HEADER VIRAL PROTEIN 31-DEC-25 21VL TITLE CRYO-EM STRUCTURE OF PORTAL-ADAPTOR OF BACTERIOPHAGE PHI92 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHI92_GP120; COMPND 3 CHAIN: H; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: PHI92_GP126; COMPND 6 CHAIN: E 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 PORTAL ADAPTOR, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR Y.CHEN,H.R.LIU REVDAT 1 22-JUL-26 21VL 0 JRNL AUTH Y.CHEN,H.R.LIU JRNL TITL CRYO-EM STRUCTURE OF PORTAL-ADAPTOR OF BACTERIOPHAGE PHI92 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.30 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) : 3.300 REMARK 3 NUMBER OF PARTICLES : 32000 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 21VL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 08-JAN-26. REMARK 100 THE DEPOSITION ID IS D_1300067954. 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 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: H, E 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 H 1 REMARK 465 SER H 2 REMARK 465 THR H 3 REMARK 465 GLY H 4 REMARK 465 LYS H 5 REMARK 465 ARG H 6 REMARK 465 LYS H 7 REMARK 465 TYR H 8 REMARK 465 THR H 9 REMARK 465 LYS H 10 REMARK 465 ARG H 11 REMARK 465 SER H 12 REMARK 465 ASP H 13 REMARK 465 TYR H 14 REMARK 465 TRP H 15 REMARK 465 ASN H 16 REMARK 465 LYS H 17 REMARK 465 GLY H 18 REMARK 465 SER H 19 REMARK 465 THR H 20 REMARK 465 GLU H 21 REMARK 465 LYS H 22 REMARK 465 ALA H 23 REMARK 465 ALA H 24 REMARK 465 LEU H 25 REMARK 465 SER H 26 REMARK 465 PRO H 27 REMARK 465 THR H 28 REMARK 465 GLN H 29 REMARK 465 SER H 30 REMARK 465 ALA H 31 REMARK 465 THR H 32 REMARK 465 LYS H 33 REMARK 465 GLU H 34 REMARK 465 LYS H 35 REMARK 465 ASN H 36 REMARK 465 LEU H 37 REMARK 465 VAL H 38 REMARK 465 LEU H 39 REMARK 465 SER H 40 REMARK 465 PRO H 41 REMARK 465 GLU H 42 REMARK 465 ILE H 43 REMARK 465 GLY H 44 REMARK 465 THR H 45 REMARK 465 ILE H 46 REMARK 465 GLY H 47 REMARK 465 LEU H 48 REMARK 465 ASN H 49 REMARK 465 SER H 50 REMARK 465 ILE H 51 REMARK 465 LYS H 52 REMARK 465 ALA H 53 REMARK 465 PHE H 54 REMARK 465 THR H 55 REMARK 465 ASN H 56 REMARK 465 PHE H 57 REMARK 465 GLY H 202 REMARK 465 MET H 203 REMARK 465 VAL H 204 REMARK 465 SER H 205 REMARK 465 PRO H 206 REMARK 465 GLY H 207 REMARK 465 THR H 208 REMARK 465 ASN H 209 REMARK 465 ALA H 210 REMARK 465 THR H 491 REMARK 465 SER H 492 REMARK 465 ARG H 493 REMARK 465 SER H 494 REMARK 465 GLY H 495 REMARK 465 ASP H 496 REMARK 465 GLY H 497 REMARK 465 LEU H 498 REMARK 465 ALA H 499 REMARK 465 ALA H 500 REMARK 465 GLY H 501 REMARK 465 ALA H 502 REMARK 465 GLY H 503 REMARK 465 ASN H 504 REMARK 465 GLY H 505 REMARK 465 THR H 506 REMARK 465 SER H 507 REMARK 465 THR H 508 REMARK 465 SER H 509 REMARK 465 PRO H 510 REMARK 465 ALA H 511 REMARK 465 ALA H 512 REMARK 465 LEU H 513 REMARK 465 ASP H 514 REMARK 465 THR H 515 REMARK 465 SER H 516 REMARK 465 ALA H 517 REMARK 465 ALA H 518 REMARK 465 ASN H 519 REMARK 465 LEU H 520 REMARK 465 ALA H 521 REMARK 465 ASN H 522 REMARK 465 TYR E 178 REMARK 465 ARG E 179 REMARK 465 ARG E 180 REMARK 465 ASP E 181 REMARK 465 LYS E 182 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 H 105 -50.47 72.70 REMARK 500 ASP H 155 75.07 61.70 REMARK 500 ALA H 306 77.73 -100.77 REMARK 500 GLU H 308 -16.18 69.08 REMARK 500 GLU H 320 -130.43 53.36 REMARK 500 LEU H 414 -12.95 72.87 REMARK 500 SER H 415 -125.39 31.88 REMARK 500 ILE H 468 134.64 73.05 REMARK 500 SER E 5 -2.62 69.16 REMARK 500 PHE E 16 139.08 70.95 REMARK 500 GLN E 20 -5.56 70.02 REMARK 500 ASP E 25 -9.21 73.41 REMARK 500 ASP E 42 -151.66 42.57 REMARK 500 GLN E 96 -4.07 73.36 REMARK 500 ILE E 100 81.86 56.16 REMARK 500 PRO E 102 -172.01 -67.31 REMARK 500 ASP E 136 122.00 81.80 REMARK 500 ASP E 160 -166.56 -79.71 REMARK 500 ARG E 161 -7.51 73.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-68036 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF PORTAL-ADAPTOR OF BACTERIOPHAGE PHI92 DBREF 21VL H 1 522 UNP I7I020 I7I020_9CAUD 1 522 DBREF 21VL E 1 182 UNP I7HTD1 I7HTD1_9CAUD 1 182 SEQRES 1 H 522 MET SER THR GLY LYS ARG LYS TYR THR LYS ARG SER ASP SEQRES 2 H 522 TYR TRP ASN LYS GLY SER THR GLU LYS ALA ALA LEU SER SEQRES 3 H 522 PRO THR GLN SER ALA THR LYS GLU LYS ASN LEU VAL LEU SEQRES 4 H 522 SER PRO GLU ILE GLY THR ILE GLY LEU ASN SER ILE LYS SEQRES 5 H 522 ALA PHE THR ASN PHE MET GLN PRO TYR GLU THR ARG PHE SEQRES 6 H 522 PRO GLU ASN ILE ARG THR TYR LYS GLU MET GLY GLU ASP SEQRES 7 H 522 PRO ASP VAL ALA THR ALA LEU ASP ALA THR TYR ILE PHE SEQRES 8 H 522 VAL ASP ARG ALA PHE PHE ASP PHE LYS ILE LYS TYR ASN SEQRES 9 H 522 VAL SER SER ALA LYS SER ARG ARG ALA ALA LYS PHE VAL SEQRES 10 H 522 ASP TYR THR LEU ARG ASN MET ASN ALA PRO LEU ARG GLN SEQRES 11 H 522 TYR VAL ARG SER LEU LEU THR TYR LYS GLN PHE GLY PHE SEQRES 12 H 522 ALA PHE ALA GLU LYS VAL TYR GLU LEU ASP GLU ASP PRO SEQRES 13 H 522 LYS SER PRO TYR PHE GLY TYR TYR ARG LEU VAL LYS LEU SEQRES 14 H 522 ALA PHE ARG PRO GLN ASP THR ILE ASP LEU ALA GLN PRO SEQRES 15 H 522 PHE THR TYR SER ASP ASP GLY ARG THR ILE LEU THR VAL SEQRES 16 H 522 ASN GLN ASN ILE THR ASN GLY MET VAL SER PRO GLY THR SEQRES 17 H 522 ASN ALA THR LEU ILE GLY ARG LYS GLU ILE PRO MET GLU SEQRES 18 H 522 LYS VAL ILE TYR VAL GLY SER ASN ILE THR GLU ASN ASN SEQRES 19 H 522 PRO LEU GLY VAL SER PRO LEU LEU ALA VAL TYR ARG SER SEQRES 20 H 522 TRP ARG GLU LYS SER LEU ILE GLN GLU TYR GLU VAL VAL SEQRES 21 H 522 GLY VAL SER LYS ASP LEU GLY GLY MET PRO VAL LEU MET SEQRES 22 H 522 VAL PRO SER ASP ILE LEU ASN ARG ALA SER LEU ASN PRO SEQRES 23 H 522 SER GLY ASP GLU ALA GLN SER LEU ARG VAL LEU GLN ALA SEQRES 24 H 522 ASN ILE ALA ASN LEU HIS ALA GLY GLU GLN SER TYR MET SEQRES 25 H 522 VAL LEU PRO SER ASP VAL TYR GLU GLY THR VAL MET ARG SEQRES 26 H 522 GLN TYR ASP LEU VAL PHE GLN GLY VAL GLU GLY SER GLY SEQRES 27 H 522 LYS GLN PHE ASP THR GLN ALA LEU ILE LYS GLN ARG LYS SEQRES 28 H 522 LEU ASP ILE TYR ASN ARG PHE GLY ALA GLY VAL LEU ILE SEQRES 29 H 522 MET GLY ASP GLY GLU GLY GLY SER TYR SER LEU SER ASP SEQRES 30 H 522 ASN LYS GLN THR LEU LEU SER HIS PHE ILE GLU ARG ASP SEQRES 31 H 522 VAL ASP ILE ILE THR GLU ALA LEU ASN THR GLN VAL ILE SEQRES 32 H 522 PRO GLN LEU LEU ARG LEU ASN GLY ILE PHE LEU SER GLN SEQRES 33 H 522 GLU ASP MET PRO LYS PHE VAL SER ASP ASP ILE GLY ASP SEQRES 34 H 522 PRO ASP ILE GLU VAL ASN ALA LYS ALA ILE GLN GLN ILE SEQRES 35 H 522 VAL ALA ALA GLY ALA ILE PRO LEU THR PRO GLU VAL ILE SEQRES 36 H 522 ASN GLU PHE PHE GLU ARG LEU GLY PHE ASN TYR ARG ILE SEQRES 37 H 522 PRO ASP ASP ILE VAL ALA ASP PRO ASP LYS PHE GLN GLU SEQRES 38 H 522 PHE LEU GLU THR PHE MET PRO ASP LYS THR SER ARG SER SEQRES 39 H 522 GLY ASP GLY LEU ALA ALA GLY ALA GLY ASN GLY THR SER SEQRES 40 H 522 THR SER PRO ALA ALA LEU ASP THR SER ALA ALA ASN LEU SEQRES 41 H 522 ALA ASN SEQRES 1 E 182 MET LEU ILE ALA SER ASP LEU VAL PRO MET ILE ARG ILE SEQRES 2 E 182 LEU VAL PHE ASN PRO SER GLN GLU THR LEU PRO ASP ALA SEQRES 3 E 182 MET ILE GLU GLN ILE ILE GLN THR TRP ILE ASP VAL LEU SEQRES 4 E 182 GLY ASN ASP ASP ALA ASN LYS CYS ALA VAL LEU TRP ASN SEQRES 5 E 182 SER LEU ILE SER VAL LEU GLU TYR LEU TRP ASN THR ASP SEQRES 6 E 182 VAL LEU ASN HIS ASN THR GLN THR GLY GLY ALA LEU SER SEQRES 7 E 182 ARG LYS GLU LYS VAL GLY GLU VAL GLN VAL GLU VAL THR SEQRES 8 E 182 PHE GLY THR GLY GLN THR GLU TYR ILE SER PRO TRP GLU SEQRES 9 E 182 ASN ILE TYR LYS GLY TYR LEU ASP GLY ASP MET MET ILE SEQRES 10 E 182 PRO GLY CYS THR SER GLY ARG GLY VAL THR SER LYS VAL SEQRES 11 E 182 LEU VAL GLY GLY VAL ASP ALA ARG GLU ILE ASP ARG VAL SEQRES 12 E 182 ASN SER ASP PRO ASN SER VAL ASN GLY LEU GLY GLY VAL SEQRES 13 E 182 GLY SER VAL ASP ARG HIS THR ARG ASN ILE LYS TYR ALA SEQRES 14 E 182 ARG ASN TYR GLY PRO ILE GLY TYR TYR ARG ARG ASP LYS HELIX 1 AA1 ARG H 64 GLY H 76 1 13 HELIX 2 AA2 ASP H 78 PHE H 96 1 19 HELIX 3 AA3 SER H 107 ASN H 123 1 17 HELIX 4 AA4 PRO H 127 LEU H 136 1 10 HELIX 5 AA5 THR H 137 GLY H 142 1 6 HELIX 6 AA6 SER H 239 ALA H 243 5 5 HELIX 7 AA7 VAL H 244 LYS H 264 1 21 HELIX 8 AA8 PRO H 275 SER H 283 1 9 HELIX 9 AA9 GLY H 288 ASN H 303 1 16 HELIX 10 AB1 ASP H 342 GLY H 359 1 18 HELIX 11 AB2 THR H 381 VAL H 402 1 22 HELIX 12 AB3 VAL H 402 ASN H 410 1 9 HELIX 13 AB4 ILE H 432 ALA H 445 1 14 HELIX 14 AB5 THR H 451 GLY H 463 1 13 HELIX 15 AB6 PRO H 469 ASP H 475 1 7 HELIX 16 AB7 ASP H 475 MET H 487 1 13 HELIX 17 AB8 LEU E 7 VAL E 15 1 9 HELIX 18 AB9 ALA E 26 LEU E 39 1 14 HELIX 19 AC1 ASN E 45 THR E 73 1 29 HELIX 20 AC2 GLU E 104 ASP E 112 1 9 HELIX 21 AC3 GLY E 125 LYS E 129 5 5 HELIX 22 AC4 ASP E 136 SER E 145 1 10 HELIX 23 AC5 ARG E 164 TYR E 172 5 9 SHEET 1 AA1 2 PHE H 99 LYS H 102 0 SHEET 2 AA1 2 LYS H 421 SER H 424 -1 O VAL H 423 N LYS H 100 SHEET 1 AA2 3 TYR H 164 PHE H 171 0 SHEET 2 AA2 3 PHE H 143 LEU H 152 -1 N GLU H 147 O ALA H 170 SHEET 3 AA2 3 VAL H 223 GLY H 227 -1 O ILE H 224 N ALA H 146 SHEET 1 AA3 3 PHE H 183 TYR H 185 0 SHEET 2 AA3 3 ILE H 192 ASN H 196 -1 O LEU H 193 N THR H 184 SHEET 3 AA3 3 GLU H 217 PRO H 219 -1 O ILE H 218 N VAL H 195 SHEET 1 AA4 2 PRO H 270 MET H 273 0 SHEET 2 AA4 2 ASP H 328 PHE H 331 -1 O VAL H 330 N VAL H 271 SHEET 1 AA5 2 VAL H 318 TYR H 319 0 SHEET 2 AA5 2 THR H 322 ARG H 325 -1 O THR H 322 N TYR H 319 SHEET 1 AA6 2 SER E 78 VAL E 83 0 SHEET 2 AA6 2 VAL E 86 THR E 91 -1 O VAL E 86 N VAL E 83 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 242 0 0 23 14 0 0 6 4754 2 0 55 END