HEADER VIRUS 26-MAY-22 8A02 TITLE BACTERIOPHAGE PHICJT23 MAJOR CAPSID PROTEIN TRIMER TYPE 2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MAJOR CAPSID PROTEIN P5; COMPND 3 CHAIN: F, E, D SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: FLAVOBACTERIUM PHAGE; SOURCE 3 ORGANISM_TAXID: 908820 KEYWDS BACTERIOPHAGE, PHICJT23, VIRUS EXPDTA ELECTRON MICROSCOPY AUTHOR I.RISSANEN,N.KEJZAR,J.T.HUISKONEN REVDAT 1 14-DEC-22 8A02 0 JRNL AUTH N.KEJZAR,E.LAANTO,I.RISSANEN,V.ABRISHAMI,M.SELVARAJ, JRNL AUTH 2 S.MOINEAU,J.RAVANTTI,L.R.SUNDBERG,J.T.HUISKONEN JRNL TITL CRYO-EM STRUCTURE OF SSDNA BACTERIOPHAGE PHI CJT23 PROVIDES JRNL TITL 2 INSIGHT INTO EARLY VIRUS EVOLUTION. JRNL REF NAT COMMUN V. 13 7478 2022 JRNL REFN ESSN 2041-1723 JRNL PMID 36463224 JRNL DOI 10.1038/S41467-022-35123-6 REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : COOT, 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 : REAL REMARK 3 REFINEMENT PROTOCOL : AB INITIO MODEL 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) : 3.200 REMARK 3 NUMBER OF PARTICLES : 257197 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 8A02 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-MAY-22. REMARK 100 THE DEPOSITION ID IS D_1292123200. 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 : UNIDENTIFIED 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 : 7.20 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 TECNAI ARCTICA REMARK 245 DETECTOR TYPE : FEI FALCON III (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 300.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2200.00 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) : 1500.00 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) : 200 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: F, E, 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 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 SER F 50 156.11 67.43 REMARK 500 GLU F 91 -95.81 61.65 REMARK 500 ASP F 108 62.29 60.05 REMARK 500 GLU E 91 -95.94 56.11 REMARK 500 ILE D 3 -60.09 -101.94 REMARK 500 GLU D 91 -95.27 58.30 REMARK 500 ASP D 112 35.25 -99.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-15045 RELATED DB: EMDB REMARK 900 BACTERIOPHAGE PHICJT23 MAJOR CAPSID PROTEIN TRIMER TYPE 2 DBREF 8A02 F 1 239 PDB 8A02 8A02 1 239 DBREF 8A02 E 1 239 PDB 8A02 8A02 1 239 DBREF 8A02 D 1 239 PDB 8A02 8A02 1 239 SEQRES 1 F 239 MET LYS ILE ALA THR ILE THR GLY VAL THR LYS SER PRO SEQRES 2 F 239 GLU LEU GLN VAL THR LYS ALA ILE GLY ALA LEU ILE LEU SEQRES 3 F 239 SER SER ASP VAL ALA LEU SER ALA LEU THR THR GLU LYS SEQRES 4 F 239 ILE SER ILE TYR ILE GLU ARG GLY ASN GLY SER ASN VAL SEQRES 5 F 239 ILE LEU ALA ASN LYS VAL LEU LEU LYS ASP PHE ILE LEU SEQRES 6 F 239 ALA SER THR TYR GLY THR GLU ASN THR GLN SER ASP ALA SEQRES 7 F 239 ASP ASN ALA MET ILE ALA LEU CYS GLU LEU ALA ASP GLU SEQRES 8 F 239 GLY SER ILE TYR LEU ALA ASP LYS GLU SER ILE LYS ILE SEQRES 9 F 239 THR LEU GLU ASP LEU ILE SER ASP LYS ARG TYR ASP LEU SEQRES 10 F 239 HIS GLY ILE GLU GLU PRO GLN GLN THR ASN ASN LEU PHE SEQRES 11 F 239 PHE PHE GLU GLN LYS SER VAL ALA SER GLU GLU PHE ASN SEQRES 12 F 239 LYS LYS ILE ASP VAL GLN GLY PHE ASP LEU ALA ILE MET SEQRES 13 F 239 THR VAL ASP ASP SER VAL SER ASP LEU SER TYR GLN TYR SEQRES 14 F 239 SER ASN GLY GLN VAL VAL LYS TYR LEU PRO PHE GLU LEU SEQRES 15 F 239 GLN THR LEU SER ARG ASP ILE ASP PRO ILE GLN ALA VAL SEQRES 16 F 239 LEU SER ASP GLY LYS VAL VAL GLN GLY LEU THR ASP ARG SEQRES 17 F 239 LEU THR LEU PRO LEU VAL ALA VAL VAL GLY ILE GLU ILE SEQRES 18 F 239 ASN LYS SER GLN GLY SER ILE ILE ASN PHE VAL VAL ARG SEQRES 19 F 239 CYS LEU LYS THR VAL SEQRES 1 E 239 MET LYS ILE ALA THR ILE THR GLY VAL THR LYS SER PRO SEQRES 2 E 239 GLU LEU GLN VAL THR LYS ALA ILE GLY ALA LEU ILE LEU SEQRES 3 E 239 SER SER ASP VAL ALA LEU SER ALA LEU THR THR GLU LYS SEQRES 4 E 239 ILE SER ILE TYR ILE GLU ARG GLY ASN GLY SER ASN VAL SEQRES 5 E 239 ILE LEU ALA ASN LYS VAL LEU LEU LYS ASP PHE ILE LEU SEQRES 6 E 239 ALA SER THR TYR GLY THR GLU ASN THR GLN SER ASP ALA SEQRES 7 E 239 ASP ASN ALA MET ILE ALA LEU CYS GLU LEU ALA ASP GLU SEQRES 8 E 239 GLY SER ILE TYR LEU ALA ASP LYS GLU SER ILE LYS ILE SEQRES 9 E 239 THR LEU GLU ASP LEU ILE SER ASP LYS ARG TYR ASP LEU SEQRES 10 E 239 HIS GLY ILE GLU GLU PRO GLN GLN THR ASN ASN LEU PHE SEQRES 11 E 239 PHE PHE GLU GLN LYS SER VAL ALA SER GLU GLU PHE ASN SEQRES 12 E 239 LYS LYS ILE ASP VAL GLN GLY PHE ASP LEU ALA ILE MET SEQRES 13 E 239 THR VAL ASP ASP SER VAL SER ASP LEU SER TYR GLN TYR SEQRES 14 E 239 SER ASN GLY GLN VAL VAL LYS TYR LEU PRO PHE GLU LEU SEQRES 15 E 239 GLN THR LEU SER ARG ASP ILE ASP PRO ILE GLN ALA VAL SEQRES 16 E 239 LEU SER ASP GLY LYS VAL VAL GLN GLY LEU THR ASP ARG SEQRES 17 E 239 LEU THR LEU PRO LEU VAL ALA VAL VAL GLY ILE GLU ILE SEQRES 18 E 239 ASN LYS SER GLN GLY SER ILE ILE ASN PHE VAL VAL ARG SEQRES 19 E 239 CYS LEU LYS THR VAL SEQRES 1 D 239 MET LYS ILE ALA THR ILE THR GLY VAL THR LYS SER PRO SEQRES 2 D 239 GLU LEU GLN VAL THR LYS ALA ILE GLY ALA LEU ILE LEU SEQRES 3 D 239 SER SER ASP VAL ALA LEU SER ALA LEU THR THR GLU LYS SEQRES 4 D 239 ILE SER ILE TYR ILE GLU ARG GLY ASN GLY SER ASN VAL SEQRES 5 D 239 ILE LEU ALA ASN LYS VAL LEU LEU LYS ASP PHE ILE LEU SEQRES 6 D 239 ALA SER THR TYR GLY THR GLU ASN THR GLN SER ASP ALA SEQRES 7 D 239 ASP ASN ALA MET ILE ALA LEU CYS GLU LEU ALA ASP GLU SEQRES 8 D 239 GLY SER ILE TYR LEU ALA ASP LYS GLU SER ILE LYS ILE SEQRES 9 D 239 THR LEU GLU ASP LEU ILE SER ASP LYS ARG TYR ASP LEU SEQRES 10 D 239 HIS GLY ILE GLU GLU PRO GLN GLN THR ASN ASN LEU PHE SEQRES 11 D 239 PHE PHE GLU GLN LYS SER VAL ALA SER GLU GLU PHE ASN SEQRES 12 D 239 LYS LYS ILE ASP VAL GLN GLY PHE ASP LEU ALA ILE MET SEQRES 13 D 239 THR VAL ASP ASP SER VAL SER ASP LEU SER TYR GLN TYR SEQRES 14 D 239 SER ASN GLY GLN VAL VAL LYS TYR LEU PRO PHE GLU LEU SEQRES 15 D 239 GLN THR LEU SER ARG ASP ILE ASP PRO ILE GLN ALA VAL SEQRES 16 D 239 LEU SER ASP GLY LYS VAL VAL GLN GLY LEU THR ASP ARG SEQRES 17 D 239 LEU THR LEU PRO LEU VAL ALA VAL VAL GLY ILE GLU ILE SEQRES 18 D 239 ASN LYS SER GLN GLY SER ILE ILE ASN PHE VAL VAL ARG SEQRES 19 D 239 CYS LEU LYS THR VAL HELIX 1 AA1 ALA F 31 LEU F 35 5 5 HELIX 2 AA2 LEU F 60 ALA F 66 1 7 HELIX 3 AA3 LEU F 178 ARG F 187 1 10 HELIX 4 AA4 ALA E 31 LEU E 35 5 5 HELIX 5 AA5 LEU E 60 ALA E 66 1 7 HELIX 6 AA6 LEU E 178 ARG E 187 1 10 HELIX 7 AA7 ALA D 31 LEU D 35 5 5 HELIX 8 AA8 LEU D 60 THR D 68 1 9 HELIX 9 AA9 LEU D 178 ARG D 187 1 10 SHEET 1 AA1 4 LYS F 2 THR F 7 0 SHEET 2 AA1 4 ARG F 114 ILE F 120 -1 O TYR F 115 N ILE F 6 SHEET 3 AA1 4 ALA F 23 SER F 28 -1 N SER F 27 O ASP F 116 SHEET 4 AA1 4 MET F 82 GLU F 87 -1 O CYS F 86 N LEU F 24 SHEET 1 AA2 4 LEU F 15 VAL F 17 0 SHEET 2 AA2 4 GLU F 100 GLU F 107 -1 O ILE F 102 N VAL F 17 SHEET 3 AA2 4 LYS F 39 ARG F 46 -1 N TYR F 43 O LYS F 103 SHEET 4 AA2 4 ASN F 51 LEU F 59 -1 O VAL F 58 N ILE F 40 SHEET 1 AA3 2 SER F 93 ILE F 94 0 SHEET 2 AA3 2 GLN F 125 THR F 126 1 O THR F 126 N SER F 93 SHEET 1 AA4 4 ASN F 128 VAL F 137 0 SHEET 2 AA4 4 ILE F 229 THR F 238 -1 O PHE F 231 N LYS F 135 SHEET 3 AA4 4 LEU F 153 THR F 157 -1 N LEU F 153 O ARG F 234 SHEET 4 AA4 4 ARG F 208 PRO F 212 -1 O LEU F 211 N ALA F 154 SHEET 1 AA5 4 ASN F 143 ILE F 146 0 SHEET 2 AA5 4 VAL F 216 LYS F 223 -1 O ILE F 221 N LYS F 144 SHEET 3 AA5 4 VAL F 162 TYR F 169 -1 N GLN F 168 O VAL F 217 SHEET 4 AA5 4 VAL F 174 TYR F 177 -1 O TYR F 177 N LEU F 165 SHEET 1 AA6 2 ALA F 194 VAL F 195 0 SHEET 2 AA6 2 VAL F 201 VAL F 202 -1 O VAL F 202 N ALA F 194 SHEET 1 AA7 4 LYS E 2 THR E 7 0 SHEET 2 AA7 4 ARG E 114 ILE E 120 -1 O TYR E 115 N ILE E 6 SHEET 3 AA7 4 ALA E 23 SER E 28 -1 N SER E 27 O ASP E 116 SHEET 4 AA7 4 MET E 82 GLU E 87 -1 O CYS E 86 N LEU E 24 SHEET 1 AA8 4 LEU E 15 VAL E 17 0 SHEET 2 AA8 4 SER E 101 GLU E 107 -1 O ILE E 102 N VAL E 17 SHEET 3 AA8 4 LYS E 39 GLU E 45 -1 N TYR E 43 O LYS E 103 SHEET 4 AA8 4 VAL E 52 LEU E 59 -1 O VAL E 52 N ILE E 44 SHEET 1 AA9 2 SER E 93 ILE E 94 0 SHEET 2 AA9 2 GLN E 125 THR E 126 1 O THR E 126 N SER E 93 SHEET 1 AB1 4 ASN E 128 VAL E 137 0 SHEET 2 AB1 4 ILE E 229 THR E 238 -1 O LYS E 237 N LEU E 129 SHEET 3 AB1 4 LEU E 153 THR E 157 -1 N LEU E 153 O ARG E 234 SHEET 4 AB1 4 ARG E 208 PRO E 212 -1 O LEU E 209 N MET E 156 SHEET 1 AB2 4 ASN E 143 ILE E 146 0 SHEET 2 AB2 4 VAL E 216 LYS E 223 -1 O ILE E 221 N LYS E 144 SHEET 3 AB2 4 VAL E 162 TYR E 169 -1 N ASP E 164 O ASN E 222 SHEET 4 AB2 4 VAL E 174 TYR E 177 -1 O TYR E 177 N LEU E 165 SHEET 1 AB3 2 ALA E 194 VAL E 195 0 SHEET 2 AB3 2 VAL E 201 VAL E 202 -1 O VAL E 202 N ALA E 194 SHEET 1 AB4 4 LYS D 2 THR D 7 0 SHEET 2 AB4 4 ARG D 114 ILE D 120 -1 O LEU D 117 N ILE D 3 SHEET 3 AB4 4 ALA D 23 SER D 28 -1 N ILE D 25 O HIS D 118 SHEET 4 AB4 4 MET D 82 GLU D 87 -1 O CYS D 86 N LEU D 24 SHEET 1 AB5 4 LEU D 15 VAL D 17 0 SHEET 2 AB5 4 GLU D 100 GLU D 107 -1 O ILE D 102 N VAL D 17 SHEET 3 AB5 4 LYS D 39 ARG D 46 -1 N TYR D 43 O LYS D 103 SHEET 4 AB5 4 VAL D 52 ILE D 53 -1 O VAL D 52 N ILE D 44 SHEET 1 AB6 4 LEU D 15 VAL D 17 0 SHEET 2 AB6 4 GLU D 100 GLU D 107 -1 O ILE D 102 N VAL D 17 SHEET 3 AB6 4 LYS D 39 ARG D 46 -1 N TYR D 43 O LYS D 103 SHEET 4 AB6 4 VAL D 58 LEU D 59 -1 O VAL D 58 N ILE D 40 SHEET 1 AB7 2 SER D 93 ILE D 94 0 SHEET 2 AB7 2 GLN D 125 THR D 126 1 O THR D 126 N SER D 93 SHEET 1 AB8 4 ASN D 128 VAL D 137 0 SHEET 2 AB8 4 ILE D 229 THR D 238 -1 O ILE D 229 N VAL D 137 SHEET 3 AB8 4 LEU D 153 THR D 157 -1 N LEU D 153 O ARG D 234 SHEET 4 AB8 4 ARG D 208 PRO D 212 -1 O LEU D 209 N MET D 156 SHEET 1 AB9 4 ASN D 143 ILE D 146 0 SHEET 2 AB9 4 VAL D 216 LYS D 223 -1 O ILE D 221 N LYS D 144 SHEET 3 AB9 4 VAL D 162 TYR D 169 -1 N ASP D 164 O ASN D 222 SHEET 4 AB9 4 VAL D 174 TYR D 177 -1 O TYR D 177 N LEU D 165 SHEET 1 AC1 2 ALA D 194 VAL D 195 0 SHEET 2 AC1 2 VAL D 201 VAL D 202 -1 O VAL D 202 N ALA D 194 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