HEADER VIRUS 13-NOV-18 6I5A TITLE TOBACCO MOSAIC VIRUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAPSID PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: COAT PROTEIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TOBACCO MOSAIC VIRUS (STRAIN VULGARE); SOURCE 3 ORGANISM_COMMON: TMV; SOURCE 4 ORGANISM_TAXID: 12243; SOURCE 5 STRAIN: VULGARE KEYWDS TMV, HELICAL VIRUS, COAT PROTEIN, PLANT PATHOGEN, VIRUS EXPDTA ELECTRON MICROSCOPY AUTHOR B.SONG,V.FLEGLER,C.MAKBUL,T.RASMUSSEN,B.BOTTCHER REVDAT 4 15-MAY-24 6I5A 1 REMARK REVDAT 3 18-DEC-19 6I5A 1 SCALE REVDAT 2 01-MAY-19 6I5A 1 JRNL REVDAT 1 20-FEB-19 6I5A 0 JRNL AUTH B.SONG,J.LENHART,V.J.FLEGLER,C.MAKBUL,T.RASMUSSEN,B.BOTTCHER JRNL TITL CAPABILITIES OF THE FALCON III DETECTOR FOR SINGLE-PARTICLE JRNL TITL 2 STRUCTURE DETERMINATION. JRNL REF ULTRAMICROSCOPY V. 203 145 2019 JRNL REFN ISSN 0304-3991 JRNL PMID 30738626 JRNL DOI 10.1016/J.ULTRAMIC.2019.01.002 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, EPU, RELION, WARP, WARP, REMARK 3 RELION, RELION, RELION, 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 : RECIPROCAL REMARK 3 REFINEMENT PROTOCOL : AB INITIO MODEL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : 105.000 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) : 2.300 REMARK 3 NUMBER OF PARTICLES : 91927 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 6I5A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-NOV-18. REMARK 100 THE DEPOSITION ID IS D_1200012852. 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) : 10.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : QUANTIFOIL 400 MESH COPPER REMARK 245 GRIDS R 1.2/1.3 WERE USED REMARK 245 (QUANTIFOIL MICRO TOOLS GMBH, REMARK 245 JENA, GERMANY). GRIDS WERE GLOW REMARK 245 DISCHARGED IN AIR AT A PRESSURE REMARK 245 OF 2.2X10-2 TORR FOR 2 MIN AT REMARK 245 MEDIUM POWER WITH A HARRICK REMARK 245 PLASMA CLEANER (PDC-002). REMARK 245 SUBSEQUENTLY, 3-4 UL OF THE REMARK 245 SAMPLE WAS PIPETTED ONTO THE REMARK 245 GLOW DISCHARGED GRIDS AND REMARK 245 PLUNGE FROZEN IN LIQUID ETHANE REMARK 245 WITH A VITROBOT IV (FEI). THE REMARK 245 SAMPLE CHAMBER OF THE VITROBOT REMARK 245 WAS MAINTAINED AT 4C AND 100% REMARK 245 HUMIDITY. WAIT TIME BETWEEN REMARK 245 SAMPLE APPLICATION AND BLOTTING REMARK 245 WAS 45 S, THE DRAIN TIME 0 S, REMARK 245 THE BLOT TIME 3 S AND THE BLOT REMARK 245 FORCE 0. 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 : 1001 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) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1800.00 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) : 5500.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 75000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 155 REMARK 465 GLY A 156 REMARK 465 PRO A 157 REMARK 465 ALA A 158 REMARK 465 THR A 159 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 SER A 56 -84.09 -123.97 REMARK 500 ARG A 93 -71.03 -34.08 REMARK 500 ASN A 102 99.51 70.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-4413 RELATED DB: EMDB REMARK 900 TOBACCO MOSAIC VIRUS DBREF 6I5A A 1 159 UNP P69687 CAPSD_TMV 1 159 SEQRES 1 A 159 MET SER TYR SER ILE THR THR PRO SER GLN PHE VAL PHE SEQRES 2 A 159 LEU SER SER ALA TRP ALA ASP PRO ILE GLU LEU ILE ASN SEQRES 3 A 159 LEU CYS THR ASN ALA LEU GLY ASN GLN PHE GLN THR GLN SEQRES 4 A 159 GLN ALA ARG THR VAL VAL GLN ARG GLN PHE SER GLU VAL SEQRES 5 A 159 TRP LYS PRO SER PRO GLN VAL THR VAL ARG PHE PRO ASP SEQRES 6 A 159 SER ASP PHE LYS VAL TYR ARG TYR ASN ALA VAL LEU ASP SEQRES 7 A 159 PRO LEU VAL THR ALA LEU LEU GLY ALA PHE ASP THR ARG SEQRES 8 A 159 ASN ARG ILE ILE GLU VAL GLU ASN GLN ALA ASN PRO THR SEQRES 9 A 159 THR ALA GLU THR LEU ASP ALA THR ARG ARG VAL ASP ASP SEQRES 10 A 159 ALA THR VAL ALA ILE ARG SER ALA ILE ASN ASN LEU ILE SEQRES 11 A 159 VAL GLU LEU ILE ARG GLY THR GLY SER TYR ASN ARG SER SEQRES 12 A 159 SER PHE GLU SER SER SER GLY LEU VAL TRP THR SER GLY SEQRES 13 A 159 PRO ALA THR HELIX 1 AA1 THR A 7 SER A 15 5 9 HELIX 2 AA2 ASP A 20 LEU A 32 1 13 HELIX 3 AA3 THR A 38 VAL A 52 1 15 HELIX 4 AA4 VAL A 76 PHE A 88 1 13 HELIX 5 AA5 ASN A 92 VAL A 97 1 6 HELIX 6 AA6 THR A 104 GLY A 136 1 33 HELIX 7 AA7 ASN A 141 GLY A 150 1 10 SHEET 1 AA1 3 TRP A 18 ALA A 19 0 SHEET 2 AA1 3 LYS A 69 TYR A 71 -1 O VAL A 70 N ALA A 19 SHEET 3 AA1 3 SER A 139 TYR A 140 -1 O TYR A 140 N LYS A 69 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