HEADER VIRAL PROTEIN 28-DEC-25 21UY TITLE CRYO-EM STRUCTURE OF BACTERIOPHAGE PHI92 MATURE HEAD COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHI92_GP123; COMPND 3 CHAIN: E, F, G; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: PHI92_GP124; COMPND 6 CHAIN: N SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA PHAGE PHI92; SOURCE 3 ORGANISM_TAXID: 948870; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: ESCHERICHIA PHAGE PHI92; SOURCE 6 ORGANISM_TAXID: 948870 KEYWDS HEAD, PHAGE, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR Y.CHEN,H.R.LIU REVDAT 1 22-JUL-26 21UY 0 JRNL AUTH Y.CHEN,H.R.LIU JRNL TITL THE IN STIU STRUCTURE OF THE MATURE HEAD OF BACTERIOPHAGE JRNL TITL 2 PHI92 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, PHENIX, RELION 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) : 3.000 REMARK 3 NUMBER OF PARTICLES : 118800 REMARK 3 CTF CORRECTION METHOD : NONE REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 21UY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 02-JAN-26. REMARK 100 THE DEPOSITION ID IS D_1300067830. 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 : ESCHERICHIA PHAGE PHI92 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 : 7.00 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1800.00 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) : 3200.00 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 300 THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR REMARK 300 CYCLIC POINT SYMMETRY (SCHOENFLIES SYMBOL = C5). 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 APPLY THE FOLLOWING TO CHAINS: E, F, G, N 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 0.309017 -0.951057 0.000000 325.12382 REMARK 350 BIOMT2 2 0.951057 0.309017 0.000000 -51.49456 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.809017 -0.587785 0.000000 474.56684 REMARK 350 BIOMT2 3 0.587785 -0.809017 0.000000 241.80387 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -0.809017 0.587785 0.000000 241.80389 REMARK 350 BIOMT2 4 -0.587785 -0.809017 0.000000 474.56683 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 5 0.309017 0.951057 0.000000 -51.49455 REMARK 350 BIOMT2 5 -0.951057 0.309017 0.000000 325.12382 REMARK 350 BIOMT3 5 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 E 1 REMARK 465 SER E 130 REMARK 465 MET F 1 REMARK 465 SER F 130 REMARK 465 MET G 1 REMARK 465 SER G 130 REMARK 465 MET N 1 REMARK 465 PRO N 2 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 E 14 -9.64 73.14 REMARK 500 CYS E 30 -4.41 80.53 REMARK 500 VAL E 62 -55.34 -125.84 REMARK 500 ASP E 76 51.53 -91.48 REMARK 500 PHE F 14 -9.49 74.77 REMARK 500 CYS F 30 -3.93 81.35 REMARK 500 VAL F 62 -57.03 -125.55 REMARK 500 ASP F 76 52.68 -94.20 REMARK 500 PHE G 14 -10.21 73.39 REMARK 500 CYS G 30 -3.31 81.04 REMARK 500 VAL G 62 -57.63 -126.10 REMARK 500 ASP G 76 53.27 -93.81 REMARK 500 GLU N 20 -152.46 59.56 REMARK 500 ALA N 56 144.64 84.92 REMARK 500 PHE N 65 164.46 81.07 REMARK 500 VAL N 145 -112.21 56.61 REMARK 500 GLN N 222 21.31 -140.35 REMARK 500 LEU N 238 54.93 -92.64 REMARK 500 ASP N 243 140.23 111.16 REMARK 500 THR N 287 142.85 75.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-68019 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF BACTERIOPHAGE PHI92 MATURE HEAD DBREF 21UY E 1 130 UNP I7HXF2 I7HXF2_9CAUD 1 130 DBREF 21UY F 1 130 UNP I7HXF2 I7HXF2_9CAUD 1 130 DBREF 21UY G 1 130 UNP I7HXF2 I7HXF2_9CAUD 1 130 DBREF 21UY N 1 333 UNP I7HJD6 I7HJD6_9CAUD 1 333 SEQRES 1 E 130 MET ALA THR GLY ILE SER LEU SER ASN TYR ARG GLN GLU SEQRES 2 E 130 PHE GLY HIS LEU VAL LEU GLY GLY VAL PHE SER SER ASP SEQRES 3 E 130 LEU GLY HIS CYS VAL ARG GLU VAL ASN LEU VAL LYS THR SEQRES 4 E 130 ALA THR MET LYS ILE GLY SER VAL LEU LYS ALA ASP ASN SEQRES 5 E 130 THR GLU ALA THR ALA ALA GLY GLU ALA VAL LYS VAL LEU SEQRES 6 E 130 LEU TRP THR ASP ALA LEU PHE GLY ILE ASP ASP VAL ALA SEQRES 7 E 130 VAL GLY ASP THR PHE THR ALA VAL VAL GLY VAL ARG ASP SEQRES 8 E 130 LEU THR LEU ASN ARG TYR ALA VAL TYR TYR LYS SER GLY SEQRES 9 E 130 ASP LEU ILE ASP ASP ALA GLY VAL ALA ALA LEU GLU THR SEQRES 10 E 130 HIS ASP LEU LYS LEU THR GLU LYS VAL VAL PHE THR SER SEQRES 1 F 130 MET ALA THR GLY ILE SER LEU SER ASN TYR ARG GLN GLU SEQRES 2 F 130 PHE GLY HIS LEU VAL LEU GLY GLY VAL PHE SER SER ASP SEQRES 3 F 130 LEU GLY HIS CYS VAL ARG GLU VAL ASN LEU VAL LYS THR SEQRES 4 F 130 ALA THR MET LYS ILE GLY SER VAL LEU LYS ALA ASP ASN SEQRES 5 F 130 THR GLU ALA THR ALA ALA GLY GLU ALA VAL LYS VAL LEU SEQRES 6 F 130 LEU TRP THR ASP ALA LEU PHE GLY ILE ASP ASP VAL ALA SEQRES 7 F 130 VAL GLY ASP THR PHE THR ALA VAL VAL GLY VAL ARG ASP SEQRES 8 F 130 LEU THR LEU ASN ARG TYR ALA VAL TYR TYR LYS SER GLY SEQRES 9 F 130 ASP LEU ILE ASP ASP ALA GLY VAL ALA ALA LEU GLU THR SEQRES 10 F 130 HIS ASP LEU LYS LEU THR GLU LYS VAL VAL PHE THR SER SEQRES 1 G 130 MET ALA THR GLY ILE SER LEU SER ASN TYR ARG GLN GLU SEQRES 2 G 130 PHE GLY HIS LEU VAL LEU GLY GLY VAL PHE SER SER ASP SEQRES 3 G 130 LEU GLY HIS CYS VAL ARG GLU VAL ASN LEU VAL LYS THR SEQRES 4 G 130 ALA THR MET LYS ILE GLY SER VAL LEU LYS ALA ASP ASN SEQRES 5 G 130 THR GLU ALA THR ALA ALA GLY GLU ALA VAL LYS VAL LEU SEQRES 6 G 130 LEU TRP THR ASP ALA LEU PHE GLY ILE ASP ASP VAL ALA SEQRES 7 G 130 VAL GLY ASP THR PHE THR ALA VAL VAL GLY VAL ARG ASP SEQRES 8 G 130 LEU THR LEU ASN ARG TYR ALA VAL TYR TYR LYS SER GLY SEQRES 9 G 130 ASP LEU ILE ASP ASP ALA GLY VAL ALA ALA LEU GLU THR SEQRES 10 G 130 HIS ASP LEU LYS LEU THR GLU LYS VAL VAL PHE THR SER SEQRES 1 N 333 MET PRO ALA ILE ILE LEU ASP GLN VAL VAL ASP PHE SER SEQRES 2 N 333 PRO MET ILE GLU LEU GLN GLU THR PRO ASP THR LEU ILE SEQRES 3 N 333 ALA SER LEU ASN LEU PHE ASP VAL GLN TYR HIS ALA THR SEQRES 4 N 333 THR ALA ILE GLU ILE GLY ARG GLN LYS ASN ALA ASP GLY SEQRES 5 N 333 LEU ILE PRO ALA ARG GLU ARG GLY GLY GLU ARG ASN PHE SEQRES 6 N 333 LEU THR MET ASP ALA PRO SER VAL LYS VAL PHE ARG ILE SEQRES 7 N 333 PRO PHE PHE PRO LEU ASP LYS ASN ILE LYS ALA GLN ASP SEQRES 8 N 333 ILE GLN SER PHE ARG SER PHE ALA MET GLY GLY ILE ASN SEQRES 9 N 333 ASP ASN LEU ARG THR GLU ALA GLU VAL VAL ASN ARG TYR SEQRES 10 N 333 MET THR GLN ILE LEU ARG ASP VAL ALA LYS THR LYS GLU SEQRES 11 N 333 LYS ILE PHE ALA GLU ALA VAL MET GLY ARG ALA TYR ASN SEQRES 12 N 333 GLY VAL GLY GLY ALA ALA ASN SER ALA TYR ASP TRP TYR SEQRES 13 N 333 THR GLU TRP GLY ALA SER GLN LYS SER VAL SER VAL ASP SEQRES 14 N 333 PHE SER SER THR THR VAL SER PRO ALA ALA THR ILE GLU SEQRES 15 N 333 GLN GLU ALA ARG ALA TYR ILE ILE ASP GLN LYS GLN ASP SEQRES 16 N 333 GLY SER THR ALA THR ARG ILE VAL ALA LEU CYS SER ARG SEQRES 17 N 333 GLU PHE PHE ALA SER LEU VAL ASN SER PRO PHE VAL ARG SEQRES 18 N 333 GLN ALA TYR GLN TYR PHE GLN GLY THR PRO ASN LEU LEU SEQRES 19 N 333 ARG ASP ARG LEU SER GLY ASN MET ASP VAL GLN VAL PHE SEQRES 20 N 333 GLU TRP ASN GLY VAL THR TYR ILE GLU ASP ILE HIS GLY SEQRES 21 N 333 ASN ILE PRO ALA GLY GLU ALA PHE VAL LEU PRO MET GLY SEQRES 22 N 333 ILE PRO ASP MET PHE GLN ALA HIS TYR ALA PRO ALA ASP SEQRES 23 N 333 THR PRO GLU LEU ALA ASN THR VAL ALA ARG ASP LEU TYR SEQRES 24 N 333 THR PHE MET VAL SER GLU HIS ARG THR VAL GLN LEU GLN SEQRES 25 N 333 SER GLU PHE SER LEU LEU ALA VAL ASN THR ARG PRO GLU SEQRES 26 N 333 LEU VAL VAL LYS LEU THR THR ALA HELIX 1 AA1 GLY E 73 VAL E 77 5 5 HELIX 2 AA2 TYR E 97 VAL E 99 5 3 HELIX 3 AA3 ASP E 108 THR E 117 1 10 HELIX 4 AA4 TYR F 97 VAL F 99 5 3 HELIX 5 AA5 ASP F 108 THR F 117 1 10 HELIX 6 AA6 TYR G 97 VAL G 99 5 3 HELIX 7 AA7 ASP G 108 THR G 117 1 10 HELIX 8 AA8 THR N 24 LEU N 29 1 6 HELIX 9 AA9 LYS N 88 ILE N 92 5 5 HELIX 10 AB1 THR N 109 GLY N 139 1 31 HELIX 11 AB2 ASP N 154 TRP N 159 1 6 HELIX 12 AB3 SER N 176 LYS N 193 1 18 HELIX 13 AB4 SER N 207 ASN N 216 1 10 HELIX 14 AB5 THR N 230 LEU N 238 1 9 SHEET 1 AA1 4 VAL E 31 VAL E 37 0 SHEET 2 AA1 4 THR E 82 GLY E 88 -1 O VAL E 87 N ARG E 32 SHEET 3 AA1 4 LYS E 63 THR E 68 -1 N TRP E 67 O VAL E 86 SHEET 4 AA1 4 VAL E 47 LEU E 48 -1 N LEU E 48 O LYS E 63 SHEET 1 AA2 2 THR E 93 ASN E 95 0 SHEET 2 AA2 2 LYS E 121 THR E 123 1 O LYS E 121 N LEU E 94 SHEET 1 AA3 4 VAL F 31 VAL F 37 0 SHEET 2 AA3 4 THR F 82 GLY F 88 -1 O VAL F 87 N ARG F 32 SHEET 3 AA3 4 LYS F 63 THR F 68 -1 N LEU F 66 O VAL F 86 SHEET 4 AA3 4 VAL F 47 LEU F 48 -1 N LEU F 48 O LYS F 63 SHEET 1 AA4 2 THR F 93 ASN F 95 0 SHEET 2 AA4 2 LYS F 121 THR F 123 1 O THR F 123 N LEU F 94 SHEET 1 AA5 3 VAL G 18 GLY G 21 0 SHEET 2 AA5 3 LEU G 92 ASN G 95 -1 O THR G 93 N LEU G 19 SHEET 3 AA5 3 LEU G 120 THR G 123 1 O LYS G 121 N LEU G 94 SHEET 1 AA6 4 VAL G 31 VAL G 37 0 SHEET 2 AA6 4 THR G 82 GLY G 88 -1 O VAL G 87 N ARG G 32 SHEET 3 AA6 4 LYS G 63 THR G 68 -1 N TRP G 67 O VAL G 86 SHEET 4 AA6 4 VAL G 47 LEU G 48 -1 N LEU G 48 O LYS G 63 SHEET 1 AA7 3 ASP N 33 TYR N 36 0 SHEET 2 AA7 3 PHE N 278 TYR N 282 1 O ALA N 280 N ASP N 33 SHEET 3 AA7 3 LEU N 317 ASN N 321 -1 O LEU N 318 N HIS N 281 SHEET 1 AA8 2 ALA N 41 ARG N 46 0 SHEET 2 AA8 2 SER N 72 ARG N 77 -1 O LYS N 74 N ILE N 44 SHEET 1 AA9 3 PHE N 81 ILE N 87 0 SHEET 2 AA9 3 VAL N 309 PHE N 315 -1 O VAL N 309 N ILE N 87 SHEET 3 AA9 3 TYR N 299 SER N 304 -1 N VAL N 303 O GLN N 310 SHEET 1 AB1 6 SER N 165 VAL N 168 0 SHEET 2 AB1 6 VAL N 328 THR N 332 1 O THR N 331 N VAL N 166 SHEET 3 AB1 6 GLU N 266 PRO N 271 -1 N ALA N 267 O LEU N 330 SHEET 4 AB1 6 ILE N 202 CYS N 206 -1 N LEU N 205 O PHE N 268 SHEET 5 AB1 6 VAL N 252 GLU N 256 1 O THR N 253 N ALA N 204 SHEET 6 AB1 6 VAL N 246 TRP N 249 -1 N PHE N 247 O TYR N 254 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 MASTER 161 0 0 14 33 0 0 6 5477 4 0 56 END