HEADER TRANSCRIPTION 10-JUN-24 9FND TITLE TRANSCRIPTIONAL ACTIVATOR PAFBC BOUND TO MYCOBACTERIAL RNA POLYMERASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL REGULATOR-LIKE PROTEIN; COMPND 3 CHAIN: X; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: PAFC; COMPND 7 CHAIN: Y; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOLICIBACTERIUM SMEGMATIS MC2 155; SOURCE 3 ORGANISM_TAXID: 246196; SOURCE 4 GENE: PAFB, MSMEI_3799; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: MYCOLICIBACTERIUM SMEGMATIS MC2 155; SOURCE 9 ORGANISM_TAXID: 246196; SOURCE 10 GENE: MSMEG_3888; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 12 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS PAFBC, SIGMA ADAPTATION, WYL DOMAIN, TRANSCRIPTIONAL ACTIVATOR, KEYWDS 2 TRANSCRIPTION EXPDTA ELECTRON MICROSCOPY AUTHOR R.ZDANOWICZ,C.M.SCHILLING,J.RABL,A.U.MUELLER,D.BOEHRINGER, AUTHOR 2 R.GLOCKSHUBER,E.WEBER-BAN REVDAT 2 19-FEB-25 9FND 1 JRNL REVDAT 1 12-FEB-25 9FND 0 JRNL AUTH C.M.SCHILLING,R.ZDANOWICZ,J.RABL,A.U.MULLER,D.BOEHRINGER, JRNL AUTH 2 R.GLOCKSHUBER,E.WEBER-BAN JRNL TITL SINGLE-STRANDED DNA BINDING TO THE TRANSCRIPTION FACTOR JRNL TITL 2 PAFBC TRIGGERS THE MYCOBACTERIAL DNA DAMAGE RESPONSE. JRNL REF SCI ADV V. 11 Q9054 2025 JRNL REFN ESSN 2375-2548 JRNL PMID 39919186 JRNL DOI 10.1126/SCIADV.ADQ9054 REMARK 2 REMARK 2 RESOLUTION. 4.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : EPU, CRYOSPARC, CRYOSPARC, CRYOSPARC, REMARK 3 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) : 4.000 REMARK 3 NUMBER OF PARTICLES : 154302 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 9FND COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-JUN-24. REMARK 100 THE DEPOSITION ID IS D_1292138140. 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 : TRANSCRIPTIONAL ACTIVATOR PAFBC REMARK 245 BOUND TO MYCOBACTERIAL RNA REMARK 245 POLYMERASE; PAFBC; DNA-DIRECTED REMARK 245 RNA POLYMERASE; RNAP POLYMERASE REMARK 245 SIGMA FACTOR A AND RNA REMARK 245 POLYMERASE-BINDING PROTEIN RBPA 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 : 8.00 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3000.00 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) : 7800.00 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: X, Y 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 GLY X -1 REMARK 465 LEU X 0 REMARK 465 SER X 1 REMARK 465 MET Y 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 VAL X 146 -61.54 -92.01 REMARK 500 MET Y 49 36.37 -99.10 REMARK 500 ARG Y 126 1.51 -67.71 REMARK 500 SER Y 137 8.90 59.23 REMARK 500 ILE Y 176 -54.89 -121.12 REMARK 500 VAL Y 222 -65.22 -120.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-50590 RELATED DB: EMDB REMARK 900 TRANSCRIPTIONAL ACTIVATOR PAFBC BOUND TO MYCOBACTERIAL RNA REMARK 900 POLYMERASE DBREF 9FND X 2 331 UNP I7G3U5 I7G3U5_MYCS2 2 331 DBREF 9FND Y 1 318 UNP A0QZ41 A0QZ41_MYCS2 1 318 SEQADV 9FND GLY X -1 UNP I7G3U5 EXPRESSION TAG SEQADV 9FND LEU X 0 UNP I7G3U5 EXPRESSION TAG SEQADV 9FND SER X 1 UNP I7G3U5 EXPRESSION TAG SEQRES 1 X 333 GLY LEU SER ALA VAL SER LYS VAL GLU ARG LEU MET ASN SEQRES 2 X 333 LEU VAL ILE ALA LEU LEU SER THR ARG THR TYR LEU PRO SEQRES 3 X 333 ALA GLU LYS ILE ARG THR THR VAL ALA GLY TYR ALA ASP SEQRES 4 X 333 SER PRO SER ASP GLU ALA PHE SER ARG MET PHE GLU ARG SEQRES 5 X 333 ASP LYS ASN GLU LEU ARG ASP LEU GLY ILE PRO LEU GLU SEQRES 6 X 333 THR GLY ARG VAL SER LYS TRP ASP SER THR GLU GLY TYR SEQRES 7 X 333 ARG ILE ASN ARG ASP SER TYR ALA LEU PRO PRO ILE GLY SEQRES 8 X 333 LEU THR ALA ASP GLU ALA ALA ALA VAL ALA VAL ALA THR SEQRES 9 X 333 GLN LEU TRP GLN SER PRO GLU LEU VAL THR ALA THR GLN SEQRES 10 X 333 ASN ALA VAL LEU LYS LEU ARG ALA ALA GLY VAL ASP VAL SEQRES 11 X 333 ASP ALA ASP GLY VAL GLY VAL ALA ILE ALA SER THR ALA SEQRES 12 X 333 THR LEU PRO GLY VAL ARG GLY SER GLU GLU VAL LEU GLN SEQRES 13 X 333 SER LEU LEU SER ALA ILE ASP GLU GLY ARG ALA VAL GLN SEQRES 14 X 333 PHE GLU HIS ARG PRO SER ARG SER ALA ASP TYR THR THR SEQRES 15 X 333 ARG THR VAL GLU PRO TRP GLY VAL VAL THR HIS ARG GLY SEQRES 16 X 333 ARG TRP TYR LEU VAL GLY HIS ASP ARG ASP ARG GLU ASP SEQRES 17 X 333 THR ARG THR PHE ARG LEU SER ARG ILE SER ALA ALA ALA SEQRES 18 X 333 ARG PRO ILE GLY PRO ALA GLY ALA VAL GLN LYS PRO GLN SEQRES 19 X 333 ASP VAL ASN LEU ARG ASP ILE VAL ARG ARG ALA VAL ALA SEQRES 20 X 333 GLU GLN PRO THR GLY GLU ARG ALA ARG ILE TRP ILE ALA SEQRES 21 X 333 GLY GLY ARG ALA THR ALA LEU ARG ARG GLN ALA VAL THR SEQRES 22 X 333 SER THR PRO ARG THR ILE GLY GLY ARG ALA GLY GLU GLU SEQRES 23 X 333 ILE THR VAL ASP ILE GLY THR TRP ASP ARG LEU ALA ARG SEQRES 24 X 333 GLU ILE ALA SER TYR GLY SER ASP ALA VAL ALA LEU GLU SEQRES 25 X 333 PRO SER SER LEU ARG ASP ASP VAL VAL GLU ARG LEU ARG SEQRES 26 X 333 ALA HIS ALA ALA GLY GLY GLU ARG SEQRES 1 Y 318 MET SER GLN VAL SER THR ARG LEU VAL ARG LEU LEU ASN SEQRES 2 Y 318 MET VAL PRO TYR PHE GLN ALA ASN PRO LYS VAL THR ARG SEQRES 3 Y 318 ALA GLU ALA ALA ALA ALA LEU GLY VAL THR GLY LYS GLN SEQRES 4 Y 318 LEU ASP ALA ASP LEU ASP GLN LEU TRP MET CYS GLY LEU SEQRES 5 Y 318 PRO GLY TYR SER PRO GLY ASP LEU ILE ASP PHE ASP PHE SEQRES 6 Y 318 VAL GLY ASP THR ILE GLU VAL THR PHE SER ALA GLY VAL SEQRES 7 Y 318 ASP HIS PRO LEU ARG LEU THR SER THR GLU ALA THR GLY SEQRES 8 Y 318 ILE LEU VAL ALA LEU ARG ALA LEU VAL ASP VAL PRO GLY SEQRES 9 Y 318 MET VAL ASP PRO GLU ALA ALA ARG SER ALA ILE ALA LYS SEQRES 10 Y 318 ILE GLU SER ALA VAL GLY SER GLN ARG ALA VAL VAL GLU SEQRES 11 Y 318 GLY ILE THR GLU ASP THR SER ALA GLU PRO GLY ALA ALA SEQRES 12 Y 318 ALA THR VAL ARG THR ALA VAL ARG GLU ASN ARG ALA LEU SEQRES 13 Y 318 THR LEU GLU TYR TYR SER ALA SER ARG ASP SER LEU ALA SEQRES 14 Y 318 THR ARG THR VAL ASP PRO ILE ARG VAL VAL LEU VAL GLY SEQRES 15 Y 318 ASP ASN SER TYR LEU GLU ALA TRP CYS ARG SER ALA GLU SEQRES 16 Y 318 ALA VAL ARG LEU PHE ARG PHE ASP ARG ILE VAL ASP ALA SEQRES 17 Y 318 GLN LEU LEU ASP ASP PRO ALA ALA PRO PRO PRO PRO ALA SEQRES 18 Y 318 VAL ALA ALA GLY PRO ASP THR SER LEU PHE ASP ALA ASP SEQRES 19 Y 318 PRO SER LEU PRO SER ALA THR LEU LEU ILE GLY ALA ALA SEQRES 20 Y 318 ALA ALA TRP MET PHE ASP TYR TYR PRO LEU ARG ASP ILE SEQRES 21 Y 318 THR GLU ARG PRO ASP GLY SER CYS GLU ALA THR MET THR SEQRES 22 Y 318 TYR ALA SER GLU ASP TRP MET ALA ARG PHE ILE LEU GLY SEQRES 23 Y 318 PHE GLY ALA GLU VAL GLN VAL LEU ALA PRO GLU SER LEU SEQRES 24 Y 318 ALA THR ARG VAL ARG GLN ALA ALA GLU ALA ALA LEU GLN SEQRES 25 Y 318 ALA TYR ALA ARG CYS VAL HELIX 1 AA1 SER X 4 SER X 18 1 15 HELIX 2 AA2 PRO X 24 VAL X 32 1 9 HELIX 3 AA3 SER X 40 LEU X 58 1 19 HELIX 4 AA4 ASN X 79 ALA X 84 1 6 HELIX 5 AA5 THR X 91 THR X 102 1 12 HELIX 6 AA6 SER X 107 GLY X 125 1 19 HELIX 7 AA7 GLU X 150 GLY X 163 1 14 HELIX 8 AA8 ASN X 235 ALA X 245 1 11 HELIX 9 AA9 ALA X 262 GLN X 268 1 7 HELIX 10 AB1 THR X 291 GLY X 303 1 13 HELIX 11 AB2 PRO X 311 ALA X 327 1 17 HELIX 12 AB3 GLN Y 3 ASN Y 21 1 19 HELIX 13 AB4 ARG Y 26 GLY Y 34 1 9 HELIX 14 AB5 THR Y 36 MET Y 49 1 14 HELIX 15 AB6 THR Y 85 VAL Y 100 1 16 HELIX 16 AB7 ASP Y 107 GLY Y 123 1 17 HELIX 17 AB8 GLY Y 141 ASN Y 153 1 13 HELIX 18 AB9 PRO Y 217 ALA Y 223 1 7 HELIX 19 AC1 TRP Y 250 TYR Y 255 1 6 HELIX 20 AC2 SER Y 276 GLY Y 288 1 13 HELIX 21 AC3 PRO Y 296 CYS Y 317 1 22 SHEET 1 AA1 2 LEU X 62 ARG X 66 0 SHEET 2 AA1 2 GLU X 74 ILE X 78 -1 O ARG X 77 N GLU X 63 SHEET 1 AA2 5 THR X 207 ARG X 211 0 SHEET 2 AA2 5 ARG X 194 ASP X 201 -1 N GLY X 199 O ARG X 208 SHEET 3 AA2 5 THR X 179 HIS X 191 -1 N GLU X 184 O HIS X 200 SHEET 4 AA2 5 ALA X 165 HIS X 170 -1 N VAL X 166 O VAL X 183 SHEET 5 AA2 5 ARG X 220 ILE X 222 -1 O ILE X 222 N ALA X 165 SHEET 1 AA3 4 THR X 271 ILE X 277 0 SHEET 2 AA3 4 ARG X 280 VAL X 287 -1 O GLU X 284 N THR X 273 SHEET 3 AA3 4 ALA X 253 ALA X 258 -1 N ILE X 255 O ILE X 285 SHEET 4 AA3 4 ALA X 306 GLU X 310 -1 O VAL X 307 N TRP X 256 SHEET 1 AA4 2 VAL Y 24 THR Y 25 0 SHEET 2 AA4 2 THR Y 69 ILE Y 70 -1 O ILE Y 70 N VAL Y 24 SHEET 1 AA5 5 ALA Y 196 ARG Y 201 0 SHEET 2 AA5 5 ASN Y 184 CYS Y 191 -1 N CYS Y 191 O ALA Y 196 SHEET 3 AA5 5 SER Y 167 VAL Y 181 -1 N ASP Y 174 O TRP Y 190 SHEET 4 AA5 5 LEU Y 156 SER Y 162 -1 N TYR Y 160 O ALA Y 169 SHEET 5 AA5 5 ILE Y 205 LEU Y 210 -1 O GLN Y 209 N THR Y 157 SHEET 1 AA6 3 ALA Y 270 THR Y 273 0 SHEET 2 AA6 3 SER Y 239 ILE Y 244 -1 N LEU Y 242 O ALA Y 270 SHEET 3 AA6 3 VAL Y 291 ALA Y 295 -1 O GLN Y 292 N LEU Y 243 CISPEP 1 GLU X 310 PRO X 311 0 1.34 CISPEP 2 ALA Y 295 PRO Y 296 0 0.03 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 TER 2532 ARG X 331 TER 4916 VAL Y 318 MASTER 141 0 0 21 21 0 0 6 4914 2 0 51 END