HEADER HYDROLASE 06-MAY-22 7UXU TITLE CRYOEM STRUCTURE OF THE TIR DOMAIN FROM ABTIR IN COMPLEX WITH 3AD COMPND MOL_ID: 1; COMPND 2 MOLECULE: MOLECULAR CHAPERONE TIR; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: TIR DOMAIN-CONTAINING PROTEIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACINETOBACTER BAUMANNII; SOURCE 3 ORGANISM_TAXID: 470; SOURCE 4 GENE: APD31_10100, H0529_09530; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS 2' CADPR, NADASE, BACTERIAL TIR, HYDROLASE EXPDTA ELECTRON MICROSCOPY AUTHOR S.LI,J.D.NANSON,M.K.MANIK,W.GU,M.J.LANDSBERG,T.VE,B.KOBE REVDAT 4 12-JUN-24 7UXU 1 REMARK REVDAT 3 12-OCT-22 7UXU 1 JRNL REVDAT 2 14-SEP-22 7UXU 1 JRNL REVDAT 1 07-SEP-22 7UXU 0 JRNL AUTH M.K.MANIK,Y.SHI,S.LI,M.A.ZAYDMAN,N.DAMARAJU,S.EASTMAN, JRNL AUTH 2 T.G.SMITH,W.GU,V.MASIC,T.MOSAIAB,J.S.WEAGLEY,S.J.HANCOCK, JRNL AUTH 3 E.VASQUEZ,L.HARTLEY-TASSELL,N.KARGIOS,N.MARUTA,B.Y.J.LIM, JRNL AUTH 4 H.BURDETT,M.J.LANDSBERG,M.A.SCHEMBRI,I.PROKES,L.SONG, JRNL AUTH 5 M.GRANT,A.DIANTONIO,J.D.NANSON,M.GUO,J.MILBRANDT,T.VE,B.KOBE JRNL TITL CYCLIC ADP RIBOSE ISOMERS: PRODUCTION, CHEMICAL STRUCTURES, JRNL TITL 2 AND IMMUNE SIGNALING. JRNL REF SCIENCE V. 377 C8969 2022 JRNL REFN ESSN 1095-9203 JRNL PMID 36048923 JRNL DOI 10.1126/SCIENCE.ADC8969 REMARK 2 REMARK 2 RESOLUTION. 2.74 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : ISOLDE, CRYOSPARC, PHENIX 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) : 2.740 REMARK 3 NUMBER OF PARTICLES : 272949 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 7UXU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-MAY-22. REMARK 100 THE DEPOSITION ID IS D_1000265135. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : HELICAL REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : FILAMENT REMARK 245 PARTICLE TYPE : HELICAL REMARK 245 NAME OF SAMPLE : FILAMENT OF THE ABTIR TIR REMARK 245 DOMAIN IN COMPLEX WITH 3AD REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 2.50 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 : JEOL CRYO ARM 300 REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 100.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 4000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : OTHER REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 4090.00 REMARK 245 ILLUMINATION MODE : OTHER 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 300 THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR REMARK 300 HELICAL SYMMETRY WITH THE FOLLOWING PARAMETERS: REMARK 300 ROTATION PER SUBUNIT (TWIST) = 174.00 DEGREES REMARK 300 RISE PER SUBUNIT (HEIGHT) = 17.80 ANGSTROMS 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 SER A 131 REMARK 465 ASN A 132 REMARK 465 ALA A 133 REMARK 465 SER B 131 REMARK 465 ASN B 132 REMARK 465 ALA B 133 REMARK 465 SER C 131 REMARK 465 ASN C 132 REMARK 465 ALA C 133 REMARK 465 SER D 131 REMARK 465 ASN D 132 REMARK 465 ALA D 133 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 PHE A 149 -56.52 -143.29 REMARK 500 MET A 222 -41.01 -137.39 REMARK 500 PHE B 149 -57.74 -141.49 REMARK 500 MET B 222 -41.07 -137.87 REMARK 500 PHE C 149 -57.06 -144.48 REMARK 500 MET C 222 -41.24 -137.30 REMARK 500 PHE D 149 -57.12 -144.81 REMARK 500 MET D 222 -40.35 -137.48 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-26862 RELATED DB: EMDB REMARK 900 CRYOEM STRUCTURE OF THE TIR DOMAIN FROM ABTIR IN COMPLEX WITH 3AD DBREF1 7UXU A 134 267 UNP A0A0Q1J3X1_ACIBA DBREF2 7UXU A A0A0Q1J3X1 157 290 DBREF1 7UXU B 134 267 UNP A0A0Q1J3X1_ACIBA DBREF2 7UXU B A0A0Q1J3X1 157 290 DBREF1 7UXU C 134 267 UNP A0A0Q1J3X1_ACIBA DBREF2 7UXU C A0A0Q1J3X1 157 290 DBREF1 7UXU D 134 267 UNP A0A0Q1J3X1_ACIBA DBREF2 7UXU D A0A0Q1J3X1 157 290 SEQADV 7UXU SER A 131 UNP A0A0Q1J3X EXPRESSION TAG SEQADV 7UXU ASN A 132 UNP A0A0Q1J3X EXPRESSION TAG SEQADV 7UXU ALA A 133 UNP A0A0Q1J3X EXPRESSION TAG SEQADV 7UXU SER B 131 UNP A0A0Q1J3X EXPRESSION TAG SEQADV 7UXU ASN B 132 UNP A0A0Q1J3X EXPRESSION TAG SEQADV 7UXU ALA B 133 UNP A0A0Q1J3X EXPRESSION TAG SEQADV 7UXU SER C 131 UNP A0A0Q1J3X EXPRESSION TAG SEQADV 7UXU ASN C 132 UNP A0A0Q1J3X EXPRESSION TAG SEQADV 7UXU ALA C 133 UNP A0A0Q1J3X EXPRESSION TAG SEQADV 7UXU SER D 131 UNP A0A0Q1J3X EXPRESSION TAG SEQADV 7UXU ASN D 132 UNP A0A0Q1J3X EXPRESSION TAG SEQADV 7UXU ALA D 133 UNP A0A0Q1J3X EXPRESSION TAG SEQRES 1 A 137 SER ASN ALA GLU TYR ASP LEU PHE ILE SER HIS ALA SER SEQRES 2 A 137 GLU ASP LYS GLU ASP PHE VAL ARG PRO LEU ALA GLU THR SEQRES 3 A 137 LEU GLN GLN LEU GLY VAL ASN VAL TRP TYR ASP GLU PHE SEQRES 4 A 137 THR LEU LYS VAL GLY ASP SER LEU ARG GLN LYS ILE ASP SEQRES 5 A 137 SER GLY LEU ARG ASN SER LYS TYR GLY THR VAL VAL LEU SEQRES 6 A 137 SER THR ASP PHE ILE LYS LYS ASP TRP THR ASN TYR GLU SEQRES 7 A 137 LEU ASP GLY LEU VAL ALA ARG GLU MET ASN GLY HIS LYS SEQRES 8 A 137 MET ILE LEU PRO ILE TRP HIS LYS ILE THR LYS ASN ASP SEQRES 9 A 137 VAL LEU ASP TYR SER PRO ASN LEU ALA ASP LYS VAL ALA SEQRES 10 A 137 LEU ASN THR SER VAL ASN SER ILE GLU GLU ILE ALA HIS SEQRES 11 A 137 GLN LEU ALA ASP VAL ILE LEU SEQRES 1 B 137 SER ASN ALA GLU TYR ASP LEU PHE ILE SER HIS ALA SER SEQRES 2 B 137 GLU ASP LYS GLU ASP PHE VAL ARG PRO LEU ALA GLU THR SEQRES 3 B 137 LEU GLN GLN LEU GLY VAL ASN VAL TRP TYR ASP GLU PHE SEQRES 4 B 137 THR LEU LYS VAL GLY ASP SER LEU ARG GLN LYS ILE ASP SEQRES 5 B 137 SER GLY LEU ARG ASN SER LYS TYR GLY THR VAL VAL LEU SEQRES 6 B 137 SER THR ASP PHE ILE LYS LYS ASP TRP THR ASN TYR GLU SEQRES 7 B 137 LEU ASP GLY LEU VAL ALA ARG GLU MET ASN GLY HIS LYS SEQRES 8 B 137 MET ILE LEU PRO ILE TRP HIS LYS ILE THR LYS ASN ASP SEQRES 9 B 137 VAL LEU ASP TYR SER PRO ASN LEU ALA ASP LYS VAL ALA SEQRES 10 B 137 LEU ASN THR SER VAL ASN SER ILE GLU GLU ILE ALA HIS SEQRES 11 B 137 GLN LEU ALA ASP VAL ILE LEU SEQRES 1 C 137 SER ASN ALA GLU TYR ASP LEU PHE ILE SER HIS ALA SER SEQRES 2 C 137 GLU ASP LYS GLU ASP PHE VAL ARG PRO LEU ALA GLU THR SEQRES 3 C 137 LEU GLN GLN LEU GLY VAL ASN VAL TRP TYR ASP GLU PHE SEQRES 4 C 137 THR LEU LYS VAL GLY ASP SER LEU ARG GLN LYS ILE ASP SEQRES 5 C 137 SER GLY LEU ARG ASN SER LYS TYR GLY THR VAL VAL LEU SEQRES 6 C 137 SER THR ASP PHE ILE LYS LYS ASP TRP THR ASN TYR GLU SEQRES 7 C 137 LEU ASP GLY LEU VAL ALA ARG GLU MET ASN GLY HIS LYS SEQRES 8 C 137 MET ILE LEU PRO ILE TRP HIS LYS ILE THR LYS ASN ASP SEQRES 9 C 137 VAL LEU ASP TYR SER PRO ASN LEU ALA ASP LYS VAL ALA SEQRES 10 C 137 LEU ASN THR SER VAL ASN SER ILE GLU GLU ILE ALA HIS SEQRES 11 C 137 GLN LEU ALA ASP VAL ILE LEU SEQRES 1 D 137 SER ASN ALA GLU TYR ASP LEU PHE ILE SER HIS ALA SER SEQRES 2 D 137 GLU ASP LYS GLU ASP PHE VAL ARG PRO LEU ALA GLU THR SEQRES 3 D 137 LEU GLN GLN LEU GLY VAL ASN VAL TRP TYR ASP GLU PHE SEQRES 4 D 137 THR LEU LYS VAL GLY ASP SER LEU ARG GLN LYS ILE ASP SEQRES 5 D 137 SER GLY LEU ARG ASN SER LYS TYR GLY THR VAL VAL LEU SEQRES 6 D 137 SER THR ASP PHE ILE LYS LYS ASP TRP THR ASN TYR GLU SEQRES 7 D 137 LEU ASP GLY LEU VAL ALA ARG GLU MET ASN GLY HIS LYS SEQRES 8 D 137 MET ILE LEU PRO ILE TRP HIS LYS ILE THR LYS ASN ASP SEQRES 9 D 137 VAL LEU ASP TYR SER PRO ASN LEU ALA ASP LYS VAL ALA SEQRES 10 D 137 LEU ASN THR SER VAL ASN SER ILE GLU GLU ILE ALA HIS SEQRES 11 D 137 GLN LEU ALA ASP VAL ILE LEU HET 1O4 A 301 74 HET 1O4 B 301 74 HET 1O4 C 301 74 HET 1O4 D 301 74 HETNAM 1O4 [[(2~{R},3~{S},4~{R},5~{R})-5-(6-AMINOPURIN-9-YL)-3,4- HETNAM 2 1O4 BIS(OXIDANYL)OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL] HETNAM 3 1O4 [(2~{R},3~{S},4~{R},5~{R})-5-(8-AZANYLISOQUINOLIN-2- HETNAM 4 1O4 YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHYL HYDROGEN HETNAM 5 1O4 PHOSPHATE FORMUL 5 1O4 4(C24 H30 N7 O13 P2 1+) HELIX 1 AA1 ALA A 142 LYS A 146 5 5 HELIX 2 AA2 PHE A 149 GLY A 161 1 13 HELIX 3 AA3 TYR A 166 LEU A 171 1 6 HELIX 4 AA4 SER A 176 ASN A 187 1 12 HELIX 5 AA5 SER A 196 LYS A 202 1 7 HELIX 6 AA6 LYS A 202 MET A 217 1 16 HELIX 7 AA7 THR A 231 SER A 239 1 9 HELIX 8 AA8 ASN A 241 LYS A 245 5 5 HELIX 9 AA9 SER A 254 LEU A 267 1 14 HELIX 10 AB1 ALA B 142 LYS B 146 5 5 HELIX 11 AB2 PHE B 149 GLY B 161 1 13 HELIX 12 AB3 TYR B 166 LEU B 171 1 6 HELIX 13 AB4 SER B 176 ASN B 187 1 12 HELIX 14 AB5 SER B 196 LYS B 202 1 7 HELIX 15 AB6 LYS B 202 MET B 217 1 16 HELIX 16 AB7 THR B 231 SER B 239 1 9 HELIX 17 AB8 ASN B 241 LYS B 245 5 5 HELIX 18 AB9 SER B 254 LEU B 267 1 14 HELIX 19 AC1 ALA C 142 LYS C 146 5 5 HELIX 20 AC2 PHE C 149 GLY C 161 1 13 HELIX 21 AC3 TYR C 166 LEU C 171 1 6 HELIX 22 AC4 SER C 176 ASN C 187 1 12 HELIX 23 AC5 SER C 196 LYS C 202 1 7 HELIX 24 AC6 LYS C 202 MET C 217 1 16 HELIX 25 AC7 THR C 231 SER C 239 1 9 HELIX 26 AC8 ASN C 241 LYS C 245 5 5 HELIX 27 AC9 SER C 254 LEU C 267 1 14 HELIX 28 AD1 ALA D 142 LYS D 146 5 5 HELIX 29 AD2 PHE D 149 GLY D 161 1 13 HELIX 30 AD3 TYR D 166 LEU D 171 1 6 HELIX 31 AD4 SER D 176 ASN D 187 1 12 HELIX 32 AD5 SER D 196 LYS D 202 1 7 HELIX 33 AD6 LYS D 202 MET D 217 1 16 HELIX 34 AD7 THR D 231 SER D 239 1 9 HELIX 35 AD8 ASN D 241 LYS D 245 5 5 HELIX 36 AD9 SER D 254 LEU D 267 1 14 SHEET 1 AA1 5 VAL A 164 TRP A 165 0 SHEET 2 AA1 5 LEU A 137 SER A 140 1 N LEU A 137 O TRP A 165 SHEET 3 AA1 5 TYR A 190 LEU A 195 1 O THR A 192 N PHE A 138 SHEET 4 AA1 5 ILE A 223 TRP A 227 1 O ILE A 226 N LEU A 195 SHEET 5 AA1 5 LEU A 248 ASN A 249 1 O LEU A 248 N TRP A 227 SHEET 1 AA2 5 VAL B 164 TRP B 165 0 SHEET 2 AA2 5 LEU B 137 SER B 140 1 N LEU B 137 O TRP B 165 SHEET 3 AA2 5 TYR B 190 LEU B 195 1 O THR B 192 N PHE B 138 SHEET 4 AA2 5 ILE B 223 TRP B 227 1 O ILE B 226 N LEU B 195 SHEET 5 AA2 5 LEU B 248 ASN B 249 1 O LEU B 248 N TRP B 227 SHEET 1 AA3 5 VAL C 164 TRP C 165 0 SHEET 2 AA3 5 LEU C 137 SER C 140 1 N LEU C 137 O TRP C 165 SHEET 3 AA3 5 TYR C 190 LEU C 195 1 O THR C 192 N PHE C 138 SHEET 4 AA3 5 ILE C 223 TRP C 227 1 O ILE C 226 N LEU C 195 SHEET 5 AA3 5 LEU C 248 ASN C 249 1 O LEU C 248 N TRP C 227 SHEET 1 AA4 5 VAL D 164 TRP D 165 0 SHEET 2 AA4 5 LEU D 137 SER D 140 1 N LEU D 137 O TRP D 165 SHEET 3 AA4 5 TYR D 190 LEU D 195 1 O THR D 192 N PHE D 138 SHEET 4 AA4 5 ILE D 223 TRP D 227 1 O ILE D 226 N LEU D 195 SHEET 5 AA4 5 LEU D 248 ASN D 249 1 O LEU D 248 N TRP D 227 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