HEADER VIRUS 10-NOV-15 5FN1 TITLE ELECTRON CRYO-MICROSCOPY OF FILAMENTOUS FLEXIBLE VIRUS PEPMV (PEPINO TITLE 2 MOSAIC VIRUS) COMPND MOL_ID: 1; COMPND 2 MOLECULE: COAT PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PEPINO MOSAIC VIRUS COAT PROTEIN; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-R(*UP*UP*UP*UP*UP)-3'; COMPND 7 CHAIN: B; COMPND 8 SYNONYM: PEPINO MOSAIC VIRUS SSRNA MODEL SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PEPINO MOSAIC VIRUS; SOURCE 3 ORGANISM_TAXID: 112229; SOURCE 4 STRAIN: PEPMV-SP13; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: PEPINO MOSAIC VIRUS; SOURCE 7 ORGANISM_TAXID: 112229; SOURCE 8 STRAIN: PEPMV-SP13 KEYWDS VIRUS, PEPMV, FILAMENTOUS PLANT VIRUS, POTEXVIRUS, HELICAL SYMMETRY EXPDTA ELECTRON MICROSCOPY AUTHOR X.AGIRREZABALA,E.MENDEZ-LOPEZ,G.LASSO,M.A.SANCHEZ-PINA,M.A.ARANDA, AUTHOR 2 M.VALLE REVDAT 3 30-AUG-17 5FN1 1 REMARK REVDAT 2 21-DEC-16 5FN1 1 JRNL REVDAT 1 30-DEC-15 5FN1 0 JRNL AUTH X.AGIRREZABALA,E.MENDEZ-LOPEZ,G.LASSO,M.A.SANCHEZ-PINA, JRNL AUTH 2 M.ARANDA,M.VALLE JRNL TITL THE NEAR-ATOMIC CRYOEM STRUCTURE OF A FLEXIBLE FILAMENTOUS JRNL TITL 2 PLANT VIRUS SHOWS HOMOLOGY OF ITS COAT PROTEIN WITH JRNL TITL 3 NUCLEOPROTEINS OF ANIMAL VIRUSES. JRNL REF ELIFE V. 4 11795 2015 JRNL REFN ESSN 2050-084X JRNL PMID 26673077 JRNL DOI 10.7554/ELIFE.11795 REMARK 2 REMARK 2 RESOLUTION. 3.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CTFTILT, EMAN, SPRING 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) : 3.900 REMARK 3 NUMBER OF PARTICLES : NULL REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD REMARK 3 -3236. (DEPOSITION ID: 14021). REMARK 4 REMARK 4 5FN1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE. REMARK 100 THE DEPOSITION ID IS D_1290065487. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : VITREOUS ICE REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : FILAMENT REMARK 245 PARTICLE TYPE : HELICAL REMARK 245 NAME OF SAMPLE : PEPINO MOSAIC VIRUS, PEPMV REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : HOLEY CARBON REMARK 245 SAMPLE VITRIFICATION DETAILS : VITRIFICATION 1 -- CRYOGEN- REMARK 245 ETHANE, HUMIDITY- 100, REMARK 245 INSTRUMENT- FEI VITROBOT MARK REMARK 245 II, REMARK 245 SAMPLE BUFFER : 100 MM TRIS-CITRIC ACID REMARK 245 PH : 8.00 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 20-FEB-14 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 II (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3500.00 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) : 25.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 59000 REMARK 245 CALIBRATED MAGNIFICATION : 102987 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 300 THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR REMARK 300 HELICAL SYMMETRY WITH THE FOLLOWING PARAMETERS: REMARK 300 ROTATION PER SUBUNIT (TWIST) = -41.10 DEGREES REMARK 300 RISE PER SUBUNIT (HEIGHT) = 3.95 ANGSTROMS 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 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 0.985109 -0.171929 0.000000 0.00000 REMARK 350 BIOMT2 1 0.171929 0.985109 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 -35.55000 REMARK 350 BIOMT1 2 0.855364 0.518027 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.518027 0.855364 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 -31.60000 REMARK 350 BIOMT1 3 0.304033 0.952661 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.952661 0.304033 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 -27.65000 REMARK 350 BIOMT1 4 -0.397148 0.917755 0.000000 0.00000 REMARK 350 BIOMT2 4 -0.917755 -0.397148 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 -23.70000 REMARK 350 BIOMT1 5 -0.902585 0.430511 0.000000 0.00000 REMARK 350 BIOMT2 5 -0.430511 -0.902585 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 -19.75000 REMARK 350 BIOMT1 6 -0.963163 -0.268920 0.000000 0.00000 REMARK 350 BIOMT2 6 0.268920 -0.963163 0.000000 0.00000 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 -15.80000 REMARK 350 BIOMT1 7 -0.549023 -0.835807 0.000000 0.00000 REMARK 350 BIOMT2 7 0.835807 -0.549023 0.000000 0.00000 REMARK 350 BIOMT3 7 0.000000 0.000000 1.000000 -11.85000 REMARK 350 BIOMT1 8 0.135716 -0.990748 0.000000 0.00000 REMARK 350 BIOMT2 8 0.990748 0.135716 0.000000 0.00000 REMARK 350 BIOMT3 8 0.000000 0.000000 1.000000 -7.90000 REMARK 350 BIOMT1 9 0.753563 -0.657375 0.000000 0.00000 REMARK 350 BIOMT2 9 0.657375 0.753563 0.000000 0.00000 REMARK 350 BIOMT3 9 0.000000 0.000000 1.000000 -3.95000 REMARK 350 BIOMT1 10 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 10 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 10 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 11 0.753563 0.657375 0.000000 0.00000 REMARK 350 BIOMT2 11 -0.657375 0.753563 0.000000 0.00000 REMARK 350 BIOMT3 11 0.000000 0.000000 1.000000 3.95000 REMARK 350 BIOMT1 12 0.135716 0.990748 0.000000 0.00000 REMARK 350 BIOMT2 12 -0.990748 0.135716 0.000000 0.00000 REMARK 350 BIOMT3 12 0.000000 0.000000 1.000000 7.90000 REMARK 350 BIOMT1 13 -0.549023 0.835807 0.000000 0.00000 REMARK 350 BIOMT2 13 -0.835807 -0.549023 0.000000 0.00000 REMARK 350 BIOMT3 13 0.000000 0.000000 1.000000 11.85000 REMARK 350 BIOMT1 14 -0.963163 0.268920 0.000000 0.00000 REMARK 350 BIOMT2 14 -0.268920 -0.963163 0.000000 0.00000 REMARK 350 BIOMT3 14 0.000000 0.000000 1.000000 15.80000 REMARK 350 BIOMT1 15 -0.902585 -0.430511 0.000000 0.00000 REMARK 350 BIOMT2 15 0.430511 -0.902585 0.000000 0.00000 REMARK 350 BIOMT3 15 0.000000 0.000000 1.000000 19.75000 REMARK 350 BIOMT1 16 -0.397148 -0.917755 0.000000 0.00000 REMARK 350 BIOMT2 16 0.917755 -0.397148 0.000000 0.00000 REMARK 350 BIOMT3 16 0.000000 0.000000 1.000000 23.70000 REMARK 350 BIOMT1 17 0.304033 -0.952661 0.000000 0.00000 REMARK 350 BIOMT2 17 0.952661 0.304033 0.000000 0.00000 REMARK 350 BIOMT3 17 0.000000 0.000000 1.000000 27.65000 REMARK 350 BIOMT1 18 0.855364 -0.518027 0.000000 0.00000 REMARK 350 BIOMT2 18 0.518027 0.855364 0.000000 0.00000 REMARK 350 BIOMT3 18 0.000000 0.000000 1.000000 31.60000 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 PRO A 2 REMARK 465 ASP A 3 REMARK 465 THR A 4 REMARK 465 THR A 5 REMARK 465 PRO A 6 REMARK 465 VAL A 7 REMARK 465 ALA A 8 REMARK 465 ALA A 9 REMARK 465 THR A 10 REMARK 465 SER A 11 REMARK 465 SER A 12 REMARK 465 ALA A 13 REMARK 465 PRO A 14 REMARK 465 PRO A 15 REMARK 465 THR A 16 REMARK 465 ALA A 17 REMARK 465 LYS A 18 REMARK 465 ASP A 19 REMARK 465 ALA A 20 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 ALA A 24 72.77 70.63 REMARK 500 SER A 29 -51.50 -177.38 REMARK 500 LYS A 44 -85.99 51.61 REMARK 500 TYR A 45 -89.25 -134.09 REMARK 500 VAL A 46 -79.30 -138.27 REMARK 500 SER A 47 56.66 -161.41 REMARK 500 THR A 75 -56.28 -134.48 REMARK 500 ASP A 88 -77.92 -71.39 REMARK 500 GLN A 96 84.36 64.60 REMARK 500 ILE A 98 84.80 39.68 REMARK 500 ALA A 106 -43.86 80.53 REMARK 500 GLN A 175 77.38 43.87 REMARK 500 THR A 207 63.99 69.60 REMARK 500 THR A 213 -128.12 61.24 REMARK 500 LEU A 214 -59.78 74.21 REMARK 500 HIS A 221 -72.85 57.32 REMARK 500 MET A 222 -77.20 62.31 REMARK 500 ALA A 225 55.22 -94.94 REMARK 500 ASN A 226 166.04 63.43 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-3236 RELATED DB: EMDB DBREF 5FN1 A 1 237 UNP Q71FK2 Q71FK2_9VIRU 1 237 DBREF 5FN1 B 1 5 PDB 5FN1 5FN1 1 5 SEQRES 1 A 237 MET PRO ASP THR THR PRO VAL ALA ALA THR SER SER ALA SEQRES 2 A 237 PRO PRO THR ALA LYS ASP ALA GLY ALA LYS ALA PRO SER SEQRES 3 A 237 ASP PHE SER ASN PRO ASN THR ALA PRO SER LEU SER ASP SEQRES 4 A 237 LEU LYS LYS VAL LYS TYR VAL SER THR VAL THR SER VAL SEQRES 5 A 237 ALA THR PRO ALA GLU ILE GLU ALA LEU GLY LYS ILE PHE SEQRES 6 A 237 THR ALA MET GLY LEU ALA ALA ASN GLU THR GLY PRO ALA SEQRES 7 A 237 MET TRP ASP LEU ALA ARG ALA TYR ALA ASP VAL GLN SER SEQRES 8 A 237 SER LYS SER ALA GLN LEU ILE GLY ALA THR PRO SER ASN SEQRES 9 A 237 PRO ALA LEU SER ARG ARG ALA LEU ALA ALA GLN PHE ASP SEQRES 10 A 237 ARG ILE ASN ILE THR PRO ARG GLN PHE CYS MET TYR PHE SEQRES 11 A 237 ALA LYS VAL VAL TRP ASN ILE LEU LEU ASP SER ASN ILE SEQRES 12 A 237 PRO PRO ALA ASN TRP ALA LYS LEU GLY TYR GLN GLU ASP SEQRES 13 A 237 THR LYS PHE ALA ALA PHE ASP PHE PHE ASP GLY VAL THR SEQRES 14 A 237 ASN PRO ALA SER LEU GLN PRO ALA ASP GLY LEU ILE ARG SEQRES 15 A 237 GLN PRO ASN GLU LYS GLU LEU ALA ALA HIS SER VAL ALA SEQRES 16 A 237 LYS TYR GLY ALA LEU ALA ARG GLN LYS ILE SER THR GLY SEQRES 17 A 237 ASN TYR ILE THR THR LEU GLY GLU VAL THR ARG GLY HIS SEQRES 18 A 237 MET GLY GLY ALA ASN THR MET TYR ALA ILE ASP ALA PRO SEQRES 19 A 237 PRO GLU LEU SEQRES 1 B 5 U U U U U HELIX 1 1 ALA A 24 PHE A 28 5 5 HELIX 2 2 THR A 33 LYS A 41 1 9 HELIX 3 3 THR A 54 GLY A 69 1 16 HELIX 4 4 THR A 75 VAL A 89 1 15 HELIX 5 5 SER A 108 PHE A 116 1 9 HELIX 6 6 ASP A 117 ASN A 120 5 4 HELIX 7 7 THR A 122 MET A 128 1 7 HELIX 8 8 PHE A 130 ASP A 140 1 11 HELIX 9 9 GLN A 154 LYS A 158 5 5 HELIX 10 10 ASN A 185 SER A 206 1 22 HELIX 11 11 THR A 227 ALA A 233 1 7 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