HEADER VIRUS LIKE PARTICLE 06-MAY-21 7OG6 TITLE STRUCTURE OF ALTERNANTHERA MOSAIC VLP BY CRYOEM COMPND MOL_ID: 1; COMPND 2 MOLECULE: COAT PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: RNA (5'-R(P*UP*UP*UP*UP*U)-3'); COMPND 7 CHAIN: R; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ALTERNANTHERA MOSAIC VIRUS; SOURCE 3 ORGANISM_TAXID: 85454; SOURCE 4 GENE: CP; SOURCE 5 EXPRESSION_SYSTEM: NICOTIANA BENTHAMIANA; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 4100; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: ALTERNANTHERA MOSAIC VIRUS; SOURCE 9 ORGANISM_TAXID: 85454; SOURCE 10 EXPRESSION_SYSTEM: NICOTIANA BENTHAMIANA; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 4100 KEYWDS POTEXVIRUS, VIRUS LIKE PARTICLE, VLP. EXPDTA ELECTRON MICROSCOPY AUTHOR M.J.BYRNE,N.A.RANSON,G.P.LOMONOSSOFF,E.C.THUENEMANN REVDAT 2 10-JUL-24 7OG6 1 REMARK REVDAT 1 23-JUN-21 7OG6 0 JRNL AUTH E.C.THUENEMANN,M.J.BYRNE,H.PEYRET,K.SAUNDERS, JRNL AUTH 2 R.CASTELLS-GRAELLS,I.FERRIOL,M.SANTONI,J.F.C.STEELE, JRNL AUTH 3 N.A.RANSON,L.AVESANI,J.J.LOPEZ-MOYA,G.P.LOMONOSSOFF JRNL TITL A REPLICATING VIRAL VECTOR GREATLY ENHANCES ACCUMULATION OF JRNL TITL 2 HELICAL VIRUS-LIKE PARTICLES IN PLANTS. JRNL REF VIRUSES V. 13 2021 JRNL REFN ESSN 1999-4915 JRNL PMID 34064959 JRNL DOI 10.3390/V13050885 REMARK 2 REMARK 2 RESOLUTION. 3.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : 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) : 3.300 REMARK 3 NUMBER OF PARTICLES : 32018 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 7OG6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-MAY-21. REMARK 100 THE DEPOSITION ID IS D_1292115724. 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 : ALTERNANTHERA MOSAIC 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 : 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 : NULL 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) : NULL REMARK 245 MAXIMUM DEFOCUS (NM) : NULL 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) : 111.00 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, R 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 MET A 1 REMARK 465 SER A 2 REMARK 465 THR A 3 REMARK 465 PRO A 4 REMARK 465 PRO A 204 REMARK 465 PRO A 205 REMARK 465 PRO A 206 REMARK 465 GLU A 207 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 TYR A 202 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 GLN A 7 71.36 58.25 REMARK 500 HIS A 19 115.73 -161.33 REMARK 500 ASP A 112 10.86 58.83 REMARK 500 ASP A 134 -178.62 -67.59 REMARK 500 PHE A 135 20.25 49.41 REMARK 500 PHE A 172 46.02 -91.92 REMARK 500 ASN A 180 58.47 -96.49 REMARK 500 PRO A 198 63.99 -65.77 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PRO A 198 THR A 199 148.52 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-12879 RELATED DB: EMDB REMARK 900 STRUCTURE OF ALTERNANTHERA MOSAIC VLP BY CRYOEM DBREF 7OG6 A 1 207 UNP Q52Z61 Q52Z61_9VIRU 1 207 DBREF 7OG6 R 42 46 PDB 7OG6 7OG6 42 46 SEQRES 1 A 207 MET SER THR PRO PHE PRO GLN VAL THR GLN GLU GLN MET SEQRES 2 A 207 ASN ALA PHE THR PRO HIS THR THR SER ASN LEU LEU PRO SEQRES 3 A 207 SER PRO GLU GLN LEU THR THR ILE ALA ASN LEU LEU VAL SEQRES 4 A 207 ALA ALA LYS VAL PRO ALA ALA SER THR THR THR ILE ALA SEQRES 5 A 207 LEU GLU LEU VAL ASN PHE CYS TYR ASP ASN GLY SER SER SEQRES 6 A 207 THR TYR THR ALA VAL VAL GLY PRO SER SER LEU ALA GLU SEQRES 7 A 207 VAL SER LEU SER GLN VAL ALA ASN ILE VAL LYS ALA SER SEQRES 8 A 207 GLY THR SER LEU ARG LYS PHE CYS ARG PHE PHE ALA PRO SEQRES 9 A 207 ILE ILE TRP ASN LEU ARG THR ASP LYS THR PRO PRO ALA SEQRES 10 A 207 ASN TRP GLU ALA ASN GLY PHE LYS PRO THR GLU LYS PHE SEQRES 11 A 207 ALA ALA PHE ASP PHE PHE ASP GLY VAL GLU ASN PRO ALA SEQRES 12 A 207 ALA MET GLN PRO PRO GLY GLY LEU VAL ARG THR PRO SER SEQRES 13 A 207 GLN ALA GLU ARG ILE ALA ASN ALA THR ASN LYS GLN VAL SEQRES 14 A 207 ASN LEU PHE GLN ALA ALA ALA GLN ASP ASN ASN PHE ALA SEQRES 15 A 207 SER ASN SER ALA PHE ILE THR LYS GLY GLN LEU SER SER SEQRES 16 A 207 ASN SER PRO THR ILE GLN TYR LEU PRO PRO PRO GLU SEQRES 1 R 5 U U U U U HELIX 1 AA1 LEU A 31 ALA A 40 1 10 HELIX 2 AA2 THR A 48 GLY A 63 1 16 HELIX 3 AA3 SER A 80 LYS A 89 1 10 HELIX 4 AA4 SER A 94 THR A 111 1 18 HELIX 5 AA5 LYS A 125 ALA A 132 5 8 HELIX 6 AA6 PHE A 135 VAL A 139 5 5 HELIX 7 AA7 SER A 156 ALA A 175 1 20 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