HEADER VIRAL PROTEIN 14-OCT-24 9JZN TITLE TETRAMERIC COMPLEX OF THE BORNA DISEASE VIRUS 1 NUCLEOPROTEIN (MUTANT TITLE 2 LYS164ALA) 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 MUTATION: YES; COMPND 7 OTHER_DETAILS: FULL-LENGTH NUCLEOPROTEIN (MUTANT LYS164ALA) OF THE COMPND 8 BORNA DISEASE VIRUS 1 STRAIN HE/80 WITH N-TERMINAL EXPRESSION 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 S.H.GOTO,Y.SUGITA,Y.HIRAI,M.HORIE REVDAT 1 11-MAR-26 9JZN 0 JRNL AUTH S.H.GOTO,Y.SUGITA,Y.HIRAI,M.HORIE JRNL TITL TETRAMERIC COMPLEX OF BORNA DISEASE VIRUS 1 NUCLEOPROTEIN JRNL TITL 2 (MUTANT LYS164ALA) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, EPU, CRYOSPARC, UCSF REMARK 3 CHIMERAX, COOT, SERVALCAT, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC, CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : FOURIER SPACE 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) : 3.150 REMARK 3 NUMBER OF PARTICLES : 170764 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 9JZN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-OCT-24. REMARK 100 THE DEPOSITION ID IS D_1300050781. 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 : PURIFIED BORNA DISEASE VIRUS 1 REMARK 245 NUCLEOPROTEIN (MUTANT LYS164ALA) 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 GLACIOS REMARK 245 DETECTOR TYPE : FEI FALCON IV (4K X 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 : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 4300.00 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) : 200 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 CYCLIC POINT SYMMETRY (SCHOENFLIES SYMBOL = C4). 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 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 124.52800 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 124.52800 REMARK 350 BIOMT2 3 0.000000 -1.000000 0.000000 124.52800 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 124.52800 REMARK 350 BIOMT3 4 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 ALA A 24 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: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 275 CD GLU A 275 OE1 0.083 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 LEU A 185 51.86 -113.98 REMARK 500 PRO A 190 21.83 -79.92 REMARK 500 THR A 212 -37.11 -133.08 REMARK 500 ILE A 255 119.58 -39.79 REMARK 500 ASP A 278 -45.41 68.19 REMARK 500 LEU A 294 60.70 -106.54 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER A 217 PRO A 218 50.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-61929 RELATED DB: EMDB REMARK 900 TETRAMERIC COMPLEX OF THE BORNA DISEASE VIRUS 1 NUCLEOPROTEIN REMARK 900 (MUTANT LYS164ALA) DBREF 9JZN A 1 370 UNP P0C796 NCAP_BDV1 1 370 SEQADV 9JZN MET A -22 UNP P0C796 INITIATING METHIONINE SEQADV 9JZN GLY A -21 UNP P0C796 EXPRESSION TAG SEQADV 9JZN SER A -20 UNP P0C796 EXPRESSION TAG SEQADV 9JZN SER A -19 UNP P0C796 EXPRESSION TAG SEQADV 9JZN HIS A -18 UNP P0C796 EXPRESSION TAG SEQADV 9JZN HIS A -17 UNP P0C796 EXPRESSION TAG SEQADV 9JZN HIS A -16 UNP P0C796 EXPRESSION TAG SEQADV 9JZN HIS A -15 UNP P0C796 EXPRESSION TAG SEQADV 9JZN HIS A -14 UNP P0C796 EXPRESSION TAG SEQADV 9JZN HIS A -13 UNP P0C796 EXPRESSION TAG SEQADV 9JZN SER A -12 UNP P0C796 EXPRESSION TAG SEQADV 9JZN SER A -11 UNP P0C796 EXPRESSION TAG SEQADV 9JZN GLY A -10 UNP P0C796 EXPRESSION TAG SEQADV 9JZN LEU A -9 UNP P0C796 EXPRESSION TAG SEQADV 9JZN VAL A -8 UNP P0C796 EXPRESSION TAG SEQADV 9JZN PRO A -7 UNP P0C796 EXPRESSION TAG SEQADV 9JZN ARG A -6 UNP P0C796 EXPRESSION TAG SEQADV 9JZN GLY A -5 UNP P0C796 EXPRESSION TAG SEQADV 9JZN SER A -4 UNP P0C796 EXPRESSION TAG SEQADV 9JZN HIS A -3 UNP P0C796 EXPRESSION TAG SEQADV 9JZN MET A -2 UNP P0C796 EXPRESSION TAG SEQADV 9JZN LEU A -1 UNP P0C796 EXPRESSION TAG SEQADV 9JZN GLU A 0 UNP P0C796 EXPRESSION TAG SEQADV 9JZN ALA A 164 UNP P0C796 LYS 164 ENGINEERED MUTATION 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 ALA 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 THR A 71 ILE A 83 1 13 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 GLY A 199 1 10 HELIX 11 AB2 TRP A 202 LEU A 211 1 10 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 ILE A 255 HIS A 276 1 22 HELIX 15 AB6 LEU A 279 LEU A 283 5 5 HELIX 16 AB7 HIS A 288 LYS A 293 5 6 HELIX 17 AB8 PHE A 299 ASN A 314 1 16 HELIX 18 AB9 LYS A 332 ARG A 341 1 10 HELIX 19 AC1 SER A 354 GLY A 365 1 12 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 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 124.52800 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 124.52800 MTRIX2 3 0.000000 -1.000000 0.000000 124.52800 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 124.52800 MTRIX3 4 0.000000 0.000000 1.000000 0.00000 MASTER 229 0 0 19 2 0 0 18 2607 1 0 31 END