HEADER DNA BINDING PROTEIN 04-AUG-22 7YPQ TITLE CRYO-EM STRUCTURE OF ONE BACULOVIRUS LEF-3 MOLECULE IN COMPLEX WITH TITLE 2 SSDNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: LEF3; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'); COMPND 7 CHAIN: Q; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOVERPA ARMIGERA NUCLEOPOLYHEDROVIRUS; SOURCE 3 ORGANISM_TAXID: 51313; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 9 ORGANISM_TAXID: 32630 KEYWDS SSDNA, SSB, BACULOVIRUS, DNA BINDING PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR Y.FU,G.RAO,J.YIN,Z.LI,S.CAO REVDAT 2 03-JUL-24 7YPQ 1 REMARK REVDAT 1 25-JAN-23 7YPQ 0 JRNL AUTH J.YIN,Y.FU,G.RAO,Z.LI,K.TIAN,T.CHONG,K.KUANG,M.WANG,Z.HU, JRNL AUTH 2 S.CAO JRNL TITL STRUCTURAL TRANSITIONS DURING THE COOPERATIVE ASSEMBLY OF JRNL TITL 2 BACULOVIRUS SINGLE-STRANDED DNA-BINDING PROTEIN ON SSDNA. JRNL REF NUCLEIC ACIDS RES. V. 50 13100 2022 JRNL REFN ESSN 1362-4962 JRNL PMID 36477586 JRNL DOI 10.1093/NAR/GKAC1142 REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL 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) : 3.100 REMARK 3 NUMBER OF PARTICLES : 159174 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 7YPQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1300031236. 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 : HELICAL ARRAY REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : BACULOVIRUS LEF-3 IN COMPLEX REMARK 245 WITH SSDNA; LEF-3; SSDNA 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 : 6.30 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) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 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) : 4000.00 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: A, Q 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 A -33 REMARK 465 GLY A -32 REMARK 465 SER A -31 REMARK 465 SER A -30 REMARK 465 HIS A -29 REMARK 465 HIS A -28 REMARK 465 HIS A -27 REMARK 465 HIS A -26 REMARK 465 HIS A -25 REMARK 465 HIS A -24 REMARK 465 SER A -23 REMARK 465 SER A -22 REMARK 465 GLY A -21 REMARK 465 LEU A -20 REMARK 465 VAL A -19 REMARK 465 PRO A -18 REMARK 465 ARG A -17 REMARK 465 GLY A -16 REMARK 465 SER A -15 REMARK 465 HIS A -14 REMARK 465 MET A -13 REMARK 465 ALA A -12 REMARK 465 SER A -11 REMARK 465 MET A -10 REMARK 465 THR A -9 REMARK 465 GLY A -8 REMARK 465 GLY A -7 REMARK 465 GLN A -6 REMARK 465 GLN A -5 REMARK 465 MET A -4 REMARK 465 GLY A -3 REMARK 465 ARG A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 ASN A 3 REMARK 465 MET A 4 REMARK 465 ASP A 5 REMARK 465 ILE A 6 REMARK 465 SER A 7 REMARK 465 PRO A 8 REMARK 465 VAL A 9 REMARK 465 LYS A 10 REMARK 465 GLN A 11 REMARK 465 LEU A 12 REMARK 465 ILE A 13 REMARK 465 ASP A 14 REMARK 465 ILE A 15 REMARK 465 GLU A 16 REMARK 465 ASN A 17 REMARK 465 ASP A 18 REMARK 465 ASP A 19 REMARK 465 ALA A 20 REMARK 465 MET A 21 REMARK 465 ASN A 22 REMARK 465 THR A 23 REMARK 465 PRO A 24 REMARK 465 GLU A 25 REMARK 465 LYS A 26 REMARK 465 GLY A 27 REMARK 465 MET A 28 REMARK 465 LYS A 29 REMARK 465 ARG A 30 REMARK 465 PRO A 31 REMARK 465 LEU A 32 REMARK 465 MET A 33 REMARK 465 ARG A 34 REMARK 465 THR A 35 REMARK 465 MET A 36 REMARK 465 SER A 37 REMARK 465 SER A 38 REMARK 465 VAL A 39 REMARK 465 GLU A 40 REMARK 465 GLU A 41 REMARK 465 PRO A 42 REMARK 465 GLN A 43 REMARK 465 ALA A 44 REMARK 465 LYS A 45 REMARK 465 MET A 46 REMARK 465 ALA A 47 REMARK 465 LYS A 48 REMARK 465 GLU A 123 REMARK 465 ASP A 124 REMARK 465 LEU A 125 REMARK 465 LEU A 126 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 ASN A 67 51.75 39.68 REMARK 500 TYR A 260 51.44 -93.03 REMARK 500 LYS A 360 -7.14 -140.23 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7YNY RELATED DB: PDB REMARK 900 SSDNA-FREE LEF-3 REMARK 900 RELATED ID: EMD-34011 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF ONE BACULOVIRUS LEF-3 MOLECULE IN COMPLEX WITH REMARK 900 SSDNA DBREF 7YPQ A 1 379 UNP Q91BW6 Q91BW6_9ABAC 1 379 DBREF 7YPQ Q 1 11 PDB 7YPQ 7YPQ 1 11 SEQADV 7YPQ MET A -33 UNP Q91BW6 INITIATING METHIONINE SEQADV 7YPQ GLY A -32 UNP Q91BW6 EXPRESSION TAG SEQADV 7YPQ SER A -31 UNP Q91BW6 EXPRESSION TAG SEQADV 7YPQ SER A -30 UNP Q91BW6 EXPRESSION TAG SEQADV 7YPQ HIS A -29 UNP Q91BW6 EXPRESSION TAG SEQADV 7YPQ HIS A -28 UNP Q91BW6 EXPRESSION TAG SEQADV 7YPQ HIS A -27 UNP Q91BW6 EXPRESSION TAG SEQADV 7YPQ HIS A -26 UNP Q91BW6 EXPRESSION TAG SEQADV 7YPQ HIS A -25 UNP Q91BW6 EXPRESSION TAG SEQADV 7YPQ HIS A -24 UNP Q91BW6 EXPRESSION TAG SEQADV 7YPQ SER A -23 UNP Q91BW6 EXPRESSION TAG SEQADV 7YPQ SER A -22 UNP Q91BW6 EXPRESSION TAG SEQADV 7YPQ GLY A -21 UNP Q91BW6 EXPRESSION TAG SEQADV 7YPQ LEU A -20 UNP Q91BW6 EXPRESSION TAG SEQADV 7YPQ VAL A -19 UNP Q91BW6 EXPRESSION TAG SEQADV 7YPQ PRO A -18 UNP Q91BW6 EXPRESSION TAG SEQADV 7YPQ ARG A -17 UNP Q91BW6 EXPRESSION TAG SEQADV 7YPQ GLY A -16 UNP Q91BW6 EXPRESSION TAG SEQADV 7YPQ SER A -15 UNP Q91BW6 EXPRESSION TAG SEQADV 7YPQ HIS A -14 UNP Q91BW6 EXPRESSION TAG SEQADV 7YPQ MET A -13 UNP Q91BW6 EXPRESSION TAG SEQADV 7YPQ ALA A -12 UNP Q91BW6 EXPRESSION TAG SEQADV 7YPQ SER A -11 UNP Q91BW6 EXPRESSION TAG SEQADV 7YPQ MET A -10 UNP Q91BW6 EXPRESSION TAG SEQADV 7YPQ THR A -9 UNP Q91BW6 EXPRESSION TAG SEQADV 7YPQ GLY A -8 UNP Q91BW6 EXPRESSION TAG SEQADV 7YPQ GLY A -7 UNP Q91BW6 EXPRESSION TAG SEQADV 7YPQ GLN A -6 UNP Q91BW6 EXPRESSION TAG SEQADV 7YPQ GLN A -5 UNP Q91BW6 EXPRESSION TAG SEQADV 7YPQ MET A -4 UNP Q91BW6 EXPRESSION TAG SEQADV 7YPQ GLY A -3 UNP Q91BW6 EXPRESSION TAG SEQADV 7YPQ ARG A -2 UNP Q91BW6 EXPRESSION TAG SEQADV 7YPQ GLY A -1 UNP Q91BW6 EXPRESSION TAG SEQADV 7YPQ SER A 0 UNP Q91BW6 EXPRESSION TAG SEQRES 1 A 413 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 413 LEU VAL PRO ARG GLY SER HIS MET ALA SER MET THR GLY SEQRES 3 A 413 GLY GLN GLN MET GLY ARG GLY SER MET SER ASN MET ASP SEQRES 4 A 413 ILE SER PRO VAL LYS GLN LEU ILE ASP ILE GLU ASN ASP SEQRES 5 A 413 ASP ALA MET ASN THR PRO GLU LYS GLY MET LYS ARG PRO SEQRES 6 A 413 LEU MET ARG THR MET SER SER VAL GLU GLU PRO GLN ALA SEQRES 7 A 413 LYS MET ALA LYS LEU ARG THR LEU ASN VAL LYS GLY GLN SEQRES 8 A 413 LEU LEU THR LYS THR THR MET SER ILE ASN ASN GLU ASP SEQRES 9 A 413 TYR TYR LEU PHE LYS PHE LEU VAL ASN ASN LYS SER ILE SEQRES 10 A 413 ASP TYR TYR GLY THR GLN THR GLN PHE PHE SER LEU ILE SEQRES 11 A 413 ASN ASN LYS THR TYR GLU LEU VAL LEU GLN TYR SER ARG SEQRES 12 A 413 LYS LYS LEU LEU ILE LYS SER TYR GLU GLN CYS GLU ASP SEQRES 13 A 413 GLU ASP LEU LEU MET THR VAL CYS LYS SER VAL THR PHE SEQRES 14 A 413 GLN GLU PHE CYS ALA ASN GLU ILE LYS SER LEU LEU ALA SEQRES 15 A 413 LYS PHE LEU TYR GLY PHE LYS ILE TYR GLY SER SER ASN SEQRES 16 A 413 VAL TYR LYS LEU VAL PHE VAL ILE LEU LEU GLU ASP ASN SEQRES 17 A 413 ASN GLY THR ILE ASN GLY VAL GLN VAL GLU MET MET SER SEQRES 18 A 413 ASP PHE LYS ARG LEU SER GLY ALA PHE LYS ASN HIS VAL SEQRES 19 A 413 ILE GLU ASN GLU ASN ASP LEU PHE ASP CYS MET TYR LYS SEQRES 20 A 413 SER GLU GLU LYS TYR PHE ASN LEU TYR ARG ILE LYS CYS SEQRES 21 A 413 ASN HIS ASN ALA ASN ASN TYR LYS SER LEU SER LEU SER SEQRES 22 A 413 SER ASN SER GLN LEU GLU ARG LEU GLU THR ASP ASP SER SEQRES 23 A 413 MET PHE GLU TYR GLU PHE GLN TYR ASP TYR THR VAL ASN SEQRES 24 A 413 ILE SER ARG SER ASN LYS ILE ILE GLN LYS HIS ARG VAL SEQRES 25 A 413 THR GLY ASN PHE THR SER GLU ARG ASN ILE TYR GLN ASN SEQRES 26 A 413 SER ASP ARG PHE VAL ILE SER TYR ASP THR ALA ASN GLU SEQRES 27 A 413 LYS ILE LYS THR SER ILE TYR ASN ARG MET GLU ASN ALA SEQRES 28 A 413 GLU SER LYS THR ASP TYR ASP THR SER ILE THR LEU LYS SEQRES 29 A 413 ASP VAL THR LEU SER GLN LEU ASN SER LEU ILE GLU SER SEQRES 30 A 413 ASN LEU VAL GLN VAL ASP VAL TYR LEU VAL THR ASP PRO SEQRES 31 A 413 ASN ASN VAL LYS ASN ASN VAL ILE ALA GLY ILE THR LYS SEQRES 32 A 413 ILE GLU ILE ASP GLY THR TYR GLU PRO LEU SEQRES 1 Q 11 DA DA DA DA DA DA DA DA DA DA DA HELIX 1 AA1 THR A 88 LEU A 95 1 8 HELIX 2 AA2 PHE A 135 ALA A 140 1 6 HELIX 3 AA3 ASP A 188 PHE A 196 1 9 HELIX 4 AA4 ASN A 203 SER A 214 1 12 HELIX 5 AA5 SER A 319 GLN A 336 1 18 HELIX 6 AA6 GLN A 336 SER A 343 1 8 SHEET 1 AA1 6 THR A 51 ILE A 66 0 SHEET 2 AA1 6 GLU A 69 LEU A 77 -1 O LEU A 77 N GLN A 57 SHEET 3 AA1 6 SER A 82 GLY A 87 -1 O ILE A 83 N PHE A 76 SHEET 4 AA1 6 LYS A 111 GLN A 119 1 O ILE A 114 N TYR A 86 SHEET 5 AA1 6 THR A 100 SER A 108 -1 N VAL A 104 O SER A 116 SHEET 6 AA1 6 THR A 51 ILE A 66 -1 N VAL A 54 O LEU A 103 SHEET 1 AA2 7 VAL A 133 THR A 134 0 SHEET 2 AA2 7 TYR A 163 GLU A 172 1 O LEU A 170 N VAL A 133 SHEET 3 AA2 7 ILE A 178 SER A 187 -1 O VAL A 183 N PHE A 167 SHEET 4 AA2 7 LEU A 236 ARG A 246 1 O LEU A 236 N GLU A 184 SHEET 5 AA2 7 LYS A 217 CYS A 226 -1 N ASN A 220 O GLU A 245 SHEET 6 AA2 7 ILE A 143 LYS A 155 -1 N PHE A 150 O LYS A 217 SHEET 7 AA2 7 TYR A 163 GLU A 172 -1 O LYS A 164 N PHE A 154 SHEET 1 AA3 4 ILE A 272 VAL A 278 0 SHEET 2 AA3 4 VAL A 346 THR A 354 -1 O LEU A 352 N GLN A 274 SHEET 3 AA3 4 VAL A 363 GLU A 371 -1 O VAL A 363 N VAL A 353 SHEET 4 AA3 4 TYR A 376 GLU A 377 -1 O GLU A 377 N LYS A 369 SHEET 1 AA4 3 THR A 283 ILE A 288 0 SHEET 2 AA4 3 ASP A 293 ASP A 300 -1 O ARG A 294 N ASN A 287 SHEET 3 AA4 3 LYS A 305 TYR A 311 -1 O THR A 308 N ILE A 297 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