HEADER VIRUS 15-APR-24 9F06 TITLE CRYO-EM STRUCTURE OF STAPHYLOCOCCUS AUREUS BACTERIOPHAGE PHI812 TAIL TITLE 2 IN THE POST-CONTRACTION STATE - TUBE PROTEINS COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAPSID PROTEIN; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: TAIL TUBE PROTEIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS PHAGE 812; SOURCE 3 ORGANISM_TAXID: 307898 KEYWDS BACTERIOPHAGE, PHAGE, CONTRACTILE, PHI812, TAIL, VIRUS EXPDTA ELECTRON MICROSCOPY AUTHOR J.BINOVSKY,M.SIBOROVA,P.PLEVKA REVDAT 2 02-JUL-25 9F06 1 REMARK REVDAT 1 23-APR-25 9F06 0 JRNL AUTH J.BINOVSKY,M.SIBOROVA,P.PLEVKA JRNL TITL CELL ATTACHMENT AND TAIL CONTRACTION OF S. AUREUS PHAGE JRNL TITL 2 PHI812 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : SERIALEM, PHENIX, RELION, RELION, REMARK 3 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) : 3.600 REMARK 3 NUMBER OF PARTICLES : 12906 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 9F06 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-APR-24. REMARK 100 THE DEPOSITION ID IS D_1292136746. 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 : STAPHYLOCOCCUS PHAGE 812; TAIL; REMARK 245 TAIL TUBE 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 : 15371 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3000.00 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) : 4200.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 130000 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: 33-MERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 0.500000 -0.866025 0.000000 184.81778 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 -49.52178 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 -0.866025 0.000000 320.11379 REMARK 350 BIOMT2 3 0.866025 -0.500000 0.000000 85.77423 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 270.59202 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 270.59201 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 5 -0.500000 0.866025 0.000000 85.77424 REMARK 350 BIOMT2 5 -0.866025 -0.500000 0.000000 320.11379 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 6 0.500000 0.866025 0.000000 -49.52177 REMARK 350 BIOMT2 6 -0.866025 0.500000 0.000000 184.81778 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 7 0.500000 -0.866025 0.000000 184.81778 REMARK 350 BIOMT2 7 0.866025 0.500000 0.000000 -49.52178 REMARK 350 BIOMT3 7 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 8 -0.500000 -0.866025 0.000000 320.11379 REMARK 350 BIOMT2 8 0.866025 -0.500000 0.000000 85.77423 REMARK 350 BIOMT3 8 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 9 -1.000000 0.000000 0.000000 270.59202 REMARK 350 BIOMT2 9 0.000000 -1.000000 0.000000 270.59201 REMARK 350 BIOMT3 9 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 10 -0.500000 0.866025 0.000000 85.77424 REMARK 350 BIOMT2 10 -0.866025 -0.500000 0.000000 320.11379 REMARK 350 BIOMT3 10 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 11 0.500000 0.866025 0.000000 -49.52177 REMARK 350 BIOMT2 11 -0.866025 0.500000 0.000000 184.81778 REMARK 350 BIOMT3 11 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C REMARK 350 BIOMT1 12 0.500000 -0.866025 0.000000 184.81778 REMARK 350 BIOMT2 12 0.866025 0.500000 0.000000 -49.52178 REMARK 350 BIOMT3 12 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C REMARK 350 BIOMT1 13 -0.500000 -0.866025 0.000000 320.11379 REMARK 350 BIOMT2 13 0.866025 -0.500000 0.000000 85.77423 REMARK 350 BIOMT3 13 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C REMARK 350 BIOMT1 14 -1.000000 0.000000 0.000000 270.59202 REMARK 350 BIOMT2 14 0.000000 -1.000000 0.000000 270.59201 REMARK 350 BIOMT3 14 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C REMARK 350 BIOMT1 15 -0.500000 0.866025 0.000000 85.77424 REMARK 350 BIOMT2 15 -0.866025 -0.500000 0.000000 320.11379 REMARK 350 BIOMT3 15 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C REMARK 350 BIOMT1 16 0.500000 0.866025 0.000000 -49.52177 REMARK 350 BIOMT2 16 -0.866025 0.500000 0.000000 184.81778 REMARK 350 BIOMT3 16 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 MET B 1 REMARK 465 MET C 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-50095 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF STAPHYLOCOCCUS AUREUS BACTERIOPHAGE PHI812 REMARK 900 TAIL IN THE POST-CONTRACTION STATE - TUBE PROTEINS DBREF 9F06 A 1 142 UNP A1YTP2 A1YTP2_9CAUD 1 142 DBREF 9F06 B 1 142 UNP A1YTP2 A1YTP2_9CAUD 1 142 DBREF 9F06 C 1 142 UNP A1YTP2 A1YTP2_9CAUD 1 142 SEQRES 1 A 142 MET ALA SER GLU ALA LYS GLN THR VAL HIS THR GLY ASN SEQRES 2 A 142 THR VAL LEU LEU MET ILE LYS GLY LYS PRO VAL GLY ARG SEQRES 3 A 142 ALA GLN SER ALA SER GLY GLN ARG GLU TYR GLY THR THR SEQRES 4 A 142 GLY VAL TYR GLU ILE GLY SER ILE MET PRO GLN GLU HIS SEQRES 5 A 142 VAL TYR LEU ARG TYR GLU GLY THR ILE THR VAL GLU ARG SEQRES 6 A 142 LEU ARG MET LYS LYS GLU ASN PHE ALA ASP LEU GLY TYR SEQRES 7 A 142 ALA SER LEU GLY GLU GLU ILE LEU LYS LYS ASP ILE ILE SEQRES 8 A 142 ASP ILE LEU VAL VAL ASP ASN LEU THR LYS GLN VAL ILE SEQRES 9 A 142 ILE SER TYR HIS GLY CYS SER ALA ASN ASN TYR ASN GLU SEQRES 10 A 142 THR TRP GLN THR ASN GLU ILE VAL THR GLU GLU ILE GLU SEQRES 11 A 142 PHE SER TYR LEU THR ALA SER ASP LYS ALA ARG THR SEQRES 1 B 142 MET ALA SER GLU ALA LYS GLN THR VAL HIS THR GLY ASN SEQRES 2 B 142 THR VAL LEU LEU MET ILE LYS GLY LYS PRO VAL GLY ARG SEQRES 3 B 142 ALA GLN SER ALA SER GLY GLN ARG GLU TYR GLY THR THR SEQRES 4 B 142 GLY VAL TYR GLU ILE GLY SER ILE MET PRO GLN GLU HIS SEQRES 5 B 142 VAL TYR LEU ARG TYR GLU GLY THR ILE THR VAL GLU ARG SEQRES 6 B 142 LEU ARG MET LYS LYS GLU ASN PHE ALA ASP LEU GLY TYR SEQRES 7 B 142 ALA SER LEU GLY GLU GLU ILE LEU LYS LYS ASP ILE ILE SEQRES 8 B 142 ASP ILE LEU VAL VAL ASP ASN LEU THR LYS GLN VAL ILE SEQRES 9 B 142 ILE SER TYR HIS GLY CYS SER ALA ASN ASN TYR ASN GLU SEQRES 10 B 142 THR TRP GLN THR ASN GLU ILE VAL THR GLU GLU ILE GLU SEQRES 11 B 142 PHE SER TYR LEU THR ALA SER ASP LYS ALA ARG THR SEQRES 1 C 142 MET ALA SER GLU ALA LYS GLN THR VAL HIS THR GLY ASN SEQRES 2 C 142 THR VAL LEU LEU MET ILE LYS GLY LYS PRO VAL GLY ARG SEQRES 3 C 142 ALA GLN SER ALA SER GLY GLN ARG GLU TYR GLY THR THR SEQRES 4 C 142 GLY VAL TYR GLU ILE GLY SER ILE MET PRO GLN GLU HIS SEQRES 5 C 142 VAL TYR LEU ARG TYR GLU GLY THR ILE THR VAL GLU ARG SEQRES 6 C 142 LEU ARG MET LYS LYS GLU ASN PHE ALA ASP LEU GLY TYR SEQRES 7 C 142 ALA SER LEU GLY GLU GLU ILE LEU LYS LYS ASP ILE ILE SEQRES 8 C 142 ASP ILE LEU VAL VAL ASP ASN LEU THR LYS GLN VAL ILE SEQRES 9 C 142 ILE SER TYR HIS GLY CYS SER ALA ASN ASN TYR ASN GLU SEQRES 10 C 142 THR TRP GLN THR ASN GLU ILE VAL THR GLU GLU ILE GLU SEQRES 11 C 142 PHE SER TYR LEU THR ALA SER ASP LYS ALA ARG THR HELIX 1 AA1 THR A 11 ASN A 13 5 3 HELIX 2 AA2 ASN A 72 GLY A 77 1 6 HELIX 3 AA3 GLY A 82 LYS A 88 5 7 HELIX 4 AA4 THR B 11 ASN B 13 5 3 HELIX 5 AA5 ASN B 72 GLY B 77 1 6 HELIX 6 AA6 GLY B 82 LYS B 88 5 7 HELIX 7 AA7 SER C 3 GLN C 7 5 5 HELIX 8 AA8 ASN C 72 GLY C 77 1 6 HELIX 9 AA9 GLY C 82 LYS C 88 5 7 SHEET 1 AA1 7 LYS A 22 PRO A 23 0 SHEET 2 AA1 7 VAL A 15 ILE A 19 -1 N ILE A 19 O LYS A 22 SHEET 3 AA1 7 ILE A 91 ASP A 97 -1 O LEU A 94 N MET A 18 SHEET 4 AA1 7 VAL A 103 GLN A 120 -1 O CYS A 110 N ILE A 91 SHEET 5 AA1 7 GLU A 123 SER A 132 -1 O SER A 132 N SER A 111 SHEET 6 AA1 7 GLU A 58 LEU A 66 -1 N ARG A 65 O GLU A 127 SHEET 7 AA1 7 ALA A 27 GLU A 35 -1 N GLU A 35 O GLU A 58 SHEET 1 AA2 5 LYS A 22 PRO A 23 0 SHEET 2 AA2 5 VAL A 15 ILE A 19 -1 N ILE A 19 O LYS A 22 SHEET 3 AA2 5 ILE A 91 ASP A 97 -1 O LEU A 94 N MET A 18 SHEET 4 AA2 5 VAL A 103 GLN A 120 -1 O CYS A 110 N ILE A 91 SHEET 5 AA2 5 THR A 135 SER A 137 -1 O SER A 137 N SER A 106 SHEET 1 AA3 2 THR A 39 GLY A 40 0 SHEET 2 AA3 2 HIS A 52 VAL A 53 -1 O VAL A 53 N THR A 39 SHEET 1 AA4 7 LYS B 22 PRO B 23 0 SHEET 2 AA4 7 VAL B 15 ILE B 19 -1 N ILE B 19 O LYS B 22 SHEET 3 AA4 7 ILE B 91 ASP B 97 -1 O LEU B 94 N MET B 18 SHEET 4 AA4 7 VAL B 103 THR B 118 -1 O ILE B 104 N VAL B 95 SHEET 5 AA4 7 THR B 126 SER B 132 -1 O SER B 132 N SER B 111 SHEET 6 AA4 7 GLU B 58 LEU B 66 -1 N ARG B 65 O GLU B 127 SHEET 7 AA4 7 ALA B 27 GLU B 35 -1 N GLN B 33 O THR B 60 SHEET 1 AA5 5 LYS B 22 PRO B 23 0 SHEET 2 AA5 5 VAL B 15 ILE B 19 -1 N ILE B 19 O LYS B 22 SHEET 3 AA5 5 ILE B 91 ASP B 97 -1 O LEU B 94 N MET B 18 SHEET 4 AA5 5 VAL B 103 THR B 118 -1 O ILE B 104 N VAL B 95 SHEET 5 AA5 5 THR B 135 SER B 137 -1 O THR B 135 N HIS B 108 SHEET 1 AA6 2 THR B 38 VAL B 41 0 SHEET 2 AA6 2 GLU B 51 TYR B 54 -1 O GLU B 51 N VAL B 41 SHEET 1 AA7 7 LYS C 22 PRO C 23 0 SHEET 2 AA7 7 VAL C 15 ILE C 19 -1 N ILE C 19 O LYS C 22 SHEET 3 AA7 7 ILE C 91 ASP C 97 -1 O LEU C 94 N MET C 18 SHEET 4 AA7 7 VAL C 103 THR C 118 -1 O ILE C 104 N VAL C 95 SHEET 5 AA7 7 THR C 126 SER C 132 -1 O SER C 132 N SER C 111 SHEET 6 AA7 7 GLU C 58 LEU C 66 -1 N ARG C 65 O GLU C 127 SHEET 7 AA7 7 ALA C 27 GLU C 35 -1 N GLU C 35 O GLU C 58 SHEET 1 AA8 5 LYS C 22 PRO C 23 0 SHEET 2 AA8 5 VAL C 15 ILE C 19 -1 N ILE C 19 O LYS C 22 SHEET 3 AA8 5 ILE C 91 ASP C 97 -1 O LEU C 94 N MET C 18 SHEET 4 AA8 5 VAL C 103 THR C 118 -1 O ILE C 104 N VAL C 95 SHEET 5 AA8 5 THR C 135 SER C 137 -1 O SER C 137 N SER C 106 SHEET 1 AA9 2 THR C 38 GLU C 43 0 SHEET 2 AA9 2 SER C 46 TYR C 54 -1 O GLU C 51 N VAL C 41 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 MASTER 160 0 0 9 42 0 0 6 3330 3 0 33 END