HEADER ANTIVIRAL PROTEIN 19-MAY-23 8P45 TITLE CRYSTAL STRUCTURE OF HUMAN STING IN COMPLEX WITH THE AGONIST MD1202D 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, ANTIVIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.KLIMA,E.BOURA REVDAT 3 17-APR-24 8P45 1 JRNL REVDAT 2 14-FEB-24 8P45 1 JRNL REVDAT 1 20-DEC-23 8P45 0 JRNL AUTH M.KLIMA,M.DEJMEK,V.DUCHOSLAV,A.EISENREICHOVA,M.SALA, JRNL AUTH 2 K.CHALUPSKY,D.CHALUPSKA,B.NOVOTNA,G.BIRKUS,R.NENCKA,E.BOURA JRNL TITL FLUORINATED CGAMP ANALOGS, WHICH ACT AS STING AGONISTS AND JRNL TITL 2 ARE NOT CLEAVABLE BY POXINS: STRUCTURAL BASIS OF THEIR JRNL TITL 3 FUNCTION. JRNL REF STRUCTURE V. 32 433 2024 JRNL REFN ISSN 0969-2126 JRNL PMID 38325369 JRNL DOI 10.1016/J.STR.2024.01.008 REMARK 2 REMARK 2 RESOLUTION. 3.23 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.23 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 3917 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 195 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 44.3500 - 3.2300 1.00 3722 195 0.2069 0.2592 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 : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.348 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.315 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 90.47 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 87.15 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 1505 REMARK 3 ANGLE : 0.553 2049 REMARK 3 CHIRALITY : 0.038 224 REMARK 3 PLANARITY : 0.004 273 REMARK 3 DIHEDRAL : 11.991 595 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 8P45 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-MAY-23. REMARK 100 THE DEPOSITION ID IS D_1292130634. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-MAY-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9184 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS XDSAPP V3.1.9 REMARK 200 DATA SCALING SOFTWARE : XDS XDSAPP V3.1.9 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3917 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.230 REMARK 200 RESOLUTION RANGE LOW (A) : 44.350 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 12.10 REMARK 200 R MERGE (I) : 0.30040 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.23 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 1.94000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.220 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200 MM SODIUM CHLORIDE; 100 MM HEPES REMARK 280 PH 7.5; 20 % W/V PEG 4000; 10 MM SPERMINE, 10 MM SPERMIDINE, REMARK 280 10MM ORNITHINE, 10 MM 1,4-DIAMINOBUTANE, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z 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 44.74500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.99000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 44.74500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 38.99000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 3930 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 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 -1.000000 0.000000 0.000000 89.49000 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 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 ALA A 318 REMARK 465 ASP A 319 REMARK 465 ASP A 320 REMARK 465 SER A 321 REMARK 465 SER A 322 REMARK 465 PHE A 323 REMARK 465 GLU A 337 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 -51.41 -122.58 REMARK 500 SER A 305 54.54 -91.99 REMARK 500 REMARK 500 REMARK: NULL DBREF 8P45 A 140 343 UNP Q86WV6 STING_HUMAN 140 343 SEQADV 8P45 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 WY8 A 401 44 HETNAM WY8 9-[(1~{S},3~{R},6~{R},8~{R},9~{R},10~{R},12~{R},15~{R}, HETNAM 2 WY8 17~{R},18~{R})-8-(6-AMINOPURIN-9-YL)-9,18- HETNAM 3 WY8 BIS(FLUORANYL)-3,12-BIS(OXIDANYLIDENE)-3,12- HETNAM 4 WY8 BIS(SULFANYL)-2,4,7,11,13-PENTAOXA-3$L^{5},12$L^{5}- HETNAM 5 WY8 DIPHOSPHATRICYCLO[13.2.1.0^{6,10}]OCTADECAN-17-YL]- HETNAM 6 WY8 1~{H}-PURIN-6-ONE FORMUL 2 WY8 C21 H23 F2 N9 O8 P2 S2 HELIX 1 AA1 ASN A 154 TYR A 167 1 14 HELIX 2 AA2 TYR A 167 LEU A 172 1 6 HELIX 3 AA3 LEU A 175 TYR A 186 1 12 HELIX 4 AA4 ASN A 211 ASP A 216 1 6 HELIX 5 AA5 ALA A 262 TYR A 274 1 13 HELIX 6 AA6 SER A 280 ASP A 301 1 22 HELIX 7 AA7 LEU A 325 GLN A 335 1 11 SHEET 1 AA1 5 ILE A 219 LYS A 224 0 SHEET 2 AA1 5 SER A 243 GLU A 249 -1 O ILE A 244 N ASP A 223 SHEET 3 AA1 5 GLN A 252 TYR A 261 -1 O ALA A 254 N LEU A 247 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 89.490 77.980 35.420 90.00 97.58 90.00 C 1 2 1 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 0.011174 0.000000 0.001487 0.00000 SCALE2 0.000000 0.012824 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028482 0.00000