HEADER IMMUNE SYSTEM 10-OCT-21 7SHO TITLE CRYSTAL STRUCTURE OF HSTING IN COMPLEX WITH C[2',3'-(ARA-2'-G, RIBO- TITLE 2 3'-A)-MP] (RJ242) COMPND MOL_ID: 1; COMPND 2 MOLECULE: STIMULATOR OF INTERFERON GENES PROTEIN; COMPND 3 CHAIN: B; 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, TMEM173; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS STING, AGONIST, CGAMP ANALOGS, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR W.XIE,L.LAMA,X.J.YANG,V.KURYAVYI,I.NUDELMAN,J.F.GLICKMAN,R.A.JONES, AUTHOR 2 T.TUSCHL,D.J.PATEL REVDAT 3 18-OCT-23 7SHO 1 REMARK REVDAT 2 16-AUG-23 7SHO 1 JRNL REVDAT 1 12-OCT-22 7SHO 0 JRNL AUTH W.XIE,L.LAMA,X.YANG,V.KURYAVYI,S.BHATTACHARYA,I.NUDELMAN, JRNL AUTH 2 G.YANG,O.OUERFELLI,J.F.GLICKMAN,R.A.JONES,T.TUSCHL,D.J.PATEL JRNL TITL ARABINOSE- AND XYLOSE-MODIFIED ANALOGS OF 2',3'-CGAMP ACT AS JRNL TITL 2 STING AGONISTS. JRNL REF CELL CHEM BIOL 2023 JRNL REFN ESSN 2451-9456 JRNL PMID 37536341 JRNL DOI 10.1016/J.CHEMBIOL.2023.07.002 REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18_3855 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) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.73 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 11616 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.550 REMARK 3 FREE R VALUE TEST SET COUNT : 529 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 29.7300 - 3.5700 0.99 2802 130 0.1579 0.1707 REMARK 3 2 3.5700 - 2.8300 0.99 2759 153 0.2301 0.2948 REMARK 3 3 2.8300 - 2.4800 0.99 2758 123 0.2522 0.3087 REMARK 3 4 2.4800 - 2.2500 0.99 2768 123 0.2598 0.2669 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) : 0.252 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.950 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 53.54 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 66.94 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 : 0.006 1518 REMARK 3 ANGLE : 0.772 2068 REMARK 3 CHIRALITY : 0.045 226 REMARK 3 PLANARITY : 0.004 264 REMARK 3 DIHEDRAL : 20.762 557 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 7SHO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-OCT-21. REMARK 100 THE DEPOSITION ID IS D_1000260291. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-FEB-20 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 : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11675 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 29.730 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.04987 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.6700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.48150 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.620 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: 4KSY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M POTASSIUM SODIUM TARTRATE, 20% REMARK 280 PEG3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 44.67350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.90450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 44.67350 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 38.90450 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: 4220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 263.68216 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 35.94065 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 PRO B 317 REMARK 465 ALA B 318 REMARK 465 ASP B 319 REMARK 465 ASP B 320 REMARK 465 SER B 321 REMARK 465 GLU B 337 REMARK 465 LYS B 338 REMARK 465 GLU B 339 REMARK 465 GLU B 340 REMARK 465 VAL B 341 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 OG1 THR B 263 O2' 9UH B 401 2856 2.04 REMARK 500 REMARK 500 REMARK: NULL 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 B 167 -65.24 -146.86 REMARK 500 LEU B 222 -55.40 -120.15 REMARK 500 REMARK 500 REMARK: NULL DBREF 7SHO B 155 341 UNP Q86WV6 STING_HUMAN 155 341 SEQADV 7SHO SER B 154 UNP Q86WV6 EXPRESSION TAG SEQRES 1 B 188 SER VAL ALA HIS GLY LEU ALA TRP SER TYR TYR ILE GLY SEQRES 2 B 188 TYR LEU ARG LEU ILE LEU PRO GLU LEU GLN ALA ARG ILE SEQRES 3 B 188 ARG THR TYR ASN GLN HIS TYR ASN ASN LEU LEU ARG GLY SEQRES 4 B 188 ALA VAL SER GLN ARG LEU TYR ILE LEU LEU PRO LEU ASP SEQRES 5 B 188 CYS GLY VAL PRO ASP ASN LEU SER MET ALA ASP PRO ASN SEQRES 6 B 188 ILE ARG PHE LEU ASP LYS LEU PRO GLN GLN THR GLY ASP SEQRES 7 B 188 HIS ALA GLY ILE LYS ASP ARG VAL TYR SER ASN SER ILE SEQRES 8 B 188 TYR GLU LEU LEU GLU ASN GLY GLN ARG ALA GLY THR CYS SEQRES 9 B 188 VAL LEU GLU TYR ALA THR PRO LEU GLN THR LEU PHE ALA SEQRES 10 B 188 MET SER GLN TYR SER GLN ALA GLY PHE SER ARG GLU ASP SEQRES 11 B 188 ARG LEU GLU GLN ALA LYS LEU PHE CYS ARG THR LEU GLU SEQRES 12 B 188 ASP ILE LEU ALA ASP ALA PRO GLU SER GLN ASN ASN CYS SEQRES 13 B 188 ARG LEU ILE ALA TYR GLN GLU PRO ALA ASP ASP SER SER SEQRES 14 B 188 PHE SER LEU SER GLN GLU VAL LEU ARG HIS LEU ARG GLN SEQRES 15 B 188 GLU GLU LYS GLU GLU VAL HET 9UH B 401 45 HETNAM 9UH (2R,5R,7R,8S,10R,12AR,14R,15R,15AS,16R)-7-(2-AMINO-6- HETNAM 2 9UH OXO-1,6-DIHYDRO-9H-PURIN-9-YL)-14-(6-AMINO-9H-PURIN-9- HETNAM 3 9UH YL)-2,10,15,16-TETRAHYDROXYOCTAHYDRO-2H,10H,12H-5,8- HETNAM 4 9UH METHANO-2LAMBDA~5~,10LAMBDA~5~-FURO[3,2-L][1,3,6,9,11, HETNAM 5 9UH 2,10]PENTAOXADIPHOSPHACYCLOTETRADECINE-2,10-DIONE FORMUL 2 9UH C20 H24 N10 O13 P2 FORMUL 3 HOH *13(H2 O) HELIX 1 AA1 SER B 154 TYR B 167 1 14 HELIX 2 AA2 TYR B 167 LEU B 172 1 6 HELIX 3 AA3 GLU B 174 TYR B 186 1 13 HELIX 4 AA4 ASN B 211 ALA B 215 5 5 HELIX 5 AA5 THR B 263 TYR B 274 1 12 HELIX 6 AA6 SER B 275 GLY B 278 5 4 HELIX 7 AA7 SER B 280 ALA B 302 1 23 HELIX 8 AA8 SER B 324 GLU B 336 1 13 SHEET 1 AA1 5 ILE B 219 LYS B 224 0 SHEET 2 AA1 5 SER B 243 GLU B 249 -1 O ILE B 244 N ASP B 223 SHEET 3 AA1 5 GLN B 252 TYR B 261 -1 O ALA B 254 N LEU B 247 SHEET 4 AA1 5 LEU B 198 PRO B 203 1 N TYR B 199 O VAL B 258 SHEET 5 AA1 5 CYS B 309 TYR B 314 1 O ILE B 312 N LEU B 202 SHEET 1 AA2 2 GLN B 228 HIS B 232 0 SHEET 2 AA2 2 ILE B 235 TYR B 240 -1 O TYR B 240 N GLN B 228 CRYST1 89.347 77.809 36.204 90.00 96.92 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 0.011192 0.000000 0.001357 0.00000 SCALE2 0.000000 0.012852 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027824 0.00000