HEADER VIRUS 26-OCT-21 7Q2R TITLE CRYO IDPC-STEM STRUCTURE RECORDED WITH CSA 4.0 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAPSID PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: COAT PROTEIN; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: RNA (5'-R(P*GP*AP*A)-3'); COMPND 7 CHAIN: B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TOBACCO MOSAIC VIRUS (VULGARE); SOURCE 3 ORGANISM_TAXID: 12243; SOURCE 4 STRAIN: VULGARE; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: TOBACCO MOSAIC VIRUS (VULGARE); SOURCE 7 ORGANISM_TAXID: 12243 KEYWDS TOBACCO MOSAIC VIRUS, RNA VIRUS, VIRUS EXPDTA ELECTRON MICROSCOPY AUTHOR C.SACHSE,M.L.LEIDL REVDAT 2 17-JUL-24 7Q2R 1 REMARK REVDAT 1 21-SEP-22 7Q2R 0 JRNL AUTH I.LAZIC,M.WIRIX,M.L.LEIDL,F.DE HAAS,D.MANN,M.BECKERS, JRNL AUTH 2 E.V.PECHNIKOVA,K.MULLER-CASPARY,R.EGOAVIL,E.G.T.BOSCH, JRNL AUTH 3 C.SACHSE JRNL TITL SINGLE-PARTICLE CRYO-EM STRUCTURES FROM IDPC-STEM AT JRNL TITL 2 NEAR-ATOMIC RESOLUTION. JRNL REF NAT.METHODS V. 19 1126 2022 JRNL REFN ESSN 1548-7105 JRNL PMID 36064775 JRNL DOI 10.1038/S41592-022-01586-0 REMARK 2 REMARK 2 RESOLUTION. 3.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : EMAN2, UCSF CHIMERA, RELION REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 4UDV REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT 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) : 3.500 REMARK 3 NUMBER OF PARTICLES : 2224 REMARK 3 CTF CORRECTION METHOD : NONE REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 7Q2R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-OCT-21. REMARK 100 THE DEPOSITION ID IS D_1292118892. 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 : HELICAL ARRAY REMARK 245 PARTICLE TYPE : HELICAL REMARK 245 NAME OF SAMPLE : TOBACCO MOSAIC VIRUS REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 90.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : BLOT FORCE OF +10 AND A REMARK 245 DURATION FOR BLOTTING OF 10 REMARK 245 SECONDS REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.40 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 : OTHER REMARK 245 MINIMUM DEFOCUS (NM) : 0.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 0.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : OTHER REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 3500.00 REMARK 245 ILLUMINATION MODE : OTHER 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 : IDPC-STEM 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 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 THR A 5 -78.61 -95.11 REMARK 500 SER A 8 34.45 -89.44 REMARK 500 LEU A 13 34.11 -97.72 REMARK 500 SER A 15 83.04 -65.27 REMARK 500 ALA A 16 19.77 -150.05 REMARK 500 SER A 55 -59.30 -129.40 REMARK 500 GLN A 99 -92.32 -117.13 REMARK 500 ARG A 141 3.28 86.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-13781 RELATED DB: EMDB REMARK 900 CRYO IDPC-STEM STRUCTURE RECORDED WITH CSA 4.0 DBREF 7Q2R A 1 153 UNP P69687 CAPSD_TMV 2 154 DBREF 7Q2R B 1 3 PDB 7Q2R 7Q2R 1 3 SEQRES 1 A 153 SER TYR SER ILE THR THR PRO SER GLN PHE VAL PHE LEU SEQRES 2 A 153 SER SER ALA TRP ALA ASP PRO ILE GLU LEU ILE ASN LEU SEQRES 3 A 153 CYS THR ASN ALA LEU GLY ASN GLN PHE GLN THR GLN GLN SEQRES 4 A 153 ALA ARG THR VAL VAL GLN ARG GLN PHE SER GLU VAL TRP SEQRES 5 A 153 LYS PRO SER PRO GLN VAL THR VAL ARG PHE PRO ASP SER SEQRES 6 A 153 ASP PHE LYS VAL TYR ARG TYR ASN ALA VAL LEU ASP PRO SEQRES 7 A 153 LEU VAL THR ALA LEU LEU GLY ALA PHE ASP THR ARG ASN SEQRES 8 A 153 ARG ILE ILE GLU VAL GLU ASN GLN ALA ASN PRO THR THR SEQRES 9 A 153 ALA GLU THR LEU ASP ALA THR ARG ARG VAL ASP ASP ALA SEQRES 10 A 153 THR VAL ALA ILE ARG SER ALA ILE ASN ASN LEU ILE VAL SEQRES 11 A 153 GLU LEU ILE ARG GLY THR GLY SER TYR ASN ARG SER SER SEQRES 12 A 153 PHE GLU SER SER SER GLY LEU VAL TRP THR SEQRES 1 B 3 G A A HELIX 1 AA1 PHE A 10 SER A 14 5 5 HELIX 2 AA2 ASP A 19 ASN A 29 1 11 HELIX 3 AA3 ALA A 30 GLY A 32 5 3 HELIX 4 AA4 THR A 37 SER A 49 1 13 HELIX 5 AA5 VAL A 75 PHE A 87 1 13 HELIX 6 AA6 ARG A 92 GLU A 97 1 6 HELIX 7 AA7 THR A 103 ILE A 133 1 31 HELIX 8 AA8 SER A 142 GLY A 149 1 8 SHEET 1 AA1 3 TRP A 17 ALA A 18 0 SHEET 2 AA1 3 LYS A 68 TYR A 70 -1 O VAL A 69 N ALA A 18 SHEET 3 AA1 3 SER A 138 TYR A 139 -1 O TYR A 139 N LYS A 68 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