PDB Short entry for 4F8Q HEADER IMMUNE SYSTEM 17-MAY-12 4F8Q TITLE CRYSTAL STRUCTURE OF THE HUMAN BTN3A2 ECTODOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: BUTYROPHILIN SUBFAMILY 3 MEMBER A2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ECTODOMAIN (UNP RESIDUES 30-239); COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: BT3.2, BTF3, BTF4, BTN3A2; SOURCE 6 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PACGP67A KEYWDS B7 SUPERFAMILY, BUTYROPHILIN, CD277, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR A.PALAKODETI,A.SANDSTROM,L.SUNDARESAN,C.HARLY,S.NEDELLEC,D.OLIVE, AUTHOR 2 E.SCOTET,M.BONNEVILLE,E.J.ADAMS REVDAT 3 13-SEP-23 4F8Q 1 SEQADV REVDAT 2 19-JUN-13 4F8Q 1 JRNL REVDAT 1 08-AUG-12 4F8Q 0 JRNL AUTH A.PALAKODETI,A.SANDSTROM,L.SUNDARESAN,C.HARLY,S.NEDELLEC, JRNL AUTH 2 D.OLIVE,E.SCOTET,M.BONNEVILLE,E.J.ADAMS JRNL TITL THE MOLECULAR BASIS FOR MODULATION OF HUMAN JRNL TITL 2 V(GAMMA)9V(DELTA)2 T CELL RESPONSES BY CD277/BUTYROPHILIN-3 JRNL TITL 3 (BTN3A)-SPECIFIC ANTIBODIES JRNL REF J.BIOL.CHEM. V. 287 32780 2012 JRNL REFN ISSN 0021-9258 JRNL PMID 22846996 JRNL DOI 10.1074/JBC.M112.384354 REMARK 2 REMARK 2 RESOLUTION. 2.38 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7_650 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) : 2.38 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.31 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.8 REMARK 3 NUMBER OF REFLECTIONS : 9977 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.234 REMARK 3 R VALUE (WORKING SET) : 0.232 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 489 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 42.3197 - 3.4305 1.00 3615 182 0.2129 0.2249 REMARK 3 2 3.4305 - 2.7230 0.98 3367 155 0.2458 0.3042 REMARK 3 3 2.7230 - 2.3789 0.74 2506 152 0.2976 0.3901 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.83 REMARK 3 K_SOL : 0.36 REMARK 3 B_SOL : 47.71 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.700 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.71 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.19 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.82550 REMARK 3 B22 (A**2) : -5.72880 REMARK 3 B33 (A**2) : 2.90330 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 : 0.012 1620 REMARK 3 ANGLE : 1.321 2194 REMARK 3 CHIRALITY : 0.071 246 REMARK 3 PLANARITY : 0.010 284 REMARK 3 DIHEDRAL : 11.271 582 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 0:115) REMARK 3 ORIGIN FOR THE GROUP (A): 16.4615 -22.6466 -25.1482 REMARK 3 T TENSOR REMARK 3 T11: 0.0837 T22: 0.0521 REMARK 3 T33: 0.0804 T12: -0.0098 REMARK 3 T13: 0.0401 T23: -0.0185 REMARK 3 L TENSOR REMARK 3 L11: 0.7474 L22: 1.0566 REMARK 3 L33: 0.9449 L12: -0.1802 REMARK 3 L13: -0.0348 L23: -0.1930 REMARK 3 S TENSOR REMARK 3 S11: 0.1353 S12: 0.0698 S13: -0.0890 REMARK 3 S21: 0.0910 S22: -0.0560 S23: -0.0542 REMARK 3 S31: -0.0823 S32: 0.0847 S33: 0.0296 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 116:214) REMARK 3 ORIGIN FOR THE GROUP (A): 13.7117 13.4070 -9.2149 REMARK 3 T TENSOR REMARK 3 T11: 0.3058 T22: 0.1531 REMARK 3 T33: 0.1777 T12: 0.0355 REMARK 3 T13: -0.0212 T23: -0.0433 REMARK 3 L TENSOR REMARK 3 L11: 1.0006 L22: 0.3880 REMARK 3 L33: 1.5115 L12: -0.5491 REMARK 3 L13: 0.3470 L23: -0.0491 REMARK 3 S TENSOR REMARK 3 S11: 0.1878 S12: 0.0080 S13: 0.0784 REMARK 3 S21: 0.0853 S22: -0.0830 S23: -0.1542 REMARK 3 S31: 0.2968 S32: -0.2359 S33: -0.0031 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 4F8Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-MAY-12. REMARK 100 THE DEPOSITION ID IS D_1000072596. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-OCT-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97857 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10267 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.379 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.38 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 50.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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 REMARK 200 STARTING MODEL: PDB ENTRY 4F80 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM CITRATE PH5.6, 0.5M REMARK 280 AMMONIUM SULFATE, 1M LITHIUM SULFATE, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,-Y,-Z+1/2 REMARK 290 4555 -X+1/2,-Y,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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 16.50050 REMARK 290 SMTRY2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.48300 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 16.50050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 50.48300 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: DIMERIC 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 33.00100 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 ALA A -2 REMARK 465 ASP A -1 REMARK 465 ALA A 153 REMARK 465 LYS A 154 REMARK 465 GLY A 155 REMARK 465 GLU A 156 REMARK 465 GLY A 184 REMARK 465 SER A 185 REMARK 465 GLY A 186 REMARK 465 HIS A 215 REMARK 465 HIS A 216 DBREF 4F8Q A 1 210 UNP P78410 BT3A2_HUMAN 30 239 SEQADV 4F8Q ALA A -2 UNP P78410 EXPRESSION TAG SEQADV 4F8Q ASP A -1 UNP P78410 EXPRESSION TAG SEQADV 4F8Q LEU A 0 UNP P78410 EXPRESSION TAG SEQADV 4F8Q HIS A 211 UNP P78410 EXPRESSION TAG SEQADV 4F8Q HIS A 212 UNP P78410 EXPRESSION TAG SEQADV 4F8Q HIS A 213 UNP P78410 EXPRESSION TAG SEQADV 4F8Q HIS A 214 UNP P78410 EXPRESSION TAG SEQADV 4F8Q HIS A 215 UNP P78410 EXPRESSION TAG SEQADV 4F8Q HIS A 216 UNP P78410 EXPRESSION TAG SEQRES 1 A 219 ALA ASP LEU GLN PHE SER VAL LEU GLY PRO SER GLY PRO SEQRES 2 A 219 ILE LEU ALA MET VAL GLY GLU ASP ALA ASP LEU PRO CYS SEQRES 3 A 219 HIS LEU PHE PRO THR MET SER ALA GLU THR MET GLU LEU SEQRES 4 A 219 LYS TRP VAL SER SER SER LEU ARG GLN VAL VAL ASN VAL SEQRES 5 A 219 TYR ALA ASP GLY LYS GLU VAL GLU ASP ARG GLN SER ALA SEQRES 6 A 219 PRO TYR ARG GLY ARG THR SER ILE LEU ARG ASP GLY ILE SEQRES 7 A 219 THR ALA GLY LYS ALA ALA LEU ARG ILE HIS ASN VAL THR SEQRES 8 A 219 ALA SER ASP SER GLY LYS TYR LEU CYS TYR PHE GLN ASP SEQRES 9 A 219 GLY ASP PHE TYR GLU LYS ALA LEU VAL GLU LEU LYS VAL SEQRES 10 A 219 ALA ALA LEU GLY SER ASN LEU HIS VAL GLU VAL LYS GLY SEQRES 11 A 219 TYR GLU ASP GLY GLY ILE HIS LEU GLU CYS ARG SER THR SEQRES 12 A 219 GLY TRP TYR PRO GLN PRO GLN ILE GLN TRP SER ASN ALA SEQRES 13 A 219 LYS GLY GLU ASN ILE PRO ALA VAL GLU ALA PRO VAL VAL SEQRES 14 A 219 ALA ASP GLY VAL GLY LEU TYR GLU VAL ALA ALA SER VAL SEQRES 15 A 219 ILE MET ARG GLY GLY SER GLY GLU GLY VAL SER CYS ILE SEQRES 16 A 219 ILE ARG ASN SER LEU LEU GLY LEU GLU LYS THR ALA SER SEQRES 17 A 219 ILE SER ILE ALA ASP HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *60(H2 O) HELIX 1 1 GLU A 57 GLN A 60 5 4 HELIX 2 2 SER A 61 ARG A 65 5 5 HELIX 3 3 GLY A 74 ALA A 77 5 4 HELIX 4 4 THR A 88 SER A 92 5 5 HELIX 5 5 ALA A 209 HIS A 214 1 6 SHEET 1 A 4 SER A 3 LEU A 5 0 SHEET 2 A 4 ALA A 19 PHE A 26 -1 O HIS A 24 N LEU A 5 SHEET 3 A 4 LYS A 79 ILE A 84 -1 O LEU A 82 N LEU A 21 SHEET 4 A 4 THR A 68 LEU A 71 -1 N LEU A 71 O ALA A 81 SHEET 1 B 6 ILE A 11 MET A 14 0 SHEET 2 B 6 PHE A 104 ALA A 115 1 O LYS A 113 N ILE A 11 SHEET 3 B 6 GLY A 93 ASP A 101 -1 N TYR A 95 O VAL A 110 SHEET 4 B 6 GLU A 35 SER A 40 -1 N VAL A 39 O LEU A 96 SHEET 5 B 6 GLN A 45 ALA A 51 -1 O VAL A 47 N TRP A 38 SHEET 6 B 6 LYS A 54 GLU A 55 -1 O LYS A 54 N ALA A 51 SHEET 1 C 4 HIS A 122 GLU A 129 0 SHEET 2 C 4 GLY A 132 TRP A 142 -1 O HIS A 134 N GLY A 127 SHEET 3 C 4 TYR A 173 MET A 181 -1 O ALA A 177 N CYS A 137 SHEET 4 C 4 VAL A 161 GLU A 162 -1 N VAL A 161 O SER A 178 SHEET 1 D 4 HIS A 122 GLU A 129 0 SHEET 2 D 4 GLY A 132 TRP A 142 -1 O HIS A 134 N GLY A 127 SHEET 3 D 4 TYR A 173 MET A 181 -1 O ALA A 177 N CYS A 137 SHEET 4 D 4 VAL A 166 ALA A 167 -1 N VAL A 166 O GLU A 174 SHEET 1 E 3 GLN A 147 SER A 151 0 SHEET 2 E 3 GLY A 188 ASN A 195 -1 O ILE A 192 N GLN A 149 SHEET 3 E 3 LEU A 200 SER A 207 -1 O LYS A 202 N ILE A 193 SSBOND 1 CYS A 23 CYS A 97 1555 1555 2.03 SSBOND 2 CYS A 137 CYS A 191 1555 1555 2.02 CISPEP 1 PHE A 26 PRO A 27 0 1.95 CISPEP 2 TYR A 143 PRO A 144 0 -3.00 CRYST1 33.001 77.579 100.966 90.00 90.00 90.00 P 21 2 21 4 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 0.030302 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012890 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009904 0.00000