HEADER VIRUS LIKE PARTICLE 05-JUL-22 8ACB TITLE CRYOEM STRUCTURE OF SWEET POTATO FEATHERY MOTTLE VIRUS VLP COMPND MOL_ID: 1; COMPND 2 MOLECULE: GENOME POLYPROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: SINGLE-STRANDED RNA; COMPND 7 CHAIN: B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SWEET POTATO FEATHERY MOTTLE VIRUS; SOURCE 3 ORGANISM_TAXID: 12844; SOURCE 4 EXPRESSION_SYSTEM: NICOTIANA BENTHAMIANA; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 4100; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: IPOMOEA BATATAS; SOURCE 8 ORGANISM_TAXID: 4120 KEYWDS PLANT VIRUS, COAT PROTEIN, VIRUS LIKE PARTICLE EXPDTA ELECTRON MICROSCOPY AUTHOR A.JAVED,J.M.BYRNE,N.RANSON,G.LOMONOSOFF REVDAT 1 17-MAY-23 8ACB 0 JRNL AUTH O.CHASE,A.JAVED,M.J.BYRNE,E.C.THUENEMANN,G.P.LOMONOSSOFF, JRNL AUTH 2 N.A.RANSON,J.J.LOPEZ-MOYA JRNL TITL CRYOEM AND STABILITY ANALYSIS OF VIRUS-LIKE PARTICLES OF JRNL TITL 2 POTYVIRUS AND IPOMOVIRUS INFECTING A COMMON HOST. JRNL REF COMMUN BIOL V. 6 433 2023 JRNL REFN ESSN 2399-3642 JRNL PMID 37076658 JRNL DOI 10.1038/S42003-023-04799-X REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : EPU, CTFFIND, UCSF CHIMERA, PHENIX, REMARK 3 ISOLDE, COOT, RELION, RELION, RELION, REMARK 3 RELION 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 : REAL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE FIT REMARK 3 REFINEMENT TARGET : CORRELATION COEFFICIENT REMARK 3 OVERALL ANISOTROPIC B VALUE : 140.900 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) : 2.600 REMARK 3 NUMBER OF PARTICLES : 48042 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 8ACB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-JUL-22. REMARK 100 THE DEPOSITION ID IS D_1292123941. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : HELICAL REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : FILAMENT REMARK 245 PARTICLE TYPE : HELICAL REMARK 245 NAME OF SAMPLE : SWEET POTATO FEATHERY MOTTLE REMARK 245 VIRUS 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 : 3276 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON III (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) : 100.00 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: A, B 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 MET A 96 CG SD CE REMARK 470 LYS A 100 CG CD CE NZ REMARK 470 LYS A 101 CG CD CE NZ REMARK 470 ARG A 102 CG CD NE CZ NH1 NH2 REMARK 470 THR A 288 OG1 CG2 REMARK 470 GLN A 289 CG CD OE1 NE2 REMARK 470 GLU A 290 CG CD OE1 OE2 REMARK 470 HIS A 296 CG ND1 CD2 CE1 NE2 REMARK 470 ARG A 303 CG CD NE CZ NH1 NH2 REMARK 470 ILE A 305 CG1 CG2 CD1 REMARK 470 HIS A 306 CG ND1 CD2 CE1 NE2 REMARK 470 ASN A 307 CG OD1 ND2 REMARK 470 LEU A 309 CG CD1 CD2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 U B 1 C3' - O3' - P ANGL. DEV. = -9.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 LYS A 100 -95.45 60.14 REMARK 500 LYS A 101 -105.11 60.33 REMARK 500 GLN A 103 152.47 65.61 REMARK 500 ASN A 222 59.95 -95.31 REMARK 500 LEU A 242 49.31 -90.96 REMARK 500 ALA A 246 28.99 -142.81 REMARK 500 SER A 287 -117.21 61.11 REMARK 500 THR A 288 -155.26 60.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-15345 RELATED DB: EMDB REMARK 900 CRYOEM STRUCTURE OF SWEET POTATO FEATHERY MOTTLE VIRUS VLP DBREF 8ACB A 91 310 UNP D2CTM1 D2CTM1_9POTV 146 365 DBREF 8ACB B 1 5 PDB 8ACB 8ACB 1 5 SEQRES 1 A 220 VAL PRO ARG VAL LYS MET ASN ALA ASN LYS LYS ARG GLN SEQRES 2 A 220 PRO MET VAL ASN GLY ARG ALA ILE ILE ASN PHE GLN HIS SEQRES 3 A 220 LEU SER THR TYR GLU PRO GLU GLN PHE GLU VAL ALA ASN SEQRES 4 A 220 THR ARG SER THR GLN GLU GLN PHE GLN ALA TRP TYR GLU SEQRES 5 A 220 GLY VAL LYS GLY ASP TYR GLY VAL ASP ASP THR GLY MET SEQRES 6 A 220 GLY ILE LEU LEU ASN GLY LEU MET VAL TRP CYS ILE GLU SEQRES 7 A 220 ASN GLY THR SER PRO ASN ILE ASN GLY VAL TRP THR MET SEQRES 8 A 220 MET ASP GLY ASP GLU GLN VAL THR TYR PRO ILE LYS PRO SEQRES 9 A 220 LEU LEU ASP HIS ALA VAL PRO THR PHE ARG GLN ILE MET SEQRES 10 A 220 THR HIS PHE SER ASP VAL ALA GLU ALA TYR ILE GLU MET SEQRES 11 A 220 ARG ASN ARG THR LYS ALA TYR MET PRO ARG TYR GLY LEU SEQRES 12 A 220 GLN ARG ASN LEU THR ASP MET SER LEU ALA ARG TYR ALA SEQRES 13 A 220 PHE ASP PHE TYR GLU LEU HIS SER THR THR PRO ALA ARG SEQRES 14 A 220 ALA LYS GLU ALA HIS LEU GLN MET LYS ALA ALA ALA LEU SEQRES 15 A 220 LYS ASN ALA ARG ASN ARG LEU PHE GLY LEU ASP GLY ASN SEQRES 16 A 220 VAL SER THR GLN GLU GLU ASP THR GLU ARG HIS THR THR SEQRES 17 A 220 THR ASP VAL THR ARG ASN ILE HIS ASN LEU LEU GLY SEQRES 1 B 5 U U U U U HELIX 1 AA1 ASN A 113 TYR A 120 1 8 HELIX 2 AA2 GLU A 123 ALA A 128 5 6 HELIX 3 AA3 THR A 133 GLY A 149 1 17 HELIX 4 AA4 ASP A 151 ASN A 169 1 19 HELIX 5 AA5 ILE A 192 HIS A 198 1 7 HELIX 6 AA6 THR A 202 HIS A 209 1 8 HELIX 7 AA7 PHE A 210 ASN A 222 1 13 HELIX 8 AA8 PRO A 229 ARG A 235 1 7 HELIX 9 AA9 MET A 240 ARG A 244 5 5 HELIX 10 AB1 ARG A 259 LEU A 272 1 14 SHEET 1 AA1 2 VAL A 178 ASP A 183 0 SHEET 2 AA1 2 GLU A 186 PRO A 191 -1 O TYR A 190 N TRP A 179 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