HEADER VIRUS LIKE PARTICLE 05-JUL-22 8ACC TITLE CRYOEM STRUCTURE OF SWEET POTATO MILD MOTTLE VIRUS VLP COMPND MOL_ID: 1; COMPND 2 MOLECULE: 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 MILD MOTTLE VIRUS; SOURCE 3 ORGANISM_TAXID: 41459; SOURCE 4 EXPRESSION_SYSTEM: NICOTIANA BENTHAMIANA; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 4100; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: NICOTIANA TABACUM; SOURCE 8 ORGANISM_TAXID: 4097 KEYWDS PLANT VIRUS, COAT PROTEIN, VLP, VIRUS LIKE PARTICLE EXPDTA ELECTRON MICROSCOPY AUTHOR A.JAVED,B.M.BYRNE,N.RANSON,G.LOMONOSOFF REVDAT 2 25-OCT-23 8ACC 1 SOURCE REVDAT 1 17-MAY-23 8ACC 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. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, EPU, CTFFIND, UCSF CHIMERA, REMARK 3 RELION, RELION, RELION, RELION, PHENIX, REMARK 3 COOT, ISOLDE 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 : 123.700 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) : 2.900 REMARK 3 NUMBER OF PARTICLES : 38705 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING ONLY REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 8ACC 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_1292123942. 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 MILD MOTTLE VIRUS REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.50 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : 3UL OF SAMPLE APPLIED TO EACH REMARK 245 GRID. 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 : 2260 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 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 ALA A 1 REMARK 465 SER A 2 REMARK 465 THR A 3 REMARK 465 SER A 4 REMARK 465 LYS A 5 REMARK 465 THR A 6 REMARK 465 ILE A 7 REMARK 465 GLU A 8 REMARK 465 GLU A 9 REMARK 465 LEU A 10 REMARK 465 GLN A 11 REMARK 465 GLN A 12 REMARK 465 GLU A 13 REMARK 465 MET A 14 REMARK 465 GLU A 15 REMARK 465 ASP A 16 REMARK 465 LEU A 17 REMARK 465 ASP A 18 REMARK 465 ALA A 19 REMARK 465 ASP A 20 REMARK 465 THR A 21 REMARK 465 THR A 22 REMARK 465 ILE A 23 REMARK 465 THR A 24 REMARK 465 VAL A 25 REMARK 465 VAL A 26 REMARK 465 GLN A 27 REMARK 465 ARG A 28 REMARK 465 GLU A 29 REMARK 465 THR A 30 REMARK 465 GLN A 31 REMARK 465 LYS A 32 REMARK 465 ALA A 33 REMARK 465 ARG A 34 REMARK 465 ILE A 35 REMARK 465 ARG A 36 REMARK 465 GLU A 37 REMARK 465 GLN A 38 REMARK 465 ILE A 39 REMARK 465 GLU A 40 REMARK 465 THR A 41 REMARK 465 LEU A 42 REMARK 465 ARG A 43 REMARK 465 ALA A 44 REMARK 465 GLN A 45 REMARK 465 GLN A 46 REMARK 465 MET A 47 REMARK 465 VAL A 48 REMARK 465 ARG A 49 REMARK 465 PRO A 50 REMARK 465 SER A 51 REMARK 465 GLU A 52 REMARK 465 ALA A 53 REMARK 465 GLN A 54 REMARK 465 LEU A 55 REMARK 465 GLN A 56 REMARK 465 PRO A 57 REMARK 465 ASP A 58 REMARK 465 VAL A 59 REMARK 465 THR A 60 REMARK 465 PRO A 61 REMARK 465 THR A 62 REMARK 465 GLN A 63 REMARK 465 ILE A 64 REMARK 465 LEU A 296 REMARK 465 ARG A 297 REMARK 465 GLY A 298 REMARK 465 ALA A 299 REMARK 465 GLN A 300 REMARK 465 LEU A 301 REMARK 465 ASP A 302 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 VAL A 65 CG1 CG2 REMARK 470 THR A 66 OG1 CG2 REMARK 470 PHE A 67 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU A 68 CG CD OE1 OE2 REMARK 470 PRO A 69 CG CD REMARK 470 PRO A 70 CG CD REMARK 470 ARG A 71 CG CD NE CZ NH1 NH2 REMARK 470 VAL A 72 CG1 CG2 REMARK 470 THR A 73 OG1 CG2 REMARK 470 PHE A 75 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LEU A 78 CG CD1 CD2 REMARK 470 GLU A 94 CG CD OE1 OE2 REMARK 470 SER A 118 OG REMARK 470 GLU A 121 CG CD OE1 OE2 REMARK 470 ASN A 149 CG OD1 ND2 REMARK 470 GLN A 172 CG CD OE1 NE2 REMARK 470 ARG A 191 CG CD NE CZ NH1 NH2 REMARK 470 MET A 206 CG SD CE REMARK 470 LYS A 213 CG CD CE NZ REMARK 470 LYS A 218 CG CD CE NZ REMARK 470 GLN A 229 CG CD OE1 NE2 REMARK 470 LYS A 252 CG CD CE NZ REMARK 470 ARG A 266 CG CD NE CZ NH1 NH2 REMARK 470 VAL A 267 CG1 CG2 REMARK 470 PHE A 268 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LEU A 270 CG CD1 CD2 REMARK 470 PRO A 273 CG CD REMARK 470 ASP A 275 CG OD1 OD2 REMARK 470 ASP A 277 CG OD1 OD2 REMARK 470 GLU A 278 CG CD OE1 OE2 REMARK 470 LEU A 279 CG CD1 CD2 REMARK 470 ASP A 280 CG OD1 OD2 REMARK 470 THR A 281 OG1 CG2 REMARK 470 GLU A 282 CG CD OE1 OE2 REMARK 470 ARG A 283 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 284 CG ND1 CD2 CE1 NE2 REMARK 470 VAL A 285 CG1 CG2 REMARK 470 VAL A 286 CG1 CG2 REMARK 470 ASP A 287 CG OD1 OD2 REMARK 470 ASP A 288 CG OD1 OD2 REMARK 470 VAL A 289 CG1 CG2 REMARK 470 ARG A 291 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 293 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 294 CG ND1 CD2 CE1 NE2 REMARK 470 SER A 295 OG REMARK 470 U B 3 OP2 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 PRO A 69 N - CA - CB ANGL. DEV. = 7.2 DEGREES REMARK 500 U B 4 OP1 - P - OP2 ANGL. DEV. = -10.1 DEGREES REMARK 500 U B 6 OP1 - P - OP2 ANGL. DEV. = -10.3 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 PRO A 69 -165.64 56.81 REMARK 500 ARG A 71 -113.02 49.40 REMARK 500 PHE A 75 -108.22 45.90 REMARK 500 HIS A 159 -7.01 72.39 REMARK 500 PRO A 181 2.23 -67.39 REMARK 500 PRO A 188 57.84 -91.06 REMARK 500 THR A 189 149.84 67.12 REMARK 500 LEU A 233 -7.06 73.34 REMARK 500 LEU A 270 -166.32 53.90 REMARK 500 ASP A 277 140.56 70.99 REMARK 500 GLU A 282 -169.72 -166.01 REMARK 500 ARG A 283 178.30 64.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-15345 RELATED DB: EMDB REMARK 900 SPFMV VLP REMARK 900 RELATED ID: EMD-15346 RELATED DB: EMDB REMARK 900 CRYOEM STRUCTURE OF SWEET POTATO MILD MOTTLE VIRUS VLP DBREF 8ACC A 1 302 UNP Q599X9 Q599X9_9POTY 200 501 DBREF 8ACC B 2 6 PDB 8ACC 8ACC 2 6 SEQRES 1 A 302 ALA SER THR SER LYS THR ILE GLU GLU LEU GLN GLN GLU SEQRES 2 A 302 MET GLU ASP LEU ASP ALA ASP THR THR ILE THR VAL VAL SEQRES 3 A 302 GLN ARG GLU THR GLN LYS ALA ARG ILE ARG GLU GLN ILE SEQRES 4 A 302 GLU THR LEU ARG ALA GLN GLN MET VAL ARG PRO SER GLU SEQRES 5 A 302 ALA GLN LEU GLN PRO ASP VAL THR PRO THR GLN ILE VAL SEQRES 6 A 302 THR PHE GLU PRO PRO ARG VAL THR GLY PHE GLY ALA LEU SEQRES 7 A 302 TRP ILE PRO ARG GLN GLN ARG ASN TYR MET THR THR ALA SEQRES 8 A 302 TYR ILE GLU LYS ILE LYS ALA TYR VAL PRO HIS SER ASN SEQRES 9 A 302 LEU ILE GLU SER GLY LEU ALA SER GLU ALA GLN LEU THR SEQRES 10 A 302 SER TRP ILE GLU ASN THR CYS ARG ASP TYR GLN VAL SER SEQRES 11 A 302 MET ASP VAL PHE MET THR THR VAL LEU PRO ALA TRP ILE SEQRES 12 A 302 VAL ASN CYS ILE ILE ASN GLY THR SER GLN GLU ARG THR SEQRES 13 A 302 ASN GLU HIS THR TRP ARG ALA VAL ILE MET ALA ASN MET SEQRES 14 A 302 GLU ASP GLN GLU VAL LEU TYR TYR PRO ILE LYS PRO ILE SEQRES 15 A 302 ILE VAL ASN ALA GLN PRO THR LEU ARG GLN VAL MET ARG SEQRES 16 A 302 HIS PHE GLY GLU GLN ALA VAL ALA GLN TYR MET ASN SER SEQRES 17 A 302 LEU GLN ALA GLY LYS PRO PHE THR VAL LYS GLY ALA VAL SEQRES 18 A 302 THR ALA GLY TYR ALA ASN VAL GLN ASP ALA TRP LEU GLY SEQRES 19 A 302 ILE ASP PHE LEU ARG ASP THR MET GLN LEU THR THR LYS SEQRES 20 A 302 GLN MET GLU VAL LYS HIS GLN ILE ILE ALA ALA ASN VAL SEQRES 21 A 302 THR ARG ARG LYS ILE ARG VAL PHE ALA LEU ALA ALA PRO SEQRES 22 A 302 GLY ASP GLY ASP GLU LEU ASP THR GLU ARG HIS VAL VAL SEQRES 23 A 302 ASP ASP VAL ALA ARG GLY ARG HIS SER LEU ARG GLY ALA SEQRES 24 A 302 GLN LEU ASP SEQRES 1 B 5 U U U U U HELIX 1 AA1 PRO A 81 ARG A 85 5 5 HELIX 2 AA2 THR A 89 ALA A 98 1 10 HELIX 3 AA3 SER A 112 GLN A 128 1 17 HELIX 4 AA4 SER A 130 THR A 137 1 8 HELIX 5 AA5 THR A 137 ASN A 149 1 13 HELIX 6 AA6 SER A 152 HIS A 159 5 8 HELIX 7 AA7 ILE A 179 VAL A 184 1 6 HELIX 8 AA8 THR A 189 MET A 194 1 6 HELIX 9 AA9 PHE A 197 ALA A 211 1 15 HELIX 10 AB1 VAL A 217 GLY A 224 1 8 HELIX 11 AB2 THR A 245 ALA A 257 1 13 HELIX 12 AB3 ALA A 258 ARG A 262 5 5 SHEET 1 AA1 2 TRP A 161 MET A 166 0 SHEET 2 AA1 2 ASP A 171 TYR A 177 -1 O LEU A 175 N ALA A 163 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