HEADER IMMUNE SYSTEM 10-NOV-21 7Q85 TITLE CRYSTAL STRUCTURE OF HUMAN STING IN COMPLEX WITH MD1193 COMPND MOL_ID: 1; COMPND 2 MOLECULE: STIMULATOR OF INTERFERON GENES PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HSTING,ENDOPLASMIC RETICULUM INTERFERON STIMULATOR,ERIS, COMPND 5 MEDIATOR OF IRF3 ACTIVATION,HMITA,TRANSMEMBRANE PROTEIN 173; COMPND 6 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: STING1, ERIS, MITA, STING, TMEM173; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS STING, ANTIVIRAL, ACTIVATOR, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR M.SMOLA,M.KLIMA,E.BOURA REVDAT 4 07-FEB-24 7Q85 1 REMARK REVDAT 3 23-AUG-23 7Q85 1 JRNL REVDAT 2 31-MAY-23 7Q85 1 COMPND SOURCE DBREF SEQADV REVDAT 1 19-OCT-22 7Q85 0 JRNL AUTH M.DEJMEK,A.BRAZDOVA,T.OTAVA,M.P.POLIDAROVA,M.KLIMA,M.SMOLA, JRNL AUTH 2 Z.VAVRINA,M.BUDESINSKY,M.DRACINSKY,R.LIBOSKA,E.BOURA, JRNL AUTH 3 G.BIRKUS,R.NENCKA JRNL TITL VINYLPHOSPHONATE-BASED CYCLIC DINUCLEOTIDES ENHANCE JRNL TITL 2 STING-MEDIATED CANCER IMMUNOTHERAPY. JRNL REF EUR.J.MED.CHEM. V. 259 15685 2023 JRNL REFN ISSN 0223-5234 JRNL PMID 37567057 JRNL DOI 10.1016/J.EJMECH.2023.115685 REMARK 2 REMARK 2 RESOLUTION. 2.36 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.36 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.363 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 9486 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.976 REMARK 3 FREE R VALUE TEST SET COUNT : 472 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 33.4600 - 3.4020 1.00 3132 162 0.1966 0.2153 REMARK 3 2 3.4020 - 2.7006 1.00 2955 156 0.2773 0.3145 REMARK 3 3 2.7006 - 2.3594 1.00 2927 154 0.2877 0.3199 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.277 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.077 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 48.47 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.86 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 1503 REMARK 3 ANGLE : 0.799 2046 REMARK 3 CHIRALITY : 0.028 223 REMARK 3 PLANARITY : 0.004 265 REMARK 3 DIHEDRAL : 12.716 552 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 7Q85 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-NOV-21. REMARK 100 THE DEPOSITION ID IS D_1292119166. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-SEP-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.541870 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 200K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS XDSGUI2 REMARK 200 DATA SCALING SOFTWARE : XDS XDSGUI2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9486 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.359 REMARK 200 RESOLUTION RANGE LOW (A) : 33.460 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.60 REMARK 200 R MERGE (I) : 0.08003 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.7200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.36 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.50 REMARK 200 R MERGE FOR SHELL (I) : 0.86970 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.5 REMARK 200 STARTING MODEL: 4KSY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LITHIUM ACETATE, 20% (W/V) PEG REMARK 280 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 17.54550 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 55.51700 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 55.51700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 8.77275 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 55.51700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 55.51700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 26.31825 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 55.51700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 55.51700 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 8.77275 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 55.51700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 55.51700 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 26.31825 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 17.54550 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: 4120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL 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 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -17.54550 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 A 514 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 140 REMARK 465 PRO A 141 REMARK 465 ALA A 142 REMARK 465 GLU A 143 REMARK 465 ILE A 144 REMARK 465 SER A 145 REMARK 465 ALA A 146 REMARK 465 VAL A 147 REMARK 465 CYS A 148 REMARK 465 GLU A 149 REMARK 465 LYS A 150 REMARK 465 GLY A 151 REMARK 465 ASN A 152 REMARK 465 PHE A 153 REMARK 465 TYR A 186 REMARK 465 ASN A 187 REMARK 465 ASN A 188 REMARK 465 LEU A 189 REMARK 465 LEU A 190 REMARK 465 ARG A 191 REMARK 465 LYS A 338 REMARK 465 GLU A 339 REMARK 465 GLU A 340 REMARK 465 VAL A 341 REMARK 465 THR A 342 REMARK 465 VAL A 343 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 TYR A 167 -70.12 -132.80 REMARK 500 CYS A 206 19.17 59.02 REMARK 500 ASN A 307 23.56 49.46 REMARK 500 ASP A 319 -3.31 77.13 REMARK 500 REMARK 500 REMARK: NULL DBREF 7Q85 A 140 343 UNP Q86WV6 STING_HUMAN 140 343 SEQADV 7Q85 ARG A 232 UNP Q86WV6 HIS 232 VARIANT SEQRES 1 A 204 ALA PRO ALA GLU ILE SER ALA VAL CYS GLU LYS GLY ASN SEQRES 2 A 204 PHE ASN VAL ALA HIS GLY LEU ALA TRP SER TYR TYR ILE SEQRES 3 A 204 GLY TYR LEU ARG LEU ILE LEU PRO GLU LEU GLN ALA ARG SEQRES 4 A 204 ILE ARG THR TYR ASN GLN HIS TYR ASN ASN LEU LEU ARG SEQRES 5 A 204 GLY ALA VAL SER GLN ARG LEU TYR ILE LEU LEU PRO LEU SEQRES 6 A 204 ASP CYS GLY VAL PRO ASP ASN LEU SER MET ALA ASP PRO SEQRES 7 A 204 ASN ILE ARG PHE LEU ASP LYS LEU PRO GLN GLN THR GLY SEQRES 8 A 204 ASP ARG ALA GLY ILE LYS ASP ARG VAL TYR SER ASN SER SEQRES 9 A 204 ILE TYR GLU LEU LEU GLU ASN GLY GLN ARG ALA GLY THR SEQRES 10 A 204 CYS VAL LEU GLU TYR ALA THR PRO LEU GLN THR LEU PHE SEQRES 11 A 204 ALA MET SER GLN TYR SER GLN ALA GLY PHE SER ARG GLU SEQRES 12 A 204 ASP ARG LEU GLU GLN ALA LYS LEU PHE CYS ARG THR LEU SEQRES 13 A 204 GLU ASP ILE LEU ALA ASP ALA PRO GLU SER GLN ASN ASN SEQRES 14 A 204 CYS ARG LEU ILE ALA TYR GLN GLU PRO ALA ASP ASP SER SEQRES 15 A 204 SER PHE SER LEU SER GLN GLU VAL LEU ARG HIS LEU ARG SEQRES 16 A 204 GLN GLU GLU LYS GLU GLU VAL THR VAL HET 98F A 401 44 HETNAM 98F 9-[(1R,6R,8R,13E,15R,17R,18R)-17-(6-AMINOPURIN-9-YL)-9, HETNAM 2 98F 18-BIS(FLUORANYL)-3,12-BIS(OXIDANYL)-3,12- HETNAM 3 98F BIS(OXIDANYLIDENE)-2,4,7,11,16-PENTAOXA-3$L^{5}, HETNAM 4 98F 12$L^{5}-DIPHOSPHATRICYCLO[13.3.0.0^{6,10}]OCTADEC-13- HETNAM 5 98F EN-8-YL]PURIN-6-AMINE FORMUL 2 98F C21 H22 F2 N10 O9 P2 FORMUL 3 HOH *27(H2 O) HELIX 1 AA1 ASN A 154 TYR A 167 1 14 HELIX 2 AA2 TYR A 167 HIS A 185 1 19 HELIX 3 AA3 ASN A 211 ASP A 216 1 6 HELIX 4 AA4 THR A 263 TYR A 274 1 12 HELIX 5 AA5 SER A 275 GLY A 278 5 4 HELIX 6 AA6 SER A 280 GLU A 282 5 3 HELIX 7 AA7 ASP A 283 ALA A 302 1 20 HELIX 8 AA8 SER A 324 GLU A 337 1 14 SHEET 1 AA1 5 ILE A 219 LYS A 224 0 SHEET 2 AA1 5 SER A 243 GLU A 249 -1 O GLU A 246 N ARG A 220 SHEET 3 AA1 5 GLN A 252 TYR A 261 -1 O GLN A 252 N GLU A 249 SHEET 4 AA1 5 LEU A 198 PRO A 203 1 N LEU A 201 O GLU A 260 SHEET 5 AA1 5 CYS A 309 TYR A 314 1 O ILE A 312 N LEU A 202 SHEET 1 AA2 2 GLN A 228 ARG A 232 0 SHEET 2 AA2 2 ILE A 235 TYR A 240 -1 O TYR A 240 N GLN A 228 CRYST1 111.034 111.034 35.091 90.00 90.00 90.00 P 41 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 0.009006 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009006 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028497 0.00000