HEADER VIRAL PROTEIN/SIGNALING PROTEIN 15-AUG-09 3IOZ TITLE SIVMAC239 NEF IN COMPLEX WITH A TCR ZETA POLYPEPTIDE DP1 (L51-D93) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN NEF; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: T-CELL SURFACE GLYCOPROTEIN CD3 ZETA CHAIN; COMPND 7 CHAIN: B; COMPND 8 SYNONYM: T-CELL RECEPTOR T3 ZETA CHAIN; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SIMIAN IMMUNODEFICIENCY VIRUS; SOURCE 3 ORGANISM_TAXID: 388909; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 13 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) KEYWDS PROTEIN-PROTEIN COMPLEX, CELL MEMBRANE, LIPOPROTEIN, MEMBRANE, KEYWDS 2 MYRISTATE, VIRAL IMMUNOEVASION, VIRULENCE, DISULFIDE BOND, HOST- KEYWDS 3 VIRUS INTERACTION, PHOSPHOPROTEIN, RECEPTOR, TRANSMEMBRANE, VIRAL KEYWDS 4 PROTEIN-ANTIVIRAL PROTEIN COMPLEX, VIRAL PROTEIN-SIGNALING PROTEIN KEYWDS 5 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR W.M.KIM,A.B.SIGALOV,L.J.STERN REVDAT 4 21-FEB-24 3IOZ 1 SEQADV REVDAT 3 01-NOV-17 3IOZ 1 REMARK REVDAT 2 28-MAR-12 3IOZ 1 JRNL VERSN REVDAT 1 02-FEB-10 3IOZ 0 JRNL AUTH W.M.KIM,A.B.SIGALOV,L.J.STERN JRNL TITL PSEUDO-MEROHEDRAL TWINNING AND NONCRYSTALLOGRAPHIC SYMMETRY JRNL TITL 2 IN ORTHORHOMBIC CRYSTALS OF SIVMAC239 NEF CORE DOMAIN BOUND JRNL TITL 3 TO DIFFERENT-LENGTH TCRZETA FRAGMENTS. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 66 163 2010 JRNL REFN ISSN 0907-4449 JRNL PMID 20124696 JRNL DOI 10.1107/S090744490904880X REMARK 2 REMARK 2 RESOLUTION. 3.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.220 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 3 NUMBER OF REFLECTIONS : 2923 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.302 REMARK 3 R VALUE (WORKING SET) : 0.301 REMARK 3 FREE R VALUE : 0.329 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.380 REMARK 3 FREE R VALUE TEST SET COUNT : 128 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 0.0000 - 3.6990 0.94 2795 128 0.3010 0.3290 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.31 REMARK 3 B_SOL : 143.6 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 2.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 206.4 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 28.37900 REMARK 3 B22 (A**2) : 28.37900 REMARK 3 B33 (A**2) : -84.59200 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.003 1088 REMARK 3 ANGLE : 0.565 1478 REMARK 3 CHIRALITY : 0.040 144 REMARK 3 PLANARITY : 0.003 187 REMARK 3 DIHEDRAL : 13.315 383 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3IOZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-AUG-09. REMARK 100 THE DEPOSITION ID IS D_1000054683. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-OCT-08 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 8.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.290 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3122 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 12.60 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.70 REMARK 200 R MERGE FOR SHELL (I) : 0.39300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.1.4 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG 3350, 0.15M KF, 0.1M HEPES, PH REMARK 280 8.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 94.72450 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 25.81900 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 25.81900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 142.08675 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 25.81900 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 25.81900 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 47.36225 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 25.81900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 25.81900 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 142.08675 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 25.81900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 25.81900 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 47.36225 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 94.72450 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 93 REMARK 465 SER A 94 REMARK 465 ASP A 95 REMARK 465 ASP A 96 REMARK 465 LEU A 97 REMARK 465 VAL A 98 REMARK 465 GLY A 99 REMARK 465 VAL A 100 REMARK 465 SER A 101 REMARK 465 VAL A 102 REMARK 465 ARG A 103 REMARK 465 PRO A 104 REMARK 465 LYS A 105 REMARK 465 VAL A 106 REMARK 465 ASN A 181 REMARK 465 VAL A 182 REMARK 465 SER A 183 REMARK 465 ASP A 184 REMARK 465 GLU A 185 REMARK 465 ALA A 186 REMARK 465 GLN A 187 REMARK 465 GLU A 188 REMARK 465 ASP A 189 REMARK 465 GLU A 190 REMARK 465 GLU A 191 REMARK 465 HIS A 192 REMARK 465 TYR A 193 REMARK 465 LEU A 194 REMARK 465 MET A 195 REMARK 465 HIS A 196 REMARK 465 PRO A 197 REMARK 465 ALA A 198 REMARK 465 GLN A 199 REMARK 465 SER A 235 REMARK 465 GLY B 49 REMARK 465 SER B 50 REMARK 465 LEU B 51 REMARK 465 ARG B 52 REMARK 465 VAL B 53 REMARK 465 LYS B 54 REMARK 465 PHE B 55 REMARK 465 SER B 56 REMARK 465 ARG B 57 REMARK 465 SER B 58 REMARK 465 ALA B 59 REMARK 465 ASP B 60 REMARK 465 ALA B 61 REMARK 465 PRO B 62 REMARK 465 ARG B 79 REMARK 465 ARG B 80 REMARK 465 GLU B 81 REMARK 465 GLU B 82 REMARK 465 TYR B 83 REMARK 465 ASP B 84 REMARK 465 VAL B 85 REMARK 465 LEU B 86 REMARK 465 ASP B 87 REMARK 465 LYS B 88 REMARK 465 ARG B 89 REMARK 465 ARG B 90 REMARK 465 GLY B 91 REMARK 465 ARG B 92 REMARK 465 ASP B 93 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 ARG A 109 136.69 -179.31 REMARK 500 LEU A 115 -72.63 -63.52 REMARK 500 ILE A 117 -72.75 -55.40 REMARK 500 LEU A 129 -44.48 77.06 REMARK 500 GLU A 130 107.13 -46.88 REMARK 500 ASP A 143 -36.58 -39.74 REMARK 500 PRO A 154 29.54 -72.56 REMARK 500 PRO A 163 -143.59 -75.94 REMARK 500 ASP A 204 -169.67 -64.55 REMARK 500 ASP A 216 107.64 -160.53 REMARK 500 THR A 222 102.13 -160.25 REMARK 500 ALA A 225 -74.72 -54.43 REMARK 500 GLU A 232 44.19 -98.42 REMARK 500 ASN B 76 39.76 72.72 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3IK5 RELATED DB: PDB DBREF 3IOZ A 95 235 UNP Q5QGG3 Q5QGG3_SIVCZ 95 235 DBREF 3IOZ B 51 93 UNP P20963 CD3Z_HUMAN 51 93 SEQADV 3IOZ GLY A 93 UNP Q5QGG3 EXPRESSION TAG SEQADV 3IOZ SER A 94 UNP Q5QGG3 EXPRESSION TAG SEQADV 3IOZ GLY B 49 UNP P20963 EXPRESSION TAG SEQADV 3IOZ SER B 50 UNP P20963 EXPRESSION TAG SEQRES 1 A 143 GLY SER ASP ASP LEU VAL GLY VAL SER VAL ARG PRO LYS SEQRES 2 A 143 VAL PRO LEU ARG THR MET SER TYR LYS LEU ALA ILE ASP SEQRES 3 A 143 MET SER HIS PHE ILE LYS GLU LYS GLY GLY LEU GLU GLY SEQRES 4 A 143 ILE TYR TYR SER ALA ARG ARG HIS ARG ILE LEU ASP ILE SEQRES 5 A 143 TYR LEU GLU LYS GLU GLU GLY ILE ILE PRO ASP TRP GLN SEQRES 6 A 143 ASP TYR THR SER GLY PRO GLY ILE ARG TYR PRO LYS THR SEQRES 7 A 143 PHE GLY TRP LEU TRP LYS LEU VAL PRO VAL ASN VAL SER SEQRES 8 A 143 ASP GLU ALA GLN GLU ASP GLU GLU HIS TYR LEU MET HIS SEQRES 9 A 143 PRO ALA GLN THR SER GLN TRP ASP ASP PRO TRP GLY GLU SEQRES 10 A 143 VAL LEU ALA TRP LYS PHE ASP PRO THR LEU ALA TYR THR SEQRES 11 A 143 TYR GLU ALA TYR VAL ARG TYR PRO GLU GLU PHE GLY SER SEQRES 1 B 45 GLY SER LEU ARG VAL LYS PHE SER ARG SER ALA ASP ALA SEQRES 2 B 45 PRO ALA TYR GLN GLN GLY GLN ASN GLN LEU TYR ASN GLU SEQRES 3 B 45 LEU ASN LEU GLY ARG ARG GLU GLU TYR ASP VAL LEU ASP SEQRES 4 B 45 LYS ARG ARG GLY ARG ASP HELIX 1 1 SER A 112 GLU A 125 1 14 HELIX 2 2 SER A 135 GLY A 151 1 17 HELIX 3 3 PRO A 217 TYR A 221 5 5 HELIX 4 4 TYR A 223 TYR A 229 1 7 HELIX 5 5 GLN B 65 GLU B 74 1 10 SHEET 1 A 2 TRP A 175 VAL A 178 0 SHEET 2 A 2 ALA A 212 PHE A 215 -1 O LYS A 214 N LYS A 176 CISPEP 1 GLY A 162 PRO A 163 0 -0.02 CRYST1 51.638 51.638 189.449 90.00 90.00 90.00 P 43 21 2 8 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 0.019366 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019366 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005278 0.00000