7 DEGREES REMARK 500 33 LYS A 19 O - C - N ANGL. DEV. = -29.4 DEGREES REMARK 500 34 LYS A 19 O - C - N ANGL. DEV. = -61.4 DEGREES REMARK 500 35 LYS A 19 O - C - N ANGL. DEV. = -47.1 DEGREES REMARK 500 39 LYS A 19 O - C - N ANGL. DEV. = -27.7 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 3 30.38 -78.02 REMARK 500 1 LEU A 5 -26.28 -140.42 REMARK 500 2 ALA A 3 29.42 -79.74 REMARK 500 2 THR A 12 1.66 -68.33 REMARK 500 3 THR A 12 0.56 -68.75 REMARK 500 4 ALA A 3 27.58 -79.15 REMARK 500 5 THR A 12 1.19 -66.30 REMARK 500 7 ALA A 3 25.28 -75.59 REMARK 500 7 THR A 12 2.11 -68.58 REMARK 500 7 ILE A 18 -70.60 -76.51 REMARK 500 8 ALA A 3 24.97 -77.79 REMARK 500 9 ALA A 3 23.27 -78.20 REMARK 500 10 ALA A 3 22.13 -73.79 REMARK 500 11 ALA A 3 27.94 -75.84 REMARK 500 11 THR A 12 1.83 -67.49 REMARK 500 12 ALA A 3 5.62 -69.83 REMARK 500 13 THR A 12 0.70 -68.17 REMARK 500 14 ALA A 3 21.21 -76.55 REMARK 500 15 ALA A 3 27.72 -75.37 REMARK 500 15 THR A 12 0.61 -67.67 REMARK 500 17 THR A 12 1.82 -67.35 REMARK 500 19 TRP A 2 26.55 -153.52 REMARK 500 20 ALA A 3 21.18 -77.27 REMARK 500 21 ALA A 3 23.03 -77.48 REMARK 500 22 ALA A 3 24.78 -77.43 REMARK 500 23 ALA A 3 22.47 -78.68 REMARK 500 24 ALA A 3 29.14 -78.40 REMARK 500 24 SER A 4 53.62 -141.32 REMARK 500 24 LEU A 5 -16.47 -144.91 REMARK 500 26 SER A 4 34.39 -98.30 REMARK 500 26 THR A 12 0.63 -67.18 REMARK 500 27 ALA A 3 23.97 -77.59 REMARK 500 28 THR A 12 3.72 -68.64 REMARK 500 29 ALA A 3 25.32 -78.59 REMARK 500 30 ALA A 3 27.72 -75.39 REMARK 500 30 THR A 12 5.08 -69.43 REMARK 500 31 ALA A 3 30.76 -78.83 REMARK 500 31 LEU A 5 -3.25 -140.93 REMARK 500 31 THR A 12 2.16 -67.11 REMARK 500 32 ALA A 3 24.80 -78.56 REMARK 500 33 ALA A 3 31.10 -78.89 REMARK 500 34 ALA A 3 11.92 -69.65 REMARK 500 34 ILE A 18 -74.70 -82.87 REMARK 500 35 ALA A 3 30.26 -77.94 REMARK 500 37 SER A 4 30.71 -99.56 REMARK 500 38 ALA A 3 30.52 -79.17 REMARK 500 38 THR A 12 0.11 -68.20 REMARK 500 38 ILE A 18 -74.92 -96.07 REMARK 500 40 TRP A 2 5.01 -69.64 REMARK 500 40 ALA A 3 5.41 -68.05 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 20 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1JAV RELATED DB: PDB REMARK 900 MINIMIZED AVERAGE STRUCTURE FOR THIS DEPOSITION DBREF 1JAU A 1 19 UNP P04624 ENV_HV1H3 665 683 SEQRES 1 A 20 LYS TRP ALA SER LEU TRP ASN TRP PHE ASN ILE THR ASN SEQRES 2 A 20 TRP LEU TRP TYR ILE LYS NH2 HET NH2 A 20 3 HETNAM NH2 AMINO GROUP FORMUL 1 NH2 H2 N HELIX 1 1 LEU A 5 ASN A 10 1 6 HELIX 2 2 ASN A 10 LYS A 19 1 10 LINK C LYS A 19 N NH2 A 20 1555 1555 1.33 LINK O LYS A 19 N NH2 A 20 1555 1555 1.91 SITE 1 AC1 2 TRP A 16 LYS A 19 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