HEADER VIRUS LIKE PARTICLE 06-DEC-22 8FEH TITLE CRYOEM STRUCTURE OF BACTERIOPHAGE Q-BETA COAT PROTEIN DIMER WITH AYGG TITLE 2 LINKER COMPND MOL_ID: 1; COMPND 2 MOLECULE: MINOR CAPSID PROTEIN A1 FUSION; COMPND 3 CHAIN: D; COMPND 4 SYNONYM: A1 READ-THROUGH PROTEIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: QUBEVIRUS DURUM; SOURCE 3 ORGANISM_TAXID: 39803; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COAT PROTEIN, Q-BETA, FUSION, VIRUS LIKE PARTICLE EXPDTA ELECTRON MICROSCOPY AUTHOR T.P.NEWTON,L.ZHAO,M.G.FINN,M.KOPYLOV REVDAT 1 20-DEC-23 8FEH 0 JRNL AUTH T.P.NEWTON,L.ZHAO,M.KOPYLOV,M.G.FINN JRNL TITL CRYOEM STRUCTURE OF BACTERIOPHAGE Q-BETA COAT PROTEIN DIMER JRNL TITL 2 WITH AYGG LINKER JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.28 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL REMARK 3 RECONSTRUCTION SCHEMA : FOURIER SPACE 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) : 3.280 REMARK 3 NUMBER OF PARTICLES : 1380 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 8FEH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-DEC-22. REMARK 100 THE DEPOSITION ID IS D_1000270495. 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 : QUBEVIRUS DURUM REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 1.00 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 : GATAN K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 0.00 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 6470.00 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 ICOSAHEDRAL POINT SYMMETRY (SCHOENFLIES SYMBOL = I). 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: D 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASN D 77 CG OD1 ND2 REMARK 470 TYR D 132 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 TYR D 134 CG CD1 CD2 CE1 CE2 CZ OH 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 ASN D 10 60.67 36.76 REMARK 500 ALA D 40 -5.20 70.19 REMARK 500 ALA D 133 116.96 -162.95 REMARK 500 ARG D 160 59.53 -92.77 REMARK 500 ARG D 222 -62.53 70.05 REMARK 500 GLN D 223 -8.55 83.83 REMARK 500 TYR D 235 -6.34 75.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-29027 RELATED DB: EMDB REMARK 900 CRYOEM STRUCTURE OF BACTERIOPHAGE Q-BETA COAT PROTEIN DIMER WITH REMARK 900 AYGG LINKER DBREF 8FEH D 1 132 UNP Q8LTE1 A1_BPQBE 2 133 DBREF 8FEH D 137 268 UNP Q8LTE1 A1_BPQBE 2 133 SEQADV 8FEH ALA D 133 UNP Q8LTE1 LINKER SEQADV 8FEH TYR D 134 UNP Q8LTE1 LINKER SEQADV 8FEH GLY D 135 UNP Q8LTE1 LINKER SEQADV 8FEH GLY D 136 UNP Q8LTE1 LINKER SEQRES 1 D 268 ALA LYS LEU GLU THR VAL THR LEU GLY ASN ILE GLY LYS SEQRES 2 D 268 ASP GLY LYS GLN THR LEU VAL LEU ASN PRO ARG GLY VAL SEQRES 3 D 268 ASN PRO THR ASN GLY VAL ALA SER LEU SER GLN ALA GLY SEQRES 4 D 268 ALA VAL PRO ALA LEU GLU LYS ARG VAL THR VAL SER VAL SEQRES 5 D 268 SER GLN PRO SER ARG ASN ARG LYS ASN TYR LYS VAL GLN SEQRES 6 D 268 VAL LYS ILE GLN ASN PRO THR ALA CYS THR ALA ASN GLY SEQRES 7 D 268 SER CYS ASP PRO SER VAL THR ARG GLN ALA TYR ALA ASP SEQRES 8 D 268 VAL THR PHE SER PHE THR GLN TYR SER THR ASP GLU GLU SEQRES 9 D 268 ARG ALA PHE VAL ARG THR GLU LEU ALA ALA LEU LEU ALA SEQRES 10 D 268 SER PRO LEU LEU ILE ASP ALA ILE ASP GLN LEU ASN PRO SEQRES 11 D 268 ALA TYR ALA TYR GLY GLY ALA LYS LEU GLU THR VAL THR SEQRES 12 D 268 LEU GLY ASN ILE GLY LYS ASP GLY LYS GLN THR LEU VAL SEQRES 13 D 268 LEU ASN PRO ARG GLY VAL ASN PRO THR ASN GLY VAL ALA SEQRES 14 D 268 SER LEU SER GLN ALA GLY ALA VAL PRO ALA LEU GLU LYS SEQRES 15 D 268 ARG VAL THR VAL SER VAL SER GLN PRO SER ARG ASN ARG SEQRES 16 D 268 LYS ASN TYR LYS VAL GLN VAL LYS ILE GLN ASN PRO THR SEQRES 17 D 268 ALA CYS THR ALA ASN GLY SER CYS ASP PRO SER VAL THR SEQRES 18 D 268 ARG GLN ALA TYR ALA ASP VAL THR PHE SER PHE THR GLN SEQRES 19 D 268 TYR SER THR ASP GLU GLU ARG ALA PHE VAL ARG THR GLU SEQRES 20 D 268 LEU ALA ALA LEU LEU ALA SER PRO LEU LEU ILE ASP ALA SEQRES 21 D 268 ILE ASP GLN LEU ASN PRO ALA TYR HELIX 1 AA1 THR D 101 ALA D 117 1 17 HELIX 2 AA2 SER D 118 ASP D 126 1 9 HELIX 3 AA3 VAL D 177 GLU D 181 5 5 HELIX 4 AA4 THR D 237 LEU D 252 1 16 HELIX 5 AA5 SER D 254 ASP D 262 1 9 SHEET 1 AA1 9 VAL D 6 ILE D 11 0 SHEET 2 AA1 9 GLN D 17 ASN D 27 -1 O LEU D 19 N LEU D 8 SHEET 3 AA1 9 VAL D 32 SER D 36 -1 O SER D 36 N ASN D 22 SHEET 4 AA1 9 VAL D 48 SER D 53 -1 O VAL D 48 N LEU D 35 SHEET 5 AA1 9 TYR D 62 ILE D 68 -1 O GLN D 65 N SER D 51 SHEET 6 AA1 9 TYR D 89 PHE D 96 -1 O VAL D 92 N VAL D 66 SHEET 7 AA1 9 ALA D 226 PHE D 232 -1 O THR D 229 N ASP D 91 SHEET 8 AA1 9 TYR D 198 ILE D 204 -1 N TYR D 198 O PHE D 232 SHEET 9 AA1 9 VAL D 184 SER D 187 -1 N SER D 187 O GLN D 201 SHEET 1 AA2 2 PRO D 71 ALA D 73 0 SHEET 2 AA2 2 VAL D 84 GLN D 87 -1 O THR D 85 N THR D 72 SHEET 1 AA3 3 VAL D 142 ILE D 147 0 SHEET 2 AA3 3 GLN D 153 PRO D 159 -1 O LEU D 155 N LEU D 144 SHEET 3 AA3 3 LEU D 171 SER D 172 -1 O SER D 172 N ASN D 158 SHEET 1 AA4 2 THR D 208 ALA D 209 0 SHEET 2 AA4 2 VAL D 220 THR D 221 -1 O THR D 221 N THR D 208 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