HEADER VIRAL PROTEIN 15-OCT-24 9JZI TITLE TETRAMERIC COMPLEX (3D CLASS 1) OF THE BORNA DISEASE VIRUS 1 TITLE 2 NUCLEOPROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOPROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: N PROTEIN,NUCLEOCAPSID PROTEIN,P38,P40; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: FULL-LENGTH NUCLEOPROTEIN OF THE BORNA DISEASE VIRUS 1 COMPND 7 STRAIN HE/80 WITH N-TERMINAL HEXAHISTIDINE TAG SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BORNA DISEASE VIRUS 1; SOURCE 3 ORGANISM_TAXID: 1714621; SOURCE 4 STRAIN: HE/80; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NUCLEOPROTEIN, COMPLEX, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR Y.SUGITA,Y.HIRAI,M.HORIE REVDAT 1 11-MAR-26 9JZI 0 JRNL AUTH Y.SUGITA,Y.HIRAI,M.HORIE JRNL TITL TETRAMERIC NUCLEOPROTEIN COMPLEX OF THE BORNA DISEASE VIRUS JRNL TITL 2 1 NUCLEOPROTEIN (3D CLASS 1) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.09 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : TOPAZ, SERIALEM, CRYOSPARC, UCSF REMARK 3 CHIMERAX, COOT, SERVALCAT, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC, CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 1N93 REMARK 3 REFINEMENT SPACE : RECIPROCAL REMARK 3 REFINEMENT PROTOCOL : AB INITIO MODEL 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) : 3.090 REMARK 3 NUMBER OF PARTICLES : 154548 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 9JZI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-OCT-24. REMARK 100 THE DEPOSITION ID IS D_1300050767. 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 : NUCLEOPROTEIN COMPLEX OF THE REMARK 245 BORNA DISEASE VIRUS 1 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 : 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 600.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1600.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 0.06 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 4000.00 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: TETRAMERIC 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 350 BIOMT1 2 0.000000 -1.000000 0.000000 121.81710 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 121.81710 REMARK 350 BIOMT2 3 0.000000 -1.000000 0.000000 121.81710 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 -1.000000 0.000000 0.000000 121.81710 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 5 0.000000 -1.000000 0.000000 121.81710 REMARK 350 BIOMT2 5 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 6 -1.000000 0.000000 0.000000 121.81710 REMARK 350 BIOMT2 6 0.000000 -1.000000 0.000000 121.81710 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 7 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 7 -1.000000 0.000000 0.000000 121.81710 REMARK 350 BIOMT3 7 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 -22 REMARK 465 GLY A -21 REMARK 465 SER A -20 REMARK 465 SER A -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 SER A -12 REMARK 465 SER A -11 REMARK 465 GLY A -10 REMARK 465 LEU A -9 REMARK 465 VAL A -8 REMARK 465 PRO A -7 REMARK 465 ARG A -6 REMARK 465 GLY A -5 REMARK 465 SER A -4 REMARK 465 HIS A -3 REMARK 465 MET A -2 REMARK 465 LEU A -1 REMARK 465 GLU A 0 REMARK 465 MET A 1 REMARK 465 PRO A 2 REMARK 465 PRO A 3 REMARK 465 LYS A 4 REMARK 465 ARG A 5 REMARK 465 ARG A 6 REMARK 465 LEU A 7 REMARK 465 VAL A 8 REMARK 465 ASP A 9 REMARK 465 ASP A 10 REMARK 465 ALA A 11 REMARK 465 ASP A 12 REMARK 465 ALA A 13 REMARK 465 MET A 14 REMARK 465 GLU A 15 REMARK 465 ASP A 16 REMARK 465 GLN A 17 REMARK 465 ASP A 18 REMARK 465 LEU A 19 REMARK 465 TYR A 20 REMARK 465 GLU A 21 REMARK 465 PRO A 22 REMARK 465 PRO A 23 REMARK 465 ARG A 107 REMARK 465 GLY A 108 REMARK 465 GLU A 109 REMARK 465 GLN A 110 REMARK 465 MET A 317 REMARK 465 ALA A 318 REMARK 465 GLY A 319 REMARK 465 TYR A 320 REMARK 465 ARG A 321 REMARK 465 ALA A 322 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 ASP A 278 -2.02 71.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 66 0.13 SIDE CHAIN REMARK 500 ARG A 342 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-61914 RELATED DB: EMDB REMARK 900 TETRAMERIC COMPLEX (3D CLASS 1) OF THE BORNA DISEASE VIRUS 1 REMARK 900 NUCLEOPROTEIN BOUND TO RNA DBREF 9JZI A 1 370 UNP P0C796 NCAP_BDV1 1 370 SEQADV 9JZI MET A -22 UNP P0C796 INITIATING METHIONINE SEQADV 9JZI GLY A -21 UNP P0C796 EXPRESSION TAG SEQADV 9JZI SER A -20 UNP P0C796 EXPRESSION TAG SEQADV 9JZI SER A -19 UNP P0C796 EXPRESSION TAG SEQADV 9JZI HIS A -18 UNP P0C796 EXPRESSION TAG SEQADV 9JZI HIS A -17 UNP P0C796 EXPRESSION TAG SEQADV 9JZI HIS A -16 UNP P0C796 EXPRESSION TAG SEQADV 9JZI HIS A -15 UNP P0C796 EXPRESSION TAG SEQADV 9JZI HIS A -14 UNP P0C796 EXPRESSION TAG SEQADV 9JZI HIS A -13 UNP P0C796 EXPRESSION TAG SEQADV 9JZI SER A -12 UNP P0C796 EXPRESSION TAG SEQADV 9JZI SER A -11 UNP P0C796 EXPRESSION TAG SEQADV 9JZI GLY A -10 UNP P0C796 EXPRESSION TAG SEQADV 9JZI LEU A -9 UNP P0C796 EXPRESSION TAG SEQADV 9JZI VAL A -8 UNP P0C796 EXPRESSION TAG SEQADV 9JZI PRO A -7 UNP P0C796 EXPRESSION TAG SEQADV 9JZI ARG A -6 UNP P0C796 EXPRESSION TAG SEQADV 9JZI GLY A -5 UNP P0C796 EXPRESSION TAG SEQADV 9JZI SER A -4 UNP P0C796 EXPRESSION TAG SEQADV 9JZI HIS A -3 UNP P0C796 EXPRESSION TAG SEQADV 9JZI MET A -2 UNP P0C796 EXPRESSION TAG SEQADV 9JZI LEU A -1 UNP P0C796 EXPRESSION TAG SEQADV 9JZI GLU A 0 UNP P0C796 EXPRESSION TAG SEQRES 1 A 393 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 393 LEU VAL PRO ARG GLY SER HIS MET LEU GLU MET PRO PRO SEQRES 3 A 393 LYS ARG ARG LEU VAL ASP ASP ALA ASP ALA MET GLU ASP SEQRES 4 A 393 GLN ASP LEU TYR GLU PRO PRO ALA SER LEU PRO LYS LEU SEQRES 5 A 393 PRO GLY LYS PHE LEU GLN TYR THR VAL GLY GLY SER ASP SEQRES 6 A 393 PRO HIS PRO GLY ILE GLY HIS GLU LYS ASP ILE ARG GLN SEQRES 7 A 393 ASN ALA VAL ALA LEU LEU ASP GLN SER ARG ARG ASP MET SEQRES 8 A 393 PHE HIS THR VAL THR PRO SER LEU VAL PHE LEU CYS LEU SEQRES 9 A 393 LEU ILE PRO GLY LEU HIS ALA ALA PHE VAL HIS GLY GLY SEQRES 10 A 393 VAL PRO ARG GLU SER TYR LEU SER THR PRO VAL THR ARG SEQRES 11 A 393 GLY GLU GLN THR VAL VAL LYS THR ALA LYS PHE TYR GLY SEQRES 12 A 393 GLU LYS THR THR GLN ARG ASP LEU THR GLU LEU GLU ILE SEQRES 13 A 393 SER SER ILE PHE SER HIS CYS CYS SER LEU LEU ILE GLY SEQRES 14 A 393 VAL VAL ILE GLY SER SER SER LYS ILE LYS ALA GLY ALA SEQRES 15 A 393 GLU GLN ILE LYS LYS ARG PHE LYS THR MET MET ALA ALA SEQRES 16 A 393 LEU ASN ARG PRO SER HIS GLY GLU THR ALA THR LEU LEU SEQRES 17 A 393 GLN MET PHE ASN PRO HIS GLU ALA ILE ASP TRP ILE ASN SEQRES 18 A 393 GLY GLN PRO TRP VAL GLY SER PHE VAL LEU SER LEU LEU SEQRES 19 A 393 THR THR ASP PHE GLU SER PRO GLY LYS GLU PHE MET ASP SEQRES 20 A 393 GLN ILE LYS LEU VAL ALA SER TYR ALA GLN MET THR THR SEQRES 21 A 393 TYR THR THR ILE LYS GLU TYR LEU ALA GLU CYS MET ASP SEQRES 22 A 393 ALA THR LEU THR ILE PRO VAL VAL ALA TYR GLU ILE ARG SEQRES 23 A 393 ASP PHE LEU GLU VAL SER ALA LYS LEU LYS GLU GLU HIS SEQRES 24 A 393 ALA ASP LEU PHE PRO PHE LEU GLY ALA ILE ARG HIS PRO SEQRES 25 A 393 ASP ALA ILE LYS LEU ALA PRO ARG SER PHE PRO ASN LEU SEQRES 26 A 393 ALA SER ALA ALA PHE TYR TRP SER LYS LYS GLU ASN PRO SEQRES 27 A 393 THR MET ALA GLY TYR ARG ALA SER THR ILE GLN PRO GLY SEQRES 28 A 393 ALA SER VAL LYS GLU THR GLN LEU ALA ARG TYR ARG ARG SEQRES 29 A 393 ARG GLU ILE SER ARG GLY GLU ASP GLY ALA GLU LEU SER SEQRES 30 A 393 GLY GLU ILE SER ALA ILE MET ARG MET ILE GLY VAL THR SEQRES 31 A 393 GLY LEU ASN HELIX 1 AA1 HIS A 49 LYS A 51 5 3 HELIX 2 AA2 ASP A 52 LEU A 60 1 9 HELIX 3 AA3 ASP A 62 ASP A 67 1 6 HELIX 4 AA4 VAL A 72 ILE A 83 1 12 HELIX 5 AA5 GLY A 85 GLY A 94 1 10 HELIX 6 AA6 THR A 129 GLY A 150 1 22 HELIX 7 AA7 SER A 152 GLY A 158 1 7 HELIX 8 AA8 ALA A 159 LEU A 173 1 15 HELIX 9 AA9 SER A 177 ALA A 182 1 6 HELIX 10 AB1 PRO A 190 GLN A 200 1 11 HELIX 11 AB2 TRP A 202 THR A 213 1 12 HELIX 12 AB3 PRO A 218 ALA A 230 1 13 HELIX 13 AB4 MET A 235 CYS A 248 1 14 HELIX 14 AB5 ASP A 250 THR A 254 5 5 HELIX 15 AB6 ILE A 255 HIS A 276 1 22 HELIX 16 AB7 LEU A 279 LEU A 283 5 5 HELIX 17 AB8 HIS A 288 ALA A 295 5 8 HELIX 18 AB9 PHE A 299 ASN A 314 1 16 HELIX 19 AC1 LYS A 332 ARG A 342 1 11 HELIX 20 AC2 SER A 354 MET A 363 1 10 SHEET 1 AA1 2 SER A 99 VAL A 105 0 SHEET 2 AA1 2 VAL A 112 THR A 115 -1 O THR A 115 N SER A 99 CISPEP 1 SER A 217 PRO A 218 0 1.07 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 MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 2 0.000000 -1.000000 0.000000 121.81710 MTRIX2 2 1.000000 0.000000 0.000000 0.00000 MTRIX3 2 0.000000 0.000000 1.000000 0.00000 MTRIX1 3 -1.000000 0.000000 0.000000 121.81710 MTRIX2 3 0.000000 -1.000000 0.000000 121.81710 MTRIX3 3 0.000000 0.000000 1.000000 0.00000 MTRIX1 4 0.000000 1.000000 0.000000 0.00000 MTRIX2 4 -1.000000 0.000000 0.000000 121.81710 MTRIX3 4 0.000000 0.000000 1.000000 0.00000 MASTER 221 0 0 20 2 0 0 18 2616 1 0 31 END