HEADER VIRUS LIKE PARTICLE 18-OCT-22 8EU5 TITLE ACHETA DOMESTICUS SEGMENTED DENSOVIRUS HIGH BUOYANCY FRACTION 2 EMPTY TITLE 2 CAPSID STRUCTURE CAVEAT 8EU5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAPSID PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SOLENOPSIS INVICTA-ASSOCIATED DENSOVIRUS; SOURCE 3 ORGANISM_TAXID: 2810814; SOURCE 4 GENE: CP; SOURCE 5 EXPRESSION_SYSTEM: ACHETA DOMESTICUS; SOURCE 6 EXPRESSION_SYSTEM_COMMON: HOUSE CRICKET; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 6997 KEYWDS PARVOVIRUS, DENSOVIRUS, VIRUS CAPSID, VIRION, INSECT VIRUS, CAPSID, KEYWDS 2 INVERTEBRATE, VIRUS, VIRUS LIKE PARTICLE EXPDTA ELECTRON MICROSCOPY AUTHOR J.J.PENZES,R.MCKENNA,P.TIJSSEN REVDAT 3 19-JUN-24 8EU5 1 REMARK REVDAT 2 14-JUN-23 8EU5 1 SOURCE REVDAT 1 09-NOV-22 8EU5 0 JRNL AUTH J.J.PENZES,H.T.PHAM,P.CHIPMAN,E.SMITH,R.MCKENNA,P.TIJSSEN JRNL TITL STRUCTURAL AND MOLECULAR BIOLOGY OF ACHETA DOMESTICUS JRNL TITL 2 SEGMENTED DENSOVIRUS, THE FIRST PARVOVIRUS TO HARBOR A JRNL TITL 3 BIPARTITE GENOME JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : UCSF CHIMERA, COOT, PHENIX 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) : 3.100 REMARK 3 NUMBER OF PARTICLES : 48354 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 8EU5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-OCT-22. REMARK 100 THE DEPOSITION ID IS D_1000269206. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : UNCLASSIFIED DENSOVIRINAE REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 1.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL 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 : GATAN K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 4320.00 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) : 6000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : OTHER 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: MONOMERIC 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 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 GLU A 324 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O TRP A 105 H GLY A 108 1.51 REMARK 500 OD1 ASP A 304 H GLU A 305 1.54 REMARK 500 O ASP A 226 HH22 ARG A 290 1.55 REMARK 500 OE1 GLU A 213 HE1 TRP A 221 1.55 REMARK 500 O ILE A 128 H LYS A 328 1.55 REMARK 500 O LYS A 76 HD22 ASN A 116 1.57 REMARK 500 O PRO A 263 H GLN A 266 1.58 REMARK 500 O THR A 147 H LYS A 312 1.59 REMARK 500 OE2 GLU A 237 NZ LYS A 273 2.01 REMARK 500 O TYR A 144 OG1 THR A 217 2.04 REMARK 500 O ALA A 124 OG1 THR A 127 2.05 REMARK 500 OD1 ASN A 116 OG1 THR A 118 2.06 REMARK 500 OD1 ASP A 84 OG1 THR A 86 2.16 REMARK 500 O LYS A 76 ND2 ASN A 116 2.19 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 ALA A 90 -118.15 52.83 REMARK 500 THR A 185 -62.18 -121.80 REMARK 500 ASP A 307 73.30 56.17 REMARK 500 THR A 308 78.40 54.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-28604 RELATED DB: EMDB REMARK 900 ACHETA DOMESTICUS SEGMENTED DENSOVIRUS HIGH BUOYANCY FRACTION 2 REMARK 900 EMPTY CAPSID STRUCTURE DBREF1 8EU5 A 49 356 UNP A0A891H5C3_9VIRU DBREF2 8EU5 A A0A891H5C3 49 357 SEQADV 8EU5 A UNP A0A891H5C GLY 105 DELETION SEQADV 8EU5 LEU A 227 UNP A0A891H5C PHE 228 CONFLICT SEQADV 8EU5 CYS A 357 UNP A0A891H5C EXPRESSION TAG SEQADV 8EU5 VAL A 358 UNP A0A891H5C EXPRESSION TAG SEQADV 8EU5 PRO A 359 UNP A0A891H5C EXPRESSION TAG SEQADV 8EU5 TYR A 360 UNP A0A891H5C EXPRESSION TAG SEQADV 8EU5 GLU A 361 UNP A0A891H5C EXPRESSION TAG SEQADV 8EU5 THR A 362 UNP A0A891H5C EXPRESSION TAG SEQADV 8EU5 HIS A 363 UNP A0A891H5C EXPRESSION TAG SEQADV 8EU5 VAL A 364 UNP A0A891H5C EXPRESSION TAG SEQADV 8EU5 SER A 365 UNP A0A891H5C EXPRESSION TAG SEQADV 8EU5 GLN A 366 UNP A0A891H5C EXPRESSION TAG SEQRES 1 A 318 GLU GLY TYR GLY LYS HIS ILE THR SER MET HIS VAL ARG SEQRES 2 A 318 ASN ILE PHE ASN GLN GLY ASN GLN VAL ILE ARG ASN ILE SEQRES 3 A 318 VAL LYS GLN GLN ARG TYR GLU LEU LEU ASP PHE THR GLY SEQRES 4 A 318 THR GLU ALA GLY THR THR ASN LEU PRO LYS ILE ILE PRO SEQRES 5 A 318 TYR GLN CYS ILE TRP TRP ARG GLY LEU GLN ASN ALA ALA SEQRES 6 A 318 ASN VAL ASN GLN THR ILE ASN ASN MET ILE ALA LEU ASN SEQRES 7 A 318 THR ILE SER TYR GLY VAL ARG PHE LEU LYS ALA LYS LEU SEQRES 8 A 318 CYS ILE GLU VAL TYR ALA VAL THR ARG LYS ARG LEU ILE SEQRES 9 A 318 GLN THR GLY ALA THR SER TYR TYR THR ASP ASP PHE GLU SEQRES 10 A 318 GLN GLY GLN ASN LEU PHE ILE GLY TRP ALA ASP ARG LYS SEQRES 11 A 318 ALA GLU SER ILE PRO ILE THR THR PRO ALA ASP LEU ASP SEQRES 12 A 318 GLU THR LYS LEU THR VAL ALA ASN THR THR LEU PHE ASP SEQRES 13 A 318 ALA ASN ASN ASP ASN ILE THR LYS GLU GLU VAL PRO THR SEQRES 14 A 318 ARG GLU LYS TRP CYS HIS THR TRP ASP LEU ASP VAL LEU SEQRES 15 A 318 ASN HIS ASN TYR LEU TRP GLU PRO ASN ASN LEU ASP SER SEQRES 16 A 318 GLN TRP THR LEU ILE PRO GLY ALA GLN ALA VAL GLN PRO SEQRES 17 A 318 THR ALA THR PRO ILE GLY PRO THR TYR GLN GLU ILE VAL SEQRES 18 A 318 ILE ALA THR LYS ALA ILE GLY ALA ASN GLU SER ALA LEU SEQRES 19 A 318 VAL THR THR ILE GLN ASP ARG ARG SER TYR PRO ARG LEU SEQRES 20 A 318 MET LEU SER GLN PRO GLN ILE LYS ASP GLU THR ASP THR SEQRES 21 A 318 MET LYS PHE LYS TYR GLN ILE ARG ILE SER THR GLU LEU SEQRES 22 A 318 GLU MET GLU HIS HIS ILE LYS PRO ASP ILE ALA ASN PRO SEQRES 23 A 318 TRP LEU THR ARG GLN THR LEU PRO LEU PRO ALA LEU SER SEQRES 24 A 318 GLY ASP GLY THR THR ARG TYR VAL PRO CYS VAL PRO TYR SEQRES 25 A 318 GLU THR HIS VAL SER GLN HELIX 1 AA1 GLU A 89 THR A 93 5 5 HELIX 2 AA2 PRO A 100 GLY A 108 5 9 HELIX 3 AA3 ASN A 116 ILE A 128 1 13 HELIX 4 AA4 THR A 186 ASP A 191 5 6 HELIX 5 AA5 GLY A 262 GLN A 266 5 5 HELIX 6 AA6 ASN A 333 ARG A 338 5 6 SHEET 1 AA1 4 ILE A 74 ASP A 84 0 SHEET 2 AA1 4 PHE A 311 ILE A 327 -1 O THR A 319 N GLN A 77 SHEET 3 AA1 4 SER A 129 LEU A 151 -1 N THR A 147 O LYS A 312 SHEET 4 AA1 4 TYR A 160 ASP A 163 -1 O THR A 161 N ARG A 150 SHEET 1 AA2 4 ILE A 74 ASP A 84 0 SHEET 2 AA2 4 PHE A 311 ILE A 327 -1 O THR A 319 N GLN A 77 SHEET 3 AA2 4 SER A 129 LEU A 151 -1 N THR A 147 O LYS A 312 SHEET 4 AA2 4 GLU A 219 TRP A 225 -1 O TRP A 225 N ALA A 137 SHEET 1 AA3 4 LYS A 97 ILE A 99 0 SHEET 2 AA3 4 LEU A 295 SER A 298 -1 O LEU A 297 N LYS A 97 SHEET 3 AA3 4 LEU A 170 TRP A 174 -1 N GLY A 173 O MET A 296 SHEET 4 AA3 4 THR A 211 VAL A 215 -1 O VAL A 215 N LEU A 170 SHEET 1 AA4 2 SER A 181 ILE A 184 0 SHEET 2 AA4 2 ARG A 353 PRO A 356 -1 O ARG A 353 N ILE A 184 SHEET 1 AA5 2 LEU A 235 TRP A 236 0 SHEET 2 AA5 2 THR A 340 LEU A 341 1 O LEU A 341 N LEU A 235 SHEET 1 AA6 2 ILE A 268 LYS A 273 0 SHEET 2 AA6 2 ALA A 281 ILE A 286 -1 O THR A 285 N VAL A 269 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