PDB Short entry for 2NEF HEADER REGULATORY FACTOR 12-FEB-97 2NEF TITLE HIV-1 NEF (REGULATORY FACTOR), NMR, 40 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEGATIVE FACTOR (F-PROTEIN); COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HIV-1 NEF; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1; SOURCE 3 ORGANISM_TAXID: 11678; SOURCE 4 STRAIN: BH10; SOURCE 5 GENE: HIV-1 NEF; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: DE3; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET11A; SOURCE 10 EXPRESSION_SYSTEM_GENE: HIV-1 NEF KEYWDS REGULATORY FACTOR, AIDS, MYRISTYLATION, GTP-BINDING EXPDTA SOLUTION NMR NUMMDL 40 AUTHOR S.GRZESIEK,A.BAX,G.M.CLORE,A.M.GRONENBORN,J.S.HU,J.KAUFMAN,I.PALMER, AUTHOR 2 S.J.STAHL,N.TJANDRA,P.T.WINGFIELD REVDAT 4 29-NOV-17 2NEF 1 HELIX REVDAT 3 13-JUL-11 2NEF 1 VERSN REVDAT 2 24-FEB-09 2NEF 1 VERSN REVDAT 1 07-JUL-97 2NEF 0 SPRSDE 07-JUL-97 2NEF 1NEF JRNL AUTH S.GRZESIEK,A.BAX,J.S.HU,J.KAUFMAN,I.PALMER,S.J.STAHL, JRNL AUTH 2 N.TJANDRA,P.T.WINGFIELD JRNL TITL REFINED SOLUTION STRUCTURE AND BACKBONE DYNAMICS OF HIV-1 JRNL TITL 2 NEF. JRNL REF PROTEIN SCI. V. 6 1248 1997 JRNL REFN ISSN 0961-8368 JRNL PMID 9194185 REMARK 1 REMARK 1 REFERENCE 1 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 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURES WERE CALCULATED USING THE SIMULATED REMARK 3 ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. REMARK 3 229, 129 - 136 USING THE PROGRAM X-PLOR 3.1 (BRUNGER) REMARK 3 MODIFIED TO INCORPORATE COUPLING CONSTANT (GARRETT ET AL. REMARK 3 (1984) J. MAGN. RESON. SERIES B 104, 99 - 103) AND CARBON REMARK 3 CHEMICAL SHIFT (KUSZEWSKI ET AL. (1995) J. MAGN. RESON. REMARK 3 SERIES B 106, 92 - 96) RESTRAINTS. REMARK 3 REMARK 3 THE COORDINATES OF THE 40 FINAL SIMULATED ANNEALING REMARK 3 STRUCTURES ARE PRESENTED IN THIS ENTRY. THE B FACTOR REMARK 3 FIELD PRESENTS THE AVERAGE RMS OF THE 40 INDIVIDUAL REMARK 3 STRUCTURES ABOUT THE MEAN COORDINATE POSITIONS OBTAINED BY REMARK 3 BEST FITTING RESIDUES 76 - 94, 97 - 102, 106 -147, 181 - REMARK 3 191, AND 194 -199. THESE RESIDUES CORRESPOND TO THE REMARK 3 NON-MOBILE CORE OF THE PROTEIN AS EVIDENCED BY 15N REMARK 3 RELAXATION DATA. REMARK 4 REMARK 4 2NEF COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000178400. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : NULL REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 40 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: REMARK 210 THE 3D STRUCTURE OF THE HIV-1 NEF (DELTA2 - 39, DELTA 159 - REMARK 210 173) SOLVED BY MULTI-DIMENSIONAL HETERONUCLEAR-EDITED AND REMARK 210 -FILTERED NMR IS BASED ON 1250 EXPERIMENTAL RESTRAINTS: REMARK 210 338 SEQUENTIAL (|I-J|=1), 101 MEDIUM RANGE (1 < |I-J| <=5) REMARK 210 AND 245 LONG RANGE (|I-J| >5) INTERRESIDUES AND 70 REMARK 210 INTRARESIDUE APPROXIMATE INTERPROTON DISTANCE RESTRAINTS; REMARK 210 64 DISTANCE RESTRAINTS FOR 32 HYDROGEN BONDS; 157 TORSION REMARK 210 ANGLE (78 PHI, 10 PSI, 55 CHI1 AND 14 CHI2) RESTRAINTS; 91 REMARK 210 THREE-BOND HN-HA COUPLING CONSTANT RESTRAINTS; AND 184 (93 REMARK 210 CALPHA AND 91 CBETA) 13C SHIFT RESTRAINTS. 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HG SER A 88 HD1 HIS A 89 1.32 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 GLU A 62 -83.59 -147.98 REMARK 500 1 GLU A 64 155.34 -45.17 REMARK 500 1 VAL A 66 31.27 -81.13 REMARK 500 1 PHE A 68 43.36 -155.79 REMARK 500 1 GLN A 73 98.06 -53.11 REMARK 500 1 PRO A 75 108.43 -34.05 REMARK 500 1 LEU A 76 97.85 -61.80 REMARK 500 1 LYS A 94 28.58 -77.49 REMARK 500 1 SER A 103 -75.93 -66.39 REMARK 500 1 GLN A 104 -41.51 -170.82 REMARK 500 1 HIS A 116 11.69 -62.72 REMARK 500 1 THR A 117 -82.72 -126.03 REMARK 500 1 PRO A 122 40.33 -75.32 REMARK 500 1 PRO A 129 -168.61 -71.27 REMARK 500 1 PRO A 131 -167.45 -76.95 REMARK 500 1 ILE A 133 175.82 -48.80 REMARK 500 1 ARG A 134 102.34 -165.90 REMARK 500 1 CYS A 142 49.55 -80.28 REMARK 500 1 GLU A 151 79.94 -61.24 REMARK 500 1 LEU A 153 41.85 -82.55 REMARK 500 1 ALA A 156 -58.43 -173.58 REMARK 500 1 LYS A 158 38.46 -92.56 REMARK 500 1 ASP A 174 -121.18 -93.96 REMARK 500 1 ASP A 186 67.79 -154.67 REMARK 500 1 SER A 187 -11.19 -44.33 REMARK 500 1 PHE A 191 -33.41 -141.48 REMARK 500 1 HIS A 193 75.12 -157.92 REMARK 500 1 LEU A 198 -70.58 -76.48 REMARK 500 1 ASN A 205 -84.68 -79.98 REMARK 500 2 LEU A 58 -73.12 -81.30 REMARK 500 2 GLN A 61 -106.64 -63.62 REMARK 500 2 GLU A 62 -69.45 -170.52 REMARK 500 2 GLU A 63 -75.43 -83.71 REMARK 500 2 GLU A 64 107.49 -56.39 REMARK 500 2 GLU A 65 -165.43 -79.34 REMARK 500 2 PHE A 68 52.33 -153.04 REMARK 500 2 PRO A 69 -178.49 -68.98 REMARK 500 2 VAL A 70 -159.79 -84.35 REMARK 500 2 PRO A 72 -160.22 -77.89 REMARK 500 2 GLN A 73 97.38 -38.90 REMARK 500 2 PRO A 75 136.79 -33.90 REMARK 500 2 GLU A 93 -72.91 -72.07 REMARK 500 2 ILE A 101 107.45 -58.80 REMARK 500 2 SER A 103 -81.51 -67.14 REMARK 500 2 GLN A 104 -27.48 -156.94 REMARK 500 2 THR A 117 -94.89 -99.21 REMARK 500 2 PRO A 122 95.02 -42.92 REMARK 500 2 ASP A 123 18.96 -154.81 REMARK 500 2 PRO A 129 38.39 -76.04 REMARK 500 2 PRO A 131 -118.48 -85.25 REMARK 500 REMARK 500 THIS ENTRY HAS 1240 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE MATERIAL USED WAS A DELETION MUTANT: DELTA 2 - 39 AND REMARK 999 DELTA 159 - 173, WHICH REMOVES THE DISORDERED N-TERMINUS REMARK 999 AND REDUCES THE SIZE OF A LONG DISORDERED SOLVENT EXPOSED REMARK 999 LOOP. IT ALSO CONTAINS A CYS 206 TO ALA MUTATION TO REMARK 999 PREVENT THE FORMATION OF INTERMOLECULAR DISULFIDES. THE REMARK 999 HIV-1 STRAIN FROM WHICH THE PROTEIN WAS DERIVED IS STRAIN REMARK 999 BH10. DBREF 2NEF A 56 205 UNP Q70627 NEF_HV1LW 56 205 SEQADV 2NEF GLU A 65 UNP Q70627 LYS 65 CONFLICT SEQADV 2NEF A UNP Q70627 GLY 159 DELETION SEQADV 2NEF A UNP Q70627 GLU 160 DELETION SEQADV 2NEF A UNP Q70627 ASN 161 DELETION SEQADV 2NEF A UNP Q70627 THR 162 DELETION SEQADV 2NEF A UNP Q70627 SER 163 DELETION SEQADV 2NEF A UNP Q70627 LEU 164 DELETION SEQADV 2NEF A UNP Q70627 LEU 165 DELETION SEQADV 2NEF A UNP Q70627 HIS 166 DELETION SEQADV 2NEF A UNP Q70627 PRO 167 DELETION SEQADV 2NEF A UNP Q70627 VAL 168 DELETION SEQADV 2NEF A UNP Q70627 SER 169 DELETION SEQADV 2NEF A UNP Q70627 LEU 170 DELETION SEQADV 2NEF A UNP Q70627 HIS 171 DELETION SEQADV 2NEF A UNP Q70627 GLY 172 DELETION SEQADV 2NEF A UNP Q70627 MET 173 DELETION SEQADV 2NEF MET A 194 UNP Q70627 VAL 194 CONFLICT SEQRES 1 A 136 ALA TRP LEU GLU ALA GLN GLU GLU GLU GLU VAL GLY PHE SEQRES 2 A 136 PRO VAL THR PRO GLN VAL PRO LEU ARG PRO MET THR TYR SEQRES 3 A 136 LYS ALA ALA VAL ASP LEU SER HIS PHE LEU LYS GLU LYS SEQRES 4 A 136 GLY GLY LEU GLU GLY LEU ILE HIS SER GLN ARG ARG GLN SEQRES 5 A 136 ASP ILE LEU ASP LEU TRP ILE TYR HIS THR GLN GLY TYR SEQRES 6 A 136 PHE PRO ASP TRP GLN ASN TYR THR PRO GLY PRO GLY ILE SEQRES 7 A 136 ARG TYR PRO LEU THR PHE GLY TRP CYS TYR LYS LEU VAL SEQRES 8 A 136 PRO VAL GLU PRO GLU LYS LEU GLU GLU ALA ASN LYS ASP SEQRES 9 A 136 ASP PRO GLU ARG GLU VAL LEU GLU TRP ARG PHE ASP SER SEQRES 10 A 136 ARG LEU ALA PHE HIS HIS MET ALA ARG GLU LEU HIS PRO SEQRES 11 A 136 GLU TYR PHE LYS ASN ALA HELIX 1 1 PRO A 69 PRO A 78 10 10 HELIX 2 2 TYR A 81 LYS A 94 1 14 HELIX 3 3 ARG A 105 ILE A 114 1 10 HELIX 4 4 SER A 187 ALA A 190 5 4 HELIX 5 5 MET A 194 LEU A 198 1 5 SHEET 1 A 5 LEU A 100 HIS A 102 0 SHEET 2 A 5 LEU A 181 ASP A 186 -1 SHEET 3 A 5 TYR A 143 PRO A 147 -1 SHEET 4 A 5 ILE A 133 LEU A 137 -1 SHEET 5 A 5 ASN A 126 THR A 128 -1 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