HEADER VIRAL PROTEIN 13-FEB-25 9LWA TITLE BACTERIOPHAGE MYCOFY1 DISTAL HEAD-TO-TAIL INTERFACE (C6 SYMMETRY) COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEAD-TO-TAIL STOPPER; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: STOPPER PROTEIN GP9; COMPND 5 OTHER_DETAILS: SEQUENCE REFERENCE FOR MYCOLICIBACTERIUM PHAGE MYCOFY1 COMPND 6 IS NOT AVAILABLE AT THE TIME OF BIOCURATION. CURRENT SEQUENCE COMPND 7 REFERENCE IS FROM UNIPROT ID Q854Y9.; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: TERMINATOR PROTEIN GP11; COMPND 10 CHAIN: B; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: MAJOR TAIL PROTEIN; COMPND 13 CHAIN: C; COMPND 14 SYNONYM: TAIL TUBE PROTEIN GP12; COMPND 15 OTHER_DETAILS: SEQUENCE REFERENCE FOR MYCOLICIBACTERIUM PHAGE MYCOFY1 COMPND 16 IS NOT AVAILABLE AT THE TIME OF BIOCURATION. CURRENT SEQUENCE COMPND 17 REFERENCE IS FROM UNIPROT ID A0A0A7RVP8. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOLICIBACTERIUM PHAGE MYCOFY1; SOURCE 3 ORGANISM_TAXID: 3349809; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: MYCOLICIBACTERIUM PHAGE MYCOFY1; SOURCE 6 ORGANISM_TAXID: 3349809; SOURCE 7 MOL_ID: 3; SOURCE 8 ORGANISM_SCIENTIFIC: MYCOLICIBACTERIUM PHAGE MYCOFY1; SOURCE 9 ORGANISM_TAXID: 3349809 KEYWDS MYCOBACTERIUM, BACTERIOPHAGE, PROLATE HEAD, HEAD-TO-TAIL INTERFACE, KEYWDS 2 CONNECTOR PROTEIN, TERMINATOR PROTEIN, TAIL TUBE PROTEIN, VIRUS, KEYWDS 3 VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR X.LI,Q.SHAO,L.LI,L.XIE,Z.RUAN,Q.FANG REVDAT 2 30-APR-25 9LWA 1 JRNL REVDAT 1 16-APR-25 9LWA 0 JRNL AUTH X.LI,Q.SHAO,L.LI,L.XIE,Z.RUAN,Q.FANG JRNL TITL CRYO-EM REVEALS STRUCTURAL DIVERSITY IN PROLATE-HEADED JRNL TITL 2 MYCOBACTERIOPHAGE MYCOFY1. JRNL REF J.MOL.BIOL. V. 437 69126 2025 JRNL REFN ESSN 1089-8638 JRNL PMID 40187685 JRNL DOI 10.1016/J.JMB.2025.169126 REMARK 2 REMARK 2 RESOLUTION. 3.83 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : PHENIX, EPU, CTFFIND, 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) : 3.830 REMARK 3 NUMBER OF PARTICLES : 12594 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 9LWA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 18-FEB-25. REMARK 100 THE DEPOSITION ID IS D_1300055139. 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 : MYCOLICIBACTERIUM PHAGE MYCOFY1 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 : 7.50 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 : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 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 : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 2570.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 59000 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 = C6). 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: 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 -0.000167 224.92380 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000135 -60.28593 REMARK 350 BIOMT3 2 -0.000033 -0.000212 1.000000 0.04033 REMARK 350 BIOMT1 3 -0.500000 -0.866025 -0.000367 389.59485 REMARK 350 BIOMT2 3 0.866025 -0.500000 0.000058 104.36084 REMARK 350 BIOMT3 3 -0.000233 -0.000289 1.000000 0.08593 REMARK 350 BIOMT1 4 -1.000000 0.000000 -0.000400 329.34209 REMARK 350 BIOMT2 4 0.000000 -1.000000 -0.000154 329.29354 REMARK 350 BIOMT3 4 -0.000400 -0.000154 1.000000 0.09121 REMARK 350 BIOMT1 5 -0.500000 0.866025 -0.000233 104.41828 REMARK 350 BIOMT2 5 -0.866025 -0.500000 -0.000289 389.57946 REMARK 350 BIOMT3 5 -0.000367 0.000058 1.000000 0.05089 REMARK 350 BIOMT1 6 0.500000 0.866025 -0.000033 -60.25276 REMARK 350 BIOMT2 6 -0.866025 0.500000 -0.000212 224.93270 REMARK 350 BIOMT3 6 -0.000167 0.000135 1.000000 0.00528 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 SER A 2 REMARK 465 GLY A 131 REMARK 465 MET B 1 REMARK 465 THR B 2 REMARK 465 MET B 3 REMARK 465 ALA B 4 REMARK 465 MET C 1 REMARK 465 THR C 2 REMARK 465 GLN C 3 REMARK 465 PRO C 4 REMARK 465 GLY C 262 REMARK 465 ASP C 263 REMARK 465 GLY C 264 REMARK 465 SER C 265 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 ARG C 55 -60.25 -93.51 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-63436 RELATED DB: EMDB REMARK 900 BACTERIOPHAGE MYCOFY1 DISTAL HEAD-TO-TAIL INTERFACE (C6 SYMMETRY) DBREF 9LWA A 1 131 UNP Q854Y9 Q854Y9_9CAUD 1 131 DBREF 9LWA B 1 140 PDB 9LWA 9LWA 1 140 DBREF1 9LWA C 1 265 UNP A0A0A7RVP8_9CAUD DBREF2 9LWA C A0A0A7RVP8 1 265 SEQADV 9LWA SER A 14 UNP Q854Y9 GLY 14 CONFLICT SEQADV 9LWA VAL A 20 UNP Q854Y9 ALA 20 CONFLICT SEQADV 9LWA THR A 47 UNP Q854Y9 ILE 47 CONFLICT SEQADV 9LWA GLY A 77 UNP Q854Y9 ASP 77 CONFLICT SEQADV 9LWA SER A 90 UNP Q854Y9 ALA 90 CONFLICT SEQADV 9LWA ARG A 104 UNP Q854Y9 HIS 104 CONFLICT SEQADV 9LWA VAL A 105 UNP Q854Y9 ILE 105 CONFLICT SEQADV 9LWA ALA A 116 UNP Q854Y9 ASP 116 CONFLICT SEQADV 9LWA SER C 53 UNP A0A0A7RVP THR 53 CONFLICT SEQADV 9LWA ARG C 73 UNP A0A0A7RVP LYS 73 CONFLICT SEQADV 9LWA PHE C 216 UNP A0A0A7RVP LEU 216 CONFLICT SEQRES 1 A 131 MET SER GLU GLU PHE GLY GLY GLN VAL VAL ALA LEU VAL SEQRES 2 A 131 SER VAL ALA GLU THR GLY VAL PRO GLY TRP GLY GLY LEU SEQRES 3 A 131 LYS ALA LYS ALA ARG THR THR THR ARG GLN PRO GLY VAL SEQRES 4 A 131 HIS PHE ARG PRO ALA SER SER THR GLU THR PRO ASP GLY SEQRES 5 A 131 GLN THR ASN VAL ALA THR GLU VAL TRP LYS LEU THR ALA SEQRES 6 A 131 PRO PRO THR ALA ALA VAL LEU ALA ALA LYS PRO GLY GLY SEQRES 7 A 131 GLU LEU VAL TYR ASP GLY THR GLU HIS PRO GLU SER LEU SEQRES 8 A 131 ASP LEU ASP SER ALA ALA GLY ARG ALA ALA THR PHE ARG SEQRES 9 A 131 VAL ASP GLY PRO ILE MET PRO LYS TYR ASP LEU ALA GLY SEQRES 10 A 131 GLN VAL HIS HIS VAL THR ILE MET CYS LYS ARG GLN ALA SEQRES 11 A 131 GLY SEQRES 1 B 140 MET THR MET ALA ASP LEU HIS ASP GLN ASP ALA PRO ASP SEQRES 2 B 140 GLU GLU ASP PHE VAL VAL CYS TRP MET GLN PRO VAL MET SEQRES 3 B 140 ARG THR ALA VAL GLU ARG ASP ILE ASP ALA GLU LEU PRO SEQRES 4 B 140 PHE CYS GLU VAL THR ARG ILE ASP GLY ALA ASP ASP PRO SEQRES 5 B 140 GLU ALA GLY THR ASP ASP PRO VAL ILE GLN LEU ASP PHE SEQRES 6 B 140 TYR ALA LEU GLY ALA GLU ALA ALA LYS ALA ALA ALA LYS SEQRES 7 B 140 GLN GLY HIS ARG ARG MET LEU PHE LEU PHE ARG ASN PHE SEQRES 8 B 140 PRO THR VAL THR LEU SER ASP GLY THR LEU ALA ASP LEU SEQRES 9 B 140 ASP PHE GLY GLU THR LEU ILE LYS PRO SER ARG MET ALA SEQRES 10 B 140 PHE GLU HIS ASP GLN ILE VAL ARG TYR THR ALA ARG TYR SEQRES 11 B 140 GLN LEU GLY THR SER TYR VAL ALA VAL PRO SEQRES 1 C 265 MET THR GLN PRO LEU THR GLY THR THR PRO ALA ALA GLY SEQRES 2 C 265 GLY TYR THR THR VAL ASP ASN ARG LEU GLN GLY GLY HIS SEQRES 3 C 265 ARG THR GLY LEU ILE ALA VAL ALA PHE ARG ASP ALA LEU SEQRES 4 C 265 GLY THR SER THR ASN ILE SER PRO HIS ASN ALA ASN GLY SEQRES 5 C 265 SER VAL ARG TRP SER PRO LEU ALA GLN ASP GLY GLN LEU SEQRES 6 C 265 ARG ASP ASP LEU PHE ALA HIS ARG LEU GLU ASN GLY VAL SEQRES 7 C 265 TRP VAL GLU ASN THR ASN PRO ASN GLU GLY TRP TYR LEU SEQRES 8 C 265 ALA GLY ALA PHE GLY GLU GLY ASN GLY PRO SER SER ARG SEQRES 9 C 265 PRO SER ILE ASP THR ASP ASP GLN MET ILE GLU GLN SER SEQRES 10 C 265 ASN TRP PRO PHE GLU SER ASP ILE THR LYS GLN ASP GLU SEQRES 11 C 265 PRO PHE THR PHE GLN ALA LEU GLN ASN LEU TYR PRO ALA SEQRES 12 C 265 ILE GLN ARG LEU ALA ASN ASN LEU PRO LEU SER ASP ALA SEQRES 13 C 265 ASN GLY ASN PRO LEU VAL GLU LEU PRO GLY GLU ALA ASP SEQRES 14 C 265 GLY PHE SER GLN PRO VAL ASP ALA GLU LYS ILE GLY ARG SEQRES 15 C 265 GLN PHE LEU LEU TYR GLY ILE ARG LYS LYS GLU GLY ARG SEQRES 16 C 265 TYR LEU TYR GLU VAL ASP ALA TYR ASP LEU ALA TYR LEU SEQRES 17 C 265 ASN ASN LYS GLY GLU ARG LYS PHE GLY LYS ARG GLY THR SEQRES 18 C 265 ALA ALA GLU LEU THR PHE LYS PRO GLU PRO SER GLY TYR SEQRES 19 C 265 PHE MET ALA MET VAL ASP GLY GLU TYR LYS PRO ILE ILE SEQRES 20 C 265 LYS HIS THR PHE ILE GLY GLY PRO ALA TRP ASP ALA LEU SEQRES 21 C 265 ALA GLY ASP GLY SER HELIX 1 AA1 GLY A 22 LEU A 26 5 5 HELIX 2 AA2 THR A 68 ALA A 73 1 6 HELIX 3 AA3 SER A 95 ALA A 101 1 7 HELIX 4 AA4 ASP B 13 GLN B 23 1 11 HELIX 5 AA5 GLY B 69 PHE B 91 1 23 HELIX 6 AA6 THR C 9 GLY C 14 1 6 HELIX 7 AA7 ASP C 19 GLN C 23 5 5 HELIX 8 AA8 LEU C 39 ASN C 44 5 6 HELIX 9 AA9 TYR C 141 ASN C 149 1 9 HELIX 10 AB1 GLY C 254 ALA C 259 1 6 SHEET 1 AA1 7 GLN A 8 THR A 18 0 SHEET 2 AA1 7 ALA A 28 GLU A 48 -1 O THR A 32 N SER A 14 SHEET 3 AA1 7 ALA A 57 ALA A 65 -1 O VAL A 60 N ALA A 44 SHEET 4 AA1 7 VAL A 119 GLN A 129 -1 O CYS A 126 N TRP A 61 SHEET 5 AA1 7 THR A 102 TYR A 113 -1 N LYS A 112 O HIS A 120 SHEET 6 AA1 7 GLU A 79 VAL A 81 -1 N LEU A 80 O PHE A 103 SHEET 7 AA1 7 GLN A 8 THR A 18 -1 N VAL A 13 O GLU A 79 SHEET 1 AA2 2 GLN B 9 ASP B 10 0 SHEET 2 AA2 2 VAL B 137 ALA B 138 -1 O VAL B 137 N ASP B 10 SHEET 1 AA3 5 THR B 28 ALA B 29 0 SHEET 2 AA3 5 PHE B 40 ASP B 47 1 O CYS B 41 N ALA B 29 SHEET 3 AA3 5 VAL B 60 LEU B 68 -1 O GLN B 62 N THR B 44 SHEET 4 AA3 5 ILE B 123 GLY B 133 -1 O TYR B 126 N PHE B 65 SHEET 5 AA3 5 PHE B 106 MET B 116 -1 N GLU B 108 O GLN B 131 SHEET 1 AA4 2 ASP B 50 ASP B 51 0 SHEET 2 AA4 2 THR B 56 ASP B 57 -1 O THR B 56 N ASP B 51 SHEET 1 AA5 2 VAL B 94 THR B 95 0 SHEET 2 AA5 2 LEU B 101 ALA B 102 -1 O ALA B 102 N VAL B 94 SHEET 1 AA6 7 TYR C 90 LEU C 91 0 SHEET 2 AA6 7 LEU C 30 ASP C 37 -1 N PHE C 35 O TYR C 90 SHEET 3 AA6 7 ARG C 182 LYS C 192 -1 O TYR C 187 N ALA C 32 SHEET 4 AA6 7 ARG C 195 ASN C 210 -1 O ARG C 195 N LYS C 192 SHEET 5 AA6 7 GLU C 224 PRO C 229 -1 O LYS C 228 N TYR C 207 SHEET 6 AA6 7 PHE C 132 GLN C 135 -1 N PHE C 132 O PHE C 227 SHEET 7 AA6 7 SER C 102 SER C 103 -1 N SER C 102 O THR C 133 SHEET 1 AA7 5 TYR C 90 LEU C 91 0 SHEET 2 AA7 5 LEU C 30 ASP C 37 -1 N PHE C 35 O TYR C 90 SHEET 3 AA7 5 ARG C 182 LYS C 192 -1 O TYR C 187 N ALA C 32 SHEET 4 AA7 5 ARG C 195 ASN C 210 -1 O ARG C 195 N LYS C 192 SHEET 5 AA7 5 LYS C 248 GLY C 253 -1 O PHE C 251 N VAL C 200 SHEET 1 AA8 2 HIS C 72 GLU C 75 0 SHEET 2 AA8 2 VAL C 78 GLU C 81 -1 O VAL C 78 N GLU C 75 SHEET 1 AA9 2 SER C 106 GLN C 112 0 SHEET 2 AA9 2 GLU C 122 ASP C 129 -1 O GLU C 122 N GLN C 112 SHEET 1 AB1 2 MET C 236 MET C 238 0 SHEET 2 AB1 2 TYR C 243 PRO C 245 -1 N LYS C 244 O ALA C 237 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 TER 944 ALA A 130 TER 2017 PRO B 140 TER 4015 ALA C 261 MASTER 154 0 0 10 36 0 0 6 4012 3 0 43 END