HEADER VIRAL PROTEIN 21-JUL-25 9VYI TITLE CRYO-EM STRUCTURE OF BACTERIOPHAGE P1 BASEPLATE IN C1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UPFC; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA PHAGE P1; SOURCE 3 ORGANISM_COMMON: BACTERIOPHAGE P1; SOURCE 4 ORGANISM_TAXID: 2886926 KEYWDS BASEPLATE, PHAGE, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR Y.CHEN,H.R.LIU REVDAT 2 04-FEB-26 9VYI 1 JRNL REVDAT 1 22-OCT-25 9VYI 0 JRNL AUTH J.ZHENG,Y.CHEN,S.CHEN,J.ZHOU,H.XIAO,F.YANG,H.LIU JRNL TITL STRUCTURE OF DEFENSE AGAINST RESTRICTION PROTEINS DARA AND JRNL TITL 2 HDF IN PHAGE P1 REVEALS A NEW MOLECULAR MECHANISM DURING JRNL TITL 3 PHAGE ASSEMBLY, INFECTION AND DNA EJECTION. JRNL REF PLOS PATHOG. V. 22 13869 2026 JRNL REFN ESSN 1553-7374 JRNL PMID 41544131 JRNL DOI 10.1371/JOURNAL.PPAT.1013869 REMARK 2 REMARK 2 RESOLUTION. 3.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : EMAN, PHENIX, CRYOSPARC 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) : 3.700 REMARK 3 NUMBER OF PARTICLES : 30339 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 9VYI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 24-JUL-25. REMARK 100 THE DEPOSITION ID IS D_1300061818. 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 P1 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 : 7.40 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: MONOMERIC 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 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 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 CYS A 73 -168.57 -128.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-65454 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF BACTERIOPHAGE P1 BASEPLATE IN C1 DBREF 9VYI A 1 94 UNP Q71TL3 Q71TL3_BPP1 1 94 SEQRES 1 A 94 MET ALA SER ILE ALA THR LYS ASP SER ILE CYS SER GLY SEQRES 2 A 94 HIS GLY GLY PHE PRO SER ARG PRO PRO VAL GLU SER GLU SEQRES 3 A 94 PRO LEU LEU LYS VAL ASN GLY VAL GLU VAL LEU VAL ASP SEQRES 4 A 94 GLY LYS GLN TYR ALA GLN HIS THR ASP GLY ASN SER THR SEQRES 5 A 94 HIS GLY GLY GLN ALA ILE SER THR ARG ALA TRP PHE THR SEQRES 6 A 94 VAL ASN GLY LYS GLY ILE VAL CYS VAL GLY ASP PRO VAL SEQRES 7 A 94 SER CYS GLY SER THR VAL ALA ALA GLY ASP GLY LEU VAL SEQRES 8 A 94 GLN VAL SER SHEET 1 AA1 2 SER A 3 ILE A 4 0 SHEET 2 AA1 2 ASP A 88 GLN A 92 -1 O ASP A 88 N ILE A 4 SHEET 1 AA2 2 GLU A 26 VAL A 31 0 SHEET 2 AA2 2 VAL A 34 VAL A 36 -1 O VAL A 34 N VAL A 31 SHEET 1 AA3 2 HIS A 46 THR A 47 0 SHEET 2 AA3 2 THR A 52 HIS A 53 -1 O HIS A 53 N HIS A 46 SHEET 1 AA4 2 ARG A 61 VAL A 66 0 SHEET 2 AA4 2 LYS A 69 ILE A 71 -1 O LYS A 69 N VAL A 66 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 122 0 0 0 8 0 0 6 658 1 0 8 END