HEADER VIRAL PROTEIN 24-JAN-19 6QJT TITLE THERMOPHAGE P23-45 IN SITU PROCAPSID PORTAL PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PORTAL PROTEIN; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS VIRUS P23-45; SOURCE 3 ORGANISM_TAXID: 466051; SOURCE 4 CELL_LINE: THERMUS THERMOPHILUS HB8 KEYWDS PORTAL, TRANSLOCASE, MOTOR, PORE, BACTERIOPHAGE, THERMOPHAGE, KEYWDS 2 CAUDOVIRALES, SIPHOVIRIDAE, VIRUS, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR O.W.BAYFIELD,A.A.ANTSON REVDAT 4 15-MAY-24 6QJT 1 REMARK REVDAT 3 03-JUN-20 6QJT 1 JRNL REVDAT 2 22-APR-20 6QJT 1 JRNL REVDAT 1 25-MAR-20 6QJT 0 JRNL AUTH O.W.BAYFIELD,A.C.STEVEN,A.A.ANTSON JRNL TITL CRYO-EM STRUCTURE IN SITU REVEALS A MOLECULAR SWITCH THAT JRNL TITL 2 SAFEGUARDS VIRUS AGAINST GENOME LOSS. JRNL REF ELIFE V. 9 2020 JRNL REFN ESSN 2050-084X JRNL PMID 32286226 JRNL DOI 10.7554/ELIFE.55517 REMARK 2 REMARK 2 RESOLUTION. 3.74 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, SCIPION, EPU, CTFFIND, COOT, REMARK 3 RELION, RELION, RELION, RELION, PHENIX, REMARK 3 COOT 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) : 3.740 REMARK 3 NUMBER OF PARTICLES : 10025 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 6QJT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-JAN-19. REMARK 100 THE DEPOSITION ID IS D_1292100299. 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 : THERMUS PHAGE P2345 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 : FEI FALCON III (4K 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 : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 9900.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 75000 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: DODECAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 BIOMT1 2 0.866025 -0.500000 0.000000 69.88143 REMARK 350 BIOMT2 2 0.500000 0.866025 0.000000 -40.34606 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 0.500000 -0.866025 0.000000 150.57356 REMARK 350 BIOMT2 3 0.866025 0.500000 0.000000 -40.34606 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 -1.000000 0.000000 220.45499 REMARK 350 BIOMT2 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 5 -0.500000 -0.866025 0.000000 260.80106 REMARK 350 BIOMT2 5 0.866025 -0.500000 0.000000 69.88143 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 6 -0.866025 -0.500000 0.000000 260.80105 REMARK 350 BIOMT2 6 0.500000 -0.866025 0.000000 150.57356 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 7 -1.000000 0.000000 0.000000 220.45499 REMARK 350 BIOMT2 7 0.000000 -1.000000 0.000000 220.45499 REMARK 350 BIOMT3 7 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 8 -0.866025 0.500000 0.000000 150.57356 REMARK 350 BIOMT2 8 -0.500000 -0.866025 0.000000 260.80106 REMARK 350 BIOMT3 8 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 9 -0.500000 0.866025 0.000000 69.88143 REMARK 350 BIOMT2 9 -0.866025 -0.500000 0.000000 260.80106 REMARK 350 BIOMT3 9 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 10 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 10 -1.000000 0.000000 0.000000 220.45499 REMARK 350 BIOMT3 10 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 11 0.500000 0.866025 0.000000 -40.34607 REMARK 350 BIOMT2 11 -0.866025 0.500000 0.000000 150.57356 REMARK 350 BIOMT3 11 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 12 0.866025 0.500000 0.000000 -40.34606 REMARK 350 BIOMT2 12 -0.500000 0.866025 0.000000 69.88143 REMARK 350 BIOMT3 12 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 1 REMARK 465 ALA A 2 REMARK 465 LYS A 3 REMARK 465 ARG A 4 REMARK 465 GLY A 5 REMARK 465 ARG A 6 REMARK 465 LYS A 7 REMARK 465 PRO A 8 REMARK 465 LYS A 9 REMARK 465 GLU A 10 REMARK 465 LEU A 11 REMARK 465 VAL A 12 REMARK 465 PRO A 13 REMARK 465 GLY A 14 REMARK 465 PRO A 15 REMARK 465 GLY A 16 REMARK 465 SER A 17 REMARK 465 ILE A 18 REMARK 465 ASP A 19 REMARK 465 PRO A 20 REMARK 465 SER A 21 REMARK 465 ASP A 22 REMARK 465 VAL A 23 REMARK 465 PRO A 24 REMARK 465 LYS A 25 REMARK 465 ALA A 437 REMARK 465 ASP A 438 REMARK 465 SER A 439 REMARK 465 ARG A 440 REMARK 465 TYR A 441 REMARK 465 LEU A 442 REMARK 465 TYR A 443 REMARK 465 THR A 444 REMARK 465 ARG A 445 REMARK 465 ARG A 446 REMARK 465 ARG A 447 REMARK 465 ARG A 448 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 TYR A 116 72.13 57.46 REMARK 500 ASN A 204 51.12 32.88 REMARK 500 PRO A 273 45.32 -80.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-4445 RELATED DB: EMDB REMARK 900 CONTAINS THE PROCAPSID FROM WHICH THE PORTAL RECONSTRUCTION WAS REMARK 900 DERIVED REMARK 900 RELATED ID: EMD-4567 RELATED DB: EMDB REMARK 900 VIRAL PORE PROTEIN DBREF 6QJT A 1 448 UNP A7XXB9 A7XXB9_9CAUD 1 448 SEQRES 1 A 448 MET ALA LYS ARG GLY ARG LYS PRO LYS GLU LEU VAL PRO SEQRES 2 A 448 GLY PRO GLY SER ILE ASP PRO SER ASP VAL PRO LYS LEU SEQRES 3 A 448 GLU GLY ALA SER VAL PRO VAL MET SER THR SER TYR ASP SEQRES 4 A 448 VAL VAL VAL ASP ARG GLU PHE ASP GLU LEU LEU GLN GLY SEQRES 5 A 448 LYS ASP GLY LEU LEU VAL TYR HIS LYS MET LEU SER ASP SEQRES 6 A 448 GLY THR VAL LYS ASN ALA LEU ASN TYR ILE PHE GLY ARG SEQRES 7 A 448 ILE ARG SER ALA LYS TRP TYR VAL GLU PRO ALA SER THR SEQRES 8 A 448 ASP PRO GLU ASP ILE ALA ILE ALA ALA PHE ILE HIS ALA SEQRES 9 A 448 GLN LEU GLY ILE ASP ASP ALA SER VAL GLY LYS TYR PRO SEQRES 10 A 448 PHE GLY ARG LEU PHE ALA ILE TYR GLU ASN ALA TYR ILE SEQRES 11 A 448 TYR GLY MET ALA ALA GLY GLU ILE VAL LEU THR LEU GLY SEQRES 12 A 448 ALA ASP GLY LYS LEU ILE LEU ASP LYS ILE VAL PRO ILE SEQRES 13 A 448 HIS PRO PHE ASN ILE ASP GLU VAL LEU TYR ASP GLU GLU SEQRES 14 A 448 GLY GLY PRO LYS ALA LEU LYS LEU SER GLY GLU VAL LYS SEQRES 15 A 448 GLY GLY SER GLN PHE VAL ASN GLY LEU GLU ILE PRO ILE SEQRES 16 A 448 TRP LYS THR VAL VAL PHE LEU HIS ASN ASP ASP GLY SER SEQRES 17 A 448 PHE THR GLY GLN SER ALA LEU ARG ALA ALA VAL PRO HIS SEQRES 18 A 448 TRP LEU ALA LYS ARG ALA LEU ILE LEU LEU ILE ASN HIS SEQRES 19 A 448 GLY LEU GLU ARG PHE MET ILE GLY VAL PRO THR LEU THR SEQRES 20 A 448 ILE PRO LYS SER VAL ARG GLN GLY THR LYS GLN TRP GLU SEQRES 21 A 448 ALA ALA LYS GLU ILE VAL LYS ASN PHE VAL GLN LYS PRO SEQRES 22 A 448 ARG HIS GLY ILE ILE LEU PRO ASP ASP TRP LYS PHE ASP SEQRES 23 A 448 THR VAL ASP LEU LYS SER ALA MET PRO ASP ALA ILE PRO SEQRES 24 A 448 TYR LEU THR TYR HIS ASP ALA GLY ILE ALA ARG ALA LEU SEQRES 25 A 448 GLY ILE ASP PHE ASN THR VAL GLN LEU ASN MET GLY VAL SEQRES 26 A 448 GLN ALA VAL ASN ILE GLY GLU PHE VAL SER LEU THR GLN SEQRES 27 A 448 GLN THR ILE ILE SER LEU GLN ARG GLU PHE ALA SER ALA SEQRES 28 A 448 VAL ASN LEU TYR LEU ILE PRO LYS LEU VAL LEU PRO ASN SEQRES 29 A 448 TRP PRO GLY ALA THR ARG PHE PRO ARG LEU THR PHE GLU SEQRES 30 A 448 MET GLU GLU ARG ASN ASP PHE SER ALA ALA ALA ASN LEU SEQRES 31 A 448 MET GLY MET LEU ILE ASN ALA VAL LYS ASP SER GLU ASP SEQRES 32 A 448 ILE PRO THR GLU LEU LYS ALA LEU ILE ASP ALA LEU PRO SEQRES 33 A 448 SER LYS MET ARG ARG ALA LEU GLY VAL VAL ASP GLU VAL SEQRES 34 A 448 ARG GLU ALA VAL ARG GLN PRO ALA ASP SER ARG TYR LEU SEQRES 35 A 448 TYR THR ARG ARG ARG ARG HELIX 1 AA1 LYS A 53 MET A 62 1 10 HELIX 2 AA2 ASP A 65 ARG A 80 1 16 HELIX 3 AA3 ASP A 92 GLY A 107 1 16 HELIX 4 AA4 PRO A 117 GLY A 132 1 16 HELIX 5 AA5 ALA A 218 MET A 240 1 23 HELIX 6 AA6 THR A 256 LYS A 272 1 17 HELIX 7 AA7 ALA A 297 LEU A 312 1 16 HELIX 8 AA8 SER A 335 LEU A 356 1 22 HELIX 9 AA9 ILE A 357 LEU A 362 1 6 HELIX 10 AB1 ASP A 383 LYS A 399 1 17 HELIX 11 AB2 ASP A 403 ALA A 414 1 12 HELIX 12 AB3 PRO A 416 LEU A 423 1 8 HELIX 13 AB4 ASP A 427 GLN A 435 1 9 SHEET 1 AA1 2 TRP A 84 GLU A 87 0 SHEET 2 AA1 2 ARG A 373 PHE A 376 -1 O ARG A 373 N GLU A 87 SHEET 1 AA2 3 PRO A 155 ILE A 156 0 SHEET 2 AA2 3 MET A 133 GLU A 137 -1 N ALA A 135 O ILE A 156 SHEET 3 AA2 3 THR A 198 LEU A 202 -1 O PHE A 201 N ALA A 134 SHEET 1 AA3 2 VAL A 139 LEU A 142 0 SHEET 2 AA3 2 LEU A 148 LYS A 152 -1 O ASP A 151 N VAL A 139 SHEET 1 AA4 3 ILE A 161 TYR A 166 0 SHEET 2 AA4 3 PRO A 172 LEU A 177 -1 O ALA A 174 N LEU A 165 SHEET 3 AA4 3 LEU A 191 PRO A 194 -1 O ILE A 193 N LEU A 175 SHEET 1 AA5 2 PRO A 244 THR A 247 0 SHEET 2 AA5 2 LYS A 284 THR A 287 -1 O ASP A 286 N THR A 245 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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