HEADER IMMUNE SYSTEM 14-JUN-10 3NI0 TITLE CRYSTAL STRUCTURE OF MOUSE BST-2/TETHERIN ECTODOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: BONE MARROW STROMAL ANTIGEN 2; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 53-151; COMPND 5 SYNONYM: BST-2, HM1.24 ANTIGEN, CD317; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: BST2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) CODON PLUS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET23B KEYWDS COILED-COIL, ANTIVIRAL DEFENSE, IMMUNE SYSTEM, GPI ANCHOR EXPDTA X-RAY DIFFRACTION AUTHOR S.M.SCHEAFFER,T.J.BRETT REVDAT 4 06-SEP-23 3NI0 1 REMARK REVDAT 3 16-FEB-11 3NI0 1 JRNL REVDAT 2 19-JAN-11 3NI0 1 JRNL REVDAT 1 17-NOV-10 3NI0 0 JRNL AUTH M.SWIECKI,S.M.SCHEAFFER,M.ALLAIRE,D.H.FREMONT,M.COLONNA, JRNL AUTH 2 T.J.BRETT JRNL TITL STRUCTURAL AND BIOPHYSICAL ANALYSIS OF BST-2/TETHERIN JRNL TITL 2 ECTODOMAINS REVEALS AN EVOLUTIONARY CONSERVED DESIGN TO JRNL TITL 3 INHIBIT VIRUS RELEASE. JRNL REF J.BIOL.CHEM. V. 286 2987 2011 JRNL REFN ISSN 0021-9258 JRNL PMID 21084286 JRNL DOI 10.1074/JBC.M110.190538 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.1_357) 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.15 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.030 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.3 REMARK 3 NUMBER OF REFLECTIONS : 23628 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 1196 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 32.1605 - 3.3296 0.96 2737 133 0.2309 0.2473 REMARK 3 2 3.3296 - 2.6432 0.99 2645 166 0.2081 0.2337 REMARK 3 3 2.6432 - 2.3092 0.98 2632 140 0.1942 0.1998 REMARK 3 4 2.3092 - 2.0981 0.97 2584 123 0.1926 0.2243 REMARK 3 5 2.0981 - 1.9477 0.98 2614 135 0.1991 0.2284 REMARK 3 6 1.9477 - 1.8329 0.89 2352 122 0.2197 0.2503 REMARK 3 7 1.8329 - 1.7411 0.87 2276 135 0.2111 0.2552 REMARK 3 8 1.7411 - 1.6653 0.88 2301 120 0.2213 0.2710 REMARK 3 9 1.6653 - 1.6010 0.87 2291 122 0.2216 0.2762 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 : 0.45 REMARK 3 B_SOL : 47.10 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.75430 REMARK 3 B22 (A**2) : 9.30170 REMARK 3 B33 (A**2) : -11.05600 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 1459 REMARK 3 ANGLE : 0.564 1959 REMARK 3 CHIRALITY : 0.033 241 REMARK 3 PLANARITY : 0.001 262 REMARK 3 DIHEDRAL : 14.348 580 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 3NI0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-JUN-10. REMARK 100 THE DEPOSITION ID IS D_1000059853. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUN-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 4.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00007 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NOIR-1 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25314 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 0.36800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.100 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 1D7M REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M PHOSPHATE/CITRATE, 35% REMARK 280 ISOPROPANOL, 5% PEG 1000, PH 4.6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y+1/2,Z REMARK 290 7555 -X+1/2,Y,-Z REMARK 290 8555 X,-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 16.84250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.21600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.41550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.21600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.84250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 50.41550 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 16.84250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 50.41550 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 55.21600 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 50.41550 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 16.84250 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 55.21600 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 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 253 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 254 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 267 LIES ON A SPECIAL POSITION. 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 53 REMARK 465 ASN A 54 REMARK 465 SER A 55 REMARK 465 VAL A 56 REMARK 465 ALA B 53 REMARK 465 ASN B 54 REMARK 465 SER B 55 REMARK 465 VAL B 56 REMARK 465 ALA B 57 REMARK 465 SER B 145 REMARK 465 SER B 146 REMARK 465 THR B 147 REMARK 465 VAL B 148 REMARK 465 GLN B 149 REMARK 465 VAL B 150 REMARK 465 ASN B 151 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 O HOH B 265 O HOH B 295 1.99 REMARK 500 O HOH B 246 O HOH B 249 2.01 REMARK 500 O HOH A 266 O HOH A 281 2.13 REMARK 500 O HOH A 227 O HOH A 239 2.14 REMARK 500 O HOH B 286 O HOH B 299 2.16 REMARK 500 O HOH A 224 O HOH A 273 2.19 REMARK 500 O HOH A 283 O HOH A 294 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH B 294 O HOH B 294 6765 2.01 REMARK 500 O HOH B 231 O HOH B 235 6765 2.13 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 IPA A 1 DBREF 3NI0 A 53 151 UNP Q8R2Q8 BST2_MOUSE 53 151 DBREF 3NI0 B 53 151 UNP Q8R2Q8 BST2_MOUSE 53 151 SEQRES 1 A 99 ALA ASN SER VAL ALA CYS ARG ASP GLY LEU ARG ALA GLN SEQRES 2 A 99 ALA GLU CYS ARG ASN THR THR HIS LEU LEU GLN ARG GLN SEQRES 3 A 99 LEU THR ARG THR GLN ASP SER LEU LEU GLN ALA GLU THR SEQRES 4 A 99 GLN ALA ASN SER CYS ASN LEU THR VAL VAL THR LEU GLN SEQRES 5 A 99 GLU SER LEU GLU LYS LYS VAL SER GLN ALA LEU GLU GLN SEQRES 6 A 99 GLN ALA ARG ILE LYS GLU LEU GLU ASN GLU VAL THR LYS SEQRES 7 A 99 LEU ASN GLN GLU LEU GLU ASN LEU ARG ILE GLN LYS GLU SEQRES 8 A 99 THR SER SER THR VAL GLN VAL ASN SEQRES 1 B 99 ALA ASN SER VAL ALA CYS ARG ASP GLY LEU ARG ALA GLN SEQRES 2 B 99 ALA GLU CYS ARG ASN THR THR HIS LEU LEU GLN ARG GLN SEQRES 3 B 99 LEU THR ARG THR GLN ASP SER LEU LEU GLN ALA GLU THR SEQRES 4 B 99 GLN ALA ASN SER CYS ASN LEU THR VAL VAL THR LEU GLN SEQRES 5 B 99 GLU SER LEU GLU LYS LYS VAL SER GLN ALA LEU GLU GLN SEQRES 6 B 99 GLN ALA ARG ILE LYS GLU LEU GLU ASN GLU VAL THR LYS SEQRES 7 B 99 LEU ASN GLN GLU LEU GLU ASN LEU ARG ILE GLN LYS GLU SEQRES 8 B 99 THR SER SER THR VAL GLN VAL ASN HET IPA A 1 4 HETNAM IPA ISOPROPYL ALCOHOL HETSYN IPA 2-PROPANOL FORMUL 3 IPA C3 H8 O FORMUL 4 HOH *225(H2 O) HELIX 1 1 CYS A 58 THR A 144 1 87 HELIX 2 2 ARG B 59 LYS B 142 1 84 SSBOND 1 CYS A 58 CYS B 58 1555 1555 2.03 SSBOND 2 CYS A 68 CYS B 68 1555 1555 2.03 SSBOND 3 CYS A 96 CYS B 96 1555 1555 2.03 SITE 1 AC1 4 THR A 82 GLN B 83 LEU B 98 THR B 102 CRYST1 33.685 100.831 110.432 90.00 90.00 90.00 I 21 21 21 16 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 0.029687 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009918 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009055 0.00000