HEADER VIRAL PROTEIN 12-APR-99 1QA5 TITLE MYRISTOYLATED HIV-1 NEF ANCHOR DOMAIN, NMR, 2 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (MYRISTOYLATED HIV-1 NEF ANCHOR DOMAIN (MYRISTATE- COMPND 3 GLY2 TO TRP57)); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (ISOLATE SOURCE 4 NL4-3); SOURCE 5 ORGANISM_COMMON: HIV-1; SOURCE 6 ORGANISM_TAXID: 11676 KEYWDS HIV, AIDS, REGULATORY FACTOR, NEGATIVE FACTOR, NEF, MYRISTOYLATION, KEYWDS 2 VIRAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 2 AUTHOR M.GEYER,H.R.KALBITZER REVDAT 5 21-DEC-22 1QA5 1 SEQADV REVDAT 4 27-OCT-21 1QA5 1 SOURCE REMARK REVDAT 3 27-NOV-19 1QA5 1 JRNL REMARK SEQADV LINK REVDAT 2 24-FEB-09 1QA5 1 VERSN REVDAT 1 26-MAY-99 1QA5 0 JRNL AUTH M.GEYER,C.E.MUNTE,J.SCHORR,R.KELLNER,H.R.KALBITZER JRNL TITL STRUCTURE OF THE ANCHOR-DOMAIN OF MYRISTOYLATED AND JRNL TITL 2 NON-MYRISTOYLATED HIV-1 NEF PROTEIN. JRNL REF J.MOL.BIOL. V. 289 123 1999 JRNL REFN ISSN 0022-2836 JRNL PMID 10339411 JRNL DOI 10.1006/JMBI.1999.2740 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.GRZESIEK,A.BAX,J.S.HU,J.KAUFMAN,I.PALMER,S.J.STAHL, REMARK 1 AUTH 2 N.TJANDRA,P.T.WINGFIELD REMARK 1 TITL REFINED SOLUTION STRUCTURE AND BACKBONE DYNAMICS OF HIV-1 REMARK 1 TITL 2 NEF. REMARK 1 REF PROTEIN SCI. V. 6 1248 1997 REMARK 1 REFN ISSN 0961-8368 REMARK 1 PMID 9194185 REMARK 1 DOI 10.1002/PRO.5560060613 REMARK 1 REFERENCE 2 REMARK 1 AUTH K.J.BARNHAM,S.A.MONKS,M.G.HINDS,A.A.AZAD,R.S.NORTON REMARK 1 TITL SOLUTION STRUCTURE OF A POLYPEPTIDE FROM THE N TERMINUS OF REMARK 1 TITL 2 THE HIV PROTEIN NEF. REMARK 1 REF BIOCHEMISTRY V. 36 5970 1997 REMARK 1 REFN ISSN 0006-2960 REMARK 1 PMID 9166767 REMARK 1 DOI 10.1021/BI9629945 REMARK 1 REFERENCE 3 REMARK 1 AUTH S.AROLD,P.FRANKEN,M.P.STRUB,F.HOH,S.BENICHOU,R.BENAROUS, REMARK 1 AUTH 2 C.DUMAS REMARK 1 TITL THE CRYSTAL STRUCTURE OF HIV-1 NEF PROTEIN BOUND TO THE FYN REMARK 1 TITL 2 KINASE SH3 DOMAIN SUGGESTS A ROLE FOR THIS COMPLEX IN REMARK 1 TITL 3 ALTERED T CELL RECEPTOR SIGNALING. REMARK 1 REF STRUCTURE V. 5 1361 1997 REMARK 1 REFN ISSN 0969-2126 REMARK 1 PMID 9351809 REMARK 1 DOI 10.1016/S0969-2126(97)00286-4 REMARK 1 REFERENCE 4 REMARK 1 AUTH C.H.LEE,K.SAKSELA,U.A.MIRZA,B.T.CHAIT,J.KURIYAN REMARK 1 TITL CRYSTAL STRUCTURE OF THE CONSERVED CORE OF HIV-1 NEF REMARK 1 TITL 2 COMPLEXED WITH A SRC FAMILY SH3 DOMAIN. REMARK 1 REF CELL(CAMBRIDGE,MASS.) V. 85 931 1996 REMARK 1 REFN ISSN 0092-8674 REMARK 1 PMID 8681387 REMARK 1 DOI 10.1016/S0092-8674(00)81276-3 REMARK 1 REFERENCE 5 REMARK 1 AUTH S.GRZESIEK,A.BAX,G.M.CLORE,A.M.GRONENBORN,J.S.HU,J.KAUFMAN, REMARK 1 AUTH 2 I.PALMER,S.J.STAHL,P.T.WINGFIELD REMARK 1 TITL THE SOLUTION STRUCTURE OF HIV-1 NEF REVEALS AN UNEXPECTED REMARK 1 TITL 2 FOLD AND PERMITS DELINEATION OF THE BINDING SURFACE FOR THE REMARK 1 TITL 3 SH3 DOMAIN OF HCK TYROSINE PROTEIN KINASE. REMARK 1 REF NAT.STRUCT.BIOL. V. 3 340 1996 REMARK 1 REFN ISSN 1072-8368 REMARK 1 PMID 8599760 REMARK 1 DOI 10.1038/NSB0496-340 REMARK 1 REFERENCE 6 REMARK 1 AUTH J.FREUND,R.KELLNER,J.KONVALINKA,V.WOLBER,H.G.KRAUSSLICH, REMARK 1 AUTH 2 H.R.KALBITZER REMARK 1 TITL A POSSIBLE REGULATION OF NEGATIVE FACTOR (NEF) ACTIVITY OF REMARK 1 TITL 2 HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 BY THE VIRAL PROTEASE. REMARK 1 REF EUR.J.BIOCHEM. V. 223 589 1994 REMARK 1 REFN ISSN 0014-2956 REMARK 1 PMID 8055930 REMARK 1 DOI 10.1111/J.1432-1033.1994.TB19029.X REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURES WERE CALCULATED WITH X-PLOR, V. 3.851 (BRUNGER, REMARK 3 1992) USING A DISTANCE GEOMETRY/SIMULATED ANNEALING PROTOCOL REMARK 3 (NILGES ET AL., FEBS LETT. 229, 317 (1988)). THE 3D STRUCTURE OF REMARK 3 MYRISTOYLATED HIV-1 NEF ANCHOR REMARK 3 DOMAIN (MYR-2-57) SOLVED BY TWO-DIMENSIONAL HOMONUCLEAR NMR REMARK 3 SPECTROSCOPY IS BASED ON 540 EXPERIMENTAL RESTRAINTS: REMARK 3 332 INTRARESIDUAL, 156 SEQUENTIAL AND MEDIUM RANGE (1<=|I-J|<=4), REMARK 3 AND 10 LONG RANGE (|I-J|>=5) INTERPROTON REMARK 3 DISTANCE RESTRAINTS; 42 TORSION ANGLE RESTRAINTS (PHI). NO REMARK 3 RESTRAINTS FOR HYDROGEN BONDS WERE ADDED. REMARK 4 REMARK 4 1QA5 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-APR-99. REMARK 100 THE DEPOSITION ID IS D_1000000836. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 285 REMARK 210 PH : 4.6 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 1H REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AMX; DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : AURELIA 2.0, X-PLOR 3.851 REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 400 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 2 REMARK 210 CONFORMERS, SELECTION CRITERIA : TWO STRUCTURES WITH LOW TOTAL REMARK 210 ENERGY WERE SELECTED SHOWING THE REMARK 210 CONFORMATIONAL VARIETY OF THE REMARK 210 FLEXIBLE DOMAIN REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: REMARK 210 THE COORDINATES OF 2 SIMULATED ANNEALING STRUCTURES ARE PRESENTED REMARK 210 IN THIS ENTRY. THE STRUCTURE OF THE REMARK 210 MYRISTOYLATED HIV-1 NEF ANCHOR DOMAIN IS HIGHLY FLEXIBLE AND NOT REMARK 210 WELL DEFINED BY NMR RESTRAINTS. ONLY TWO REMARK 210 SECONDARY STRUCTURE ELEMENTS CAN BE OBSERVED: A FIRST HELIX IN REMARK 210 THE POSITIVE CLUSTER REGION FROM PRO14 TO ARG22 REMARK 210 AND A SECOND HELICAL REGION FROM ALA33 TO GLY41. ADDITIONALLY, THE REMARK 210 N-TERMINAL MYRISTIC ACID RESIDUE REMARK 210 CLOSELY INTERACTS WITH THE SIDE CHAIN OF TRP5 AND THEREBY FORMS A REMARK 210 LOOP WITH GLY2, GLY3 AND LYS4 IN THE REMARK 210 KINK REGION. TWO MODELS ARE PRESENTED TO DEMONSTRATE THE REMARK 210 CONFORMATIONAL VARIETY OF THE STRUCTURES CALCULATED. 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: 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 SER A 6 86.30 50.18 REMARK 500 1 VAL A 11 154.70 58.08 REMARK 500 1 TRP A 13 81.03 -159.42 REMARK 500 1 PRO A 14 45.22 -80.66 REMARK 500 1 ARG A 22 -76.13 -87.45 REMARK 500 1 ALA A 23 -84.36 155.77 REMARK 500 1 GLU A 24 112.44 176.77 REMARK 500 1 ASP A 28 71.65 47.03 REMARK 500 1 ALA A 33 -79.78 -76.14 REMARK 500 1 SER A 34 -77.52 -87.89 REMARK 500 1 ARG A 35 -98.68 -100.32 REMARK 500 1 ASP A 36 -62.71 -125.66 REMARK 500 1 ALA A 49 -129.50 53.28 REMARK 500 1 ALA A 50 -153.65 53.36 REMARK 500 1 ASN A 52 85.54 44.17 REMARK 500 1 ALA A 54 -167.66 57.99 REMARK 500 2 LYS A 4 104.63 53.38 REMARK 500 2 GLU A 18 -70.47 -53.72 REMARK 500 2 ALA A 23 -170.89 52.57 REMARK 500 2 ALA A 27 -156.00 -125.90 REMARK 500 2 ALA A 32 135.89 168.35 REMARK 500 2 SER A 34 -89.29 -85.44 REMARK 500 2 ARG A 35 -91.89 -108.26 REMARK 500 2 SER A 46 78.66 -160.78 REMARK 500 2 ALA A 49 -145.86 50.32 REMARK 500 2 ALA A 50 128.07 61.89 REMARK 500 2 ASN A 51 -111.58 -131.34 REMARK 500 2 ALA A 53 -122.50 -170.65 REMARK 500 2 ALA A 54 148.20 63.88 REMARK 500 2 CYS A 55 128.67 -178.53 REMARK 500 2 ALA A 56 172.56 171.61 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 ARG A 17 0.31 SIDE CHAIN REMARK 500 1 ARG A 19 0.30 SIDE CHAIN REMARK 500 1 ARG A 21 0.31 SIDE CHAIN REMARK 500 1 ARG A 22 0.32 SIDE CHAIN REMARK 500 1 ARG A 35 0.32 SIDE CHAIN REMARK 500 2 ARG A 17 0.32 SIDE CHAIN REMARK 500 2 ARG A 19 0.32 SIDE CHAIN REMARK 500 2 ARG A 21 0.31 SIDE CHAIN REMARK 500 2 ARG A 22 0.30 SIDE CHAIN REMARK 500 2 ARG A 35 0.32 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1QA5 A 2 57 UNP P04324 NEF_HV112 2 57 SEQADV 1QA5 MYR A 1 P04324 MODIFIED RESIDUE SEQADV 1QA5 NH2 A 58 P04324 AMIDATION SEQRES 1 A 58 MYR GLY GLY LYS TRP SER LYS SER SER VAL VAL GLY TRP SEQRES 2 A 58 PRO ALA VAL ARG GLU ARG MET ARG ARG ALA GLU PRO ALA SEQRES 3 A 58 ALA ASP GLY VAL GLY ALA ALA SER ARG ASP LEU GLU LYS SEQRES 4 A 58 HIS GLY ALA ILE THR SER SER ASN THR ALA ALA ASN ASN SEQRES 5 A 58 ALA ALA CYS ALA TRP NH2 HET MYR A 1 42 HET NH2 A 58 3 HETNAM MYR MYRISTIC ACID HETNAM NH2 AMINO GROUP FORMUL 1 MYR C14 H28 O2 FORMUL 1 NH2 H2 N HELIX 1 1 VAL A 16 ARG A 22 1 7 HELIX 2 2 LEU A 37 GLY A 41 1 5 LINK C1 MYR A 1 N GLY A 2 1555 1555 1.31 LINK C TRP A 57 N NH2 A 58 1555 1555 1.30 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 HETATM 1 C1 MYR A 1 63.925 -9.939 8.222 1.00-10.00 C HETATM 2 O1 MYR A 1 64.874 -10.258 7.530 1.00-10.00 O HETATM 3 C2 MYR A 1 62.639 -9.398 7.592 1.00-10.00 C HETATM 4 C3 MYR A 1 61.843 -10.556 6.981 1.00-10.00 C HETATM 5 C4 MYR A 1 60.807 -10.006 5.995 1.00-10.00 C HETATM 6 C5 MYR A 1 60.508 -11.058 4.921 1.00-10.00 C HETATM 7 C6 MYR A 1 59.031 -11.459 4.987 1.00-10.00 C HETATM 8 C7 MYR A 1 58.221 -10.588 4.021 1.00-10.00 C HETATM 9 C8 MYR A 1 56.959 -10.077 4.722 1.00-10.00 C HETATM 10 C9 MYR A 1 57.348 -9.063 5.803 1.00-10.00 C HETATM 11 C10 MYR A 1 56.340 -7.909 5.814 1.00-10.00 C HETATM 12 C11 MYR A 1 56.009 -7.529 7.260 1.00-10.00 C HETATM 13 C12 MYR A 1 57.093 -6.595 7.811 1.00-10.00 C HETATM 14 C13 MYR A 1 57.802 -7.270 8.988 1.00-10.00 C HETATM 15 C14 MYR A 1 58.680 -6.246 9.713 1.00-10.00 C HETATM 16 H21 MYR A 1 62.044 -8.913 8.352 1.00-10.00 H HETATM 17 H22 MYR A 1 62.888 -8.684 6.820 1.00-10.00 H HETATM 18 H31 MYR A 1 62.519 -11.218 6.460 1.00-10.00 H HETATM 19 H32 MYR A 1 61.339 -11.101 7.766 1.00-10.00 H HETATM 20 H41 MYR A 1 59.899 -9.765 6.528 1.00-10.00 H HETATM 21 H42 MYR A 1 61.195 -9.114 5.525 1.00-10.00 H HETATM 22 H51 MYR A 1 60.723 -10.645 3.947 1.00-10.00 H HETATM 23 H52 MYR A 1 61.124 -11.930 5.086 1.00-10.00 H HETATM 24 H61 MYR A 1 58.930 -12.497 4.707 1.00-10.00 H HETATM 25 H62 MYR A 1 58.664 -11.321 5.994 1.00-10.00 H HETATM 26 H71 MYR A 1 58.823 -9.748 3.707 1.00-10.00 H HETATM 27 H72 MYR A 1 57.941 -11.173 3.156 1.00-10.00 H HETATM 28 H81 MYR A 1 56.315 -9.603 3.997 1.00-10.00 H HETATM 29 H82 MYR A 1 56.438 -10.906 5.178 1.00-10.00 H HETATM 30 H91 MYR A 1 57.349 -9.550 6.767 1.00-10.00 H HETATM 31 H92 MYR A 1 58.335 -8.675 5.595 1.00-10.00 H HETATM 32 H101 MYR A 1 56.766 -7.058 5.305 1.00-10.00 H HETATM 33 H102 MYR A 1 55.435 -8.215 5.307 1.00-10.00 H HETATM 34 H111 MYR A 1 55.055 -7.025 7.288 1.00-10.00 H HETATM 35 H112 MYR A 1 55.961 -8.422 7.866 1.00-10.00 H HETATM 36 H121 MYR A 1 57.811 -6.381 7.033 1.00-10.00 H HETATM 37 H122 MYR A 1 56.639 -5.673 8.146 1.00-10.00 H HETATM 38 H131 MYR A 1 57.065 -7.661 9.673 1.00-10.00 H HETATM 39 H132 MYR A 1 58.420 -8.077 8.623 1.00-10.00 H HETATM 40 H141 MYR A 1 59.003 -6.654 10.660 1.00-10.00 H HETATM 41 H142 MYR A 1 58.112 -5.343 9.886 1.00-10.00 H HETATM 42 H143 MYR A 1 59.543 -6.017 9.106 1.00-10.00 H