HEADER IMMUNE SYSTEM 10-SEP-25 9WQ2 TITLE STRUCTURE OF 3TM-SAVED DIMER BOUND TO 2'3'-CGAMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2-METHYLTHIOADENINE SYNTHETASE; COMPND 3 CHAIN: B, A; COMPND 4 SYNONYM: TM-SAVED PROTEIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS THURINGIENSIS; SOURCE 3 ORGANISM_TAXID: 1428; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SAVED, IMMUNE SYSTEM EXPDTA ELECTRON MICROSCOPY AUTHOR Y.N.GAO REVDAT 1 01-APR-26 9WQ2 0 JRNL AUTH Y.N.GAO JRNL TITL STRUCTURE OF 3TM-SAVED DIMER BOUND TO 2'3'-CGAMP JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.27 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, PHENIX, CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 3.270 REMARK 3 NUMBER OF PARTICLES : 201167 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 9WQ2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 12-SEP-25. REMARK 100 THE DEPOSITION ID IS D_1300063612. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : 3TM-SAVED DIMER REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1800.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 6000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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 APPLY THE FOLLOWING TO CHAINS: B, 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 MET B 1 REMARK 465 MET A 1 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 LYS B 70 15.23 -143.08 REMARK 500 ASN B 283 62.28 61.08 REMARK 500 LYS B 359 -139.29 58.76 REMARK 500 LYS A 70 15.30 -143.11 REMARK 500 ASN A 283 62.25 61.08 REMARK 500 LYS A 359 -139.25 58.74 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-66157 RELATED DB: EMDB REMARK 900 STRUCTURE OF 3TM-SAVED DIMER BOUND TO 2'3'-CGAMP DBREF1 9WQ2 B 1 369 UNP A0A9X6VCG9_BACTU DBREF2 9WQ2 B A0A9X6VCG9 1 369 DBREF1 9WQ2 A 1 369 UNP A0A9X6VCG9_BACTU DBREF2 9WQ2 A A0A9X6VCG9 1 369 SEQRES 1 B 369 MET ASN ILE VAL THR PHE GLY ILE ILE LEU VAL VAL THR SEQRES 2 B 369 THR ILE ILE MET ILE ILE LEU TYR ALA PHE ASN ARG THR SEQRES 3 B 369 LYS GLY VAL GLU THR PHE GLY GLY HIS THR PHE ILE SER SEQRES 4 B 369 PHE GLY LEU GLY LEU ILE THR GLY SER PHE GLY THR LEU SEQRES 5 B 369 VAL ASP LYS ILE HIS SER ILE VAL ILE ALA ILE ILE LYS SEQRES 6 B 369 VAL THR ASN ASP LYS THR GLN ALA LYS THR LEU THR ASP SEQRES 7 B 369 ALA THR ASP VAL ASN TYR ILE GLN LEU VAL THR GLY VAL SEQRES 8 B 369 ALA PHE VAL ALA LEU GLY ILE TRP PHE ILE TYR LYS LEU SEQRES 9 B 369 LYS ASN ARG ILE TYR ILE LEU ASN ILE ASN GLY TYR ALA SEQRES 10 B 369 ASP HIS ARG ILE GLU ASN ASN GLN LYS SER LEU GLY LEU SEQRES 11 B 369 ASN GLU PHE ASP PHE LYS GLU ARG GLU ILE GLU PHE VAL SEQRES 12 B 369 LYS ARG PHE THR LYS ALA GLN ASP ASN SER THR GLU GLN SEQRES 13 B 369 ASN VAL VAL PRO GLU ILE ILE GLU GLU LEU VAL PHE LYS SEQRES 14 B 369 ILE GLU ALA PHE LYS ASN GLU SER THR ASN VAL LYS ARG SEQRES 15 B 369 GLY TYR THR GLY ILE ALA PRO ILE PRO PHE ILE LEU TYR SEQRES 16 B 369 ALA GLY LYS LEU PHE ASN GLY HIS LYS ILE ASN HIS PHE SEQRES 17 B 369 TYR GLU ARG ASN LYS LEU LYS GLN ASP TYR TYR LYS LEU SEQRES 18 B 369 ALA ASN LYS LYS LYS ASN PHE GLU GLU LEU THR LEU GLN SEQRES 19 B 369 THR ASN LEU GLN ALA LEU SER SER THR SER ALA THR GLU SEQRES 20 B 369 ALA ILE LEU LYS VAL SER LEU THR PHE ASP ILE SER THR SEQRES 21 B 369 HIS ASP THR SER GLN PHE GLY SER ASN VAL PRO VAL VAL SEQRES 22 B 369 ASP LEU LYS VAL ASP GLU THR LYS GLU ASN ILE ILE GLN SEQRES 23 B 369 GLY LYS ASP GLN LEU GLU GLU TYR VAL LYS VAL VAL TYR SEQRES 24 B 369 GLU THR ILE ARG LYS ILE ASN GLN SER ASN PRO SER ILE SEQRES 25 B 369 GLN ARG VAL HIS LEU LEU ILE ALA SER GLN SER CYS LEU SEQRES 26 B 369 PRO PHE GLU LEU GLY LYS LEU LEU ASP ASP THR SER MET SEQRES 27 B 369 PRO GLU VAL ILE SER TYR HIS PHE VAL ASN PRO ARG TYR SEQRES 28 B 369 LYS TRP GLY ILE ILE LEU ASN LYS HIS ASN LYS GLY THR SEQRES 29 B 369 PHE ILE THR ALA PRO SEQRES 1 A 369 MET ASN ILE VAL THR PHE GLY ILE ILE LEU VAL VAL THR SEQRES 2 A 369 THR ILE ILE MET ILE ILE LEU TYR ALA PHE ASN ARG THR SEQRES 3 A 369 LYS GLY VAL GLU THR PHE GLY GLY HIS THR PHE ILE SER SEQRES 4 A 369 PHE GLY LEU GLY LEU ILE THR GLY SER PHE GLY THR LEU SEQRES 5 A 369 VAL ASP LYS ILE HIS SER ILE VAL ILE ALA ILE ILE LYS SEQRES 6 A 369 VAL THR ASN ASP LYS THR GLN ALA LYS THR LEU THR ASP SEQRES 7 A 369 ALA THR ASP VAL ASN TYR ILE GLN LEU VAL THR GLY VAL SEQRES 8 A 369 ALA PHE VAL ALA LEU GLY ILE TRP PHE ILE TYR LYS LEU SEQRES 9 A 369 LYS ASN ARG ILE TYR ILE LEU ASN ILE ASN GLY TYR ALA SEQRES 10 A 369 ASP HIS ARG ILE GLU ASN ASN GLN LYS SER LEU GLY LEU SEQRES 11 A 369 ASN GLU PHE ASP PHE LYS GLU ARG GLU ILE GLU PHE VAL SEQRES 12 A 369 LYS ARG PHE THR LYS ALA GLN ASP ASN SER THR GLU GLN SEQRES 13 A 369 ASN VAL VAL PRO GLU ILE ILE GLU GLU LEU VAL PHE LYS SEQRES 14 A 369 ILE GLU ALA PHE LYS ASN GLU SER THR ASN VAL LYS ARG SEQRES 15 A 369 GLY TYR THR GLY ILE ALA PRO ILE PRO PHE ILE LEU TYR SEQRES 16 A 369 ALA GLY LYS LEU PHE ASN GLY HIS LYS ILE ASN HIS PHE SEQRES 17 A 369 TYR GLU ARG ASN LYS LEU LYS GLN ASP TYR TYR LYS LEU SEQRES 18 A 369 ALA ASN LYS LYS LYS ASN PHE GLU GLU LEU THR LEU GLN SEQRES 19 A 369 THR ASN LEU GLN ALA LEU SER SER THR SER ALA THR GLU SEQRES 20 A 369 ALA ILE LEU LYS VAL SER LEU THR PHE ASP ILE SER THR SEQRES 21 A 369 HIS ASP THR SER GLN PHE GLY SER ASN VAL PRO VAL VAL SEQRES 22 A 369 ASP LEU LYS VAL ASP GLU THR LYS GLU ASN ILE ILE GLN SEQRES 23 A 369 GLY LYS ASP GLN LEU GLU GLU TYR VAL LYS VAL VAL TYR SEQRES 24 A 369 GLU THR ILE ARG LYS ILE ASN GLN SER ASN PRO SER ILE SEQRES 25 A 369 GLN ARG VAL HIS LEU LEU ILE ALA SER GLN SER CYS LEU SEQRES 26 A 369 PRO PHE GLU LEU GLY LYS LEU LEU ASP ASP THR SER MET SEQRES 27 A 369 PRO GLU VAL ILE SER TYR HIS PHE VAL ASN PRO ARG TYR SEQRES 28 A 369 LYS TRP GLY ILE ILE LEU ASN LYS HIS ASN LYS GLY THR SEQRES 29 A 369 PHE ILE THR ALA PRO HET 1SY B 401 45 HET 1SY A 401 45 HETNAM 1SY CGAMP HETSYN 1SY 2',3' CGAMP; C-GMP-AMP; C[G(2',5')PA(3',5')P] FORMUL 3 1SY 2(C20 H24 N10 O13 P2) HELIX 1 AA1 ASN B 2 ASN B 24 1 23 HELIX 2 AA2 VAL B 29 PHE B 49 1 21 HELIX 3 AA3 THR B 51 ASP B 69 1 19 HELIX 4 AA4 THR B 71 LEU B 76 1 6 HELIX 5 AA5 ASN B 83 LYS B 105 1 23 HELIX 6 AA6 ARG B 120 ASN B 124 5 5 HELIX 7 AA7 GLN B 125 GLY B 129 5 5 HELIX 8 AA8 PHE B 142 ASN B 152 1 11 HELIX 9 AA9 THR B 154 SER B 177 1 24 HELIX 10 AB1 PRO B 189 LEU B 199 1 11 HELIX 11 AB2 GLN B 238 THR B 243 1 6 HELIX 12 AB3 GLY B 287 ASN B 309 1 23 HELIX 13 AB4 SER B 323 LEU B 333 1 11 HELIX 14 AB5 ILE A 3 ASN A 24 1 22 HELIX 15 AB6 VAL A 29 PHE A 49 1 21 HELIX 16 AB7 THR A 51 ASP A 69 1 19 HELIX 17 AB8 THR A 71 LEU A 76 1 6 HELIX 18 AB9 ASN A 83 LYS A 105 1 23 HELIX 19 AC1 ARG A 120 ASN A 124 5 5 HELIX 20 AC2 GLN A 125 GLY A 129 5 5 HELIX 21 AC3 PHE A 142 ASN A 152 1 11 HELIX 22 AC4 THR A 154 SER A 177 1 24 HELIX 23 AC5 PRO A 189 LEU A 199 1 11 HELIX 24 AC6 GLN A 238 THR A 243 1 6 HELIX 25 AC7 GLY A 287 ASN A 309 1 23 HELIX 26 AC8 SER A 323 LEU A 333 1 11 SHEET 1 AA1 5 PHE B 135 GLU B 141 0 SHEET 2 AA1 5 ILE B 108 ASN B 114 1 N ILE B 110 O LYS B 136 SHEET 3 AA1 5 LYS B 181 ILE B 187 1 O GLY B 183 N TYR B 109 SHEET 4 AA1 5 HIS B 207 ASN B 212 1 O TYR B 209 N TYR B 184 SHEET 5 AA1 5 ASP B 217 LYS B 220 -1 O TYR B 219 N GLU B 210 SHEET 1 AA2 7 THR B 232 LEU B 233 0 SHEET 2 AA2 7 VAL B 272 LYS B 276 -1 O LYS B 276 N THR B 232 SHEET 3 AA2 7 GLU B 247 SER B 253 1 N LYS B 251 O VAL B 273 SHEET 4 AA2 7 ARG B 314 ALA B 320 1 O HIS B 316 N LEU B 250 SHEET 5 AA2 7 GLU B 340 PHE B 346 1 O ILE B 342 N LEU B 317 SHEET 6 AA2 7 TYR B 351 ILE B 356 -1 O ILE B 355 N SER B 343 SHEET 7 AA2 7 PHE B 365 THR B 367 -1 O ILE B 366 N GLY B 354 SHEET 1 AA3 5 PHE A 135 GLU A 141 0 SHEET 2 AA3 5 ILE A 108 ASN A 114 1 N ILE A 110 O LYS A 136 SHEET 3 AA3 5 LYS A 181 ILE A 187 1 O GLY A 183 N TYR A 109 SHEET 4 AA3 5 HIS A 207 ASN A 212 1 O TYR A 209 N TYR A 184 SHEET 5 AA3 5 ASP A 217 LYS A 220 -1 O TYR A 219 N GLU A 210 SHEET 1 AA4 7 THR A 232 LEU A 233 0 SHEET 2 AA4 7 VAL A 272 LYS A 276 -1 O LYS A 276 N THR A 232 SHEET 3 AA4 7 GLU A 247 SER A 253 1 N LYS A 251 O VAL A 273 SHEET 4 AA4 7 ARG A 314 ALA A 320 1 O HIS A 316 N LEU A 250 SHEET 5 AA4 7 GLU A 340 PHE A 346 1 O ILE A 342 N LEU A 317 SHEET 6 AA4 7 TYR A 351 ILE A 356 -1 O ILE A 355 N SER A 343 SHEET 7 AA4 7 PHE A 365 THR A 367 -1 O ILE A 366 N GLY A 354 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 CONECT 5917 5920 5921 CONECT 5918 5919 CONECT 5919 5918 5920 5923 CONECT 5920 5917 5919 CONECT 5921 5917 5922 CONECT 5922 5921 5923 5926 CONECT 5923 5919 5922 5924 CONECT 5924 5923 5925 CONECT 5925 5924 5926 CONECT 5926 5922 5925 5927 CONECT 5927 5926 5928 5961 CONECT 5928 5927 5929 5930 CONECT 5929 5928 CONECT 5930 5928 5931 5944 CONECT 5931 5930 5932 5961 CONECT 5932 5931 5933 CONECT 5933 5932 5934 CONECT 5934 5933 5935 5936 5960 CONECT 5935 5934 CONECT 5936 5934 5937 CONECT 5937 5936 5938 5948 CONECT 5938 5937 5939 5940 CONECT 5939 5938 CONECT 5940 5938 5941 5947 CONECT 5941 5940 5942 CONECT 5942 5941 5943 CONECT 5943 5942 5944 5945 5946 CONECT 5944 5930 5943 CONECT 5945 5943 CONECT 5946 5943 CONECT 5947 5940 5948 CONECT 5948 5937 5947 5949 CONECT 5949 5948 5950 5952 CONECT 5950 5949 5951 CONECT 5951 5950 5953 CONECT 5952 5949 5953 5958 CONECT 5953 5951 5952 5954 CONECT 5954 5953 5955 5959 CONECT 5955 5954 5956 CONECT 5956 5955 5957 5958 CONECT 5957 5956 CONECT 5958 5952 5956 CONECT 5959 5954 CONECT 5960 5934 CONECT 5961 5927 5931 CONECT 5962 5965 5966 CONECT 5963 5964 CONECT 5964 5963 5965 5968 CONECT 5965 5962 5964 CONECT 5966 5962 5967 CONECT 5967 5966 5968 5971 CONECT 5968 5964 5967 5969 CONECT 5969 5968 5970 CONECT 5970 5969 5971 CONECT 5971 5967 5970 5972 CONECT 5972 5971 5973 6006 CONECT 5973 5972 5974 5975 CONECT 5974 5973 CONECT 5975 5973 5976 5989 CONECT 5976 5975 5977 6006 CONECT 5977 5976 5978 CONECT 5978 5977 5979 CONECT 5979 5978 5980 5981 6005 CONECT 5980 5979 CONECT 5981 5979 5982 CONECT 5982 5981 5983 5993 CONECT 5983 5982 5984 5985 CONECT 5984 5983 CONECT 5985 5983 5986 5992 CONECT 5986 5985 5987 CONECT 5987 5986 5988 CONECT 5988 5987 5989 5990 5991 CONECT 5989 5975 5988 CONECT 5990 5988 CONECT 5991 5988 CONECT 5992 5985 5993 CONECT 5993 5982 5992 5994 CONECT 5994 5993 5995 5997 CONECT 5995 5994 5996 CONECT 5996 5995 5998 CONECT 5997 5994 5998 6003 CONECT 5998 5996 5997 5999 CONECT 5999 5998 6000 6004 CONECT 6000 5999 6001 CONECT 6001 6000 6002 6003 CONECT 6002 6001 CONECT 6003 5997 6001 CONECT 6004 5999 CONECT 6005 5979 CONECT 6006 5972 5976 MASTER 129 0 2 26 24 0 0 6 6004 2 90 58 END