HEADER VIRAL PROTEIN 05-NOV-25 9T5K TITLE LOCAL REFINEMENT OF RNA-FREE ASSEMBLED LANGYA VIRUS N-CORE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOCAPSID; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NUCLEOCAPSID PROTEIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LANGYA VIRUS; SOURCE 3 ORGANISM_TAXID: 2971765; SOURCE 4 STRAIN: ISOLATE SDQD_H1801; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HENIPAVIRUS, LANGYA VIRUS, CRYO-EM, NUCLEOCAPSID, NUCLEOPROTEIN, RNA, KEYWDS 2 VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR R.B.JAYACHANDRAN,E.QUIGNON,M.RENNER REVDAT 1 22-APR-26 9T5K 0 JRNL AUTH R.B.JAYACHANDRAN,E.QUIGNON,M.RENNER JRNL TITL OPEN AND CLOSED FORMS OF ASSEMBLED HENIPAVIRUS NUCLEOPROTEIN JRNL TITL 2 SUGGEST STRUCTURAL BASIS OF GENOME ACCESS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC, CRYOSPARC, 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) : 2.600 REMARK 3 NUMBER OF PARTICLES : 703773 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 9T5K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-NOV-25. REMARK 100 THE DEPOSITION ID IS D_1292151885. 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 : LANGYA VIRUS N-CORE 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 : 7.50 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 : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2400.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 -32 REMARK 465 HIS A -31 REMARK 465 HIS A -30 REMARK 465 HIS A -29 REMARK 465 HIS A -28 REMARK 465 HIS A -27 REMARK 465 HIS A -26 REMARK 465 GLY A -25 REMARK 465 LYS A -24 REMARK 465 PRO A -23 REMARK 465 ILE A -22 REMARK 465 PRO A -21 REMARK 465 ASN A -20 REMARK 465 PRO A -19 REMARK 465 LEU A -18 REMARK 465 LEU A -17 REMARK 465 GLY A -16 REMARK 465 LEU A -15 REMARK 465 ASP A -14 REMARK 465 SER A -13 REMARK 465 THR A -12 REMARK 465 GLU A -11 REMARK 465 ASN A -10 REMARK 465 LEU A -9 REMARK 465 TYR A -8 REMARK 465 PHE A -7 REMARK 465 GLN A -6 REMARK 465 GLY A -5 REMARK 465 ILE A -4 REMARK 465 ASP A -3 REMARK 465 PRO A -2 REMARK 465 PHE A -1 REMARK 465 THR A 0 REMARK 465 MET A 1 REMARK 465 ARG A 117 REMARK 465 ARG A 118 REMARK 465 GLY A 119 REMARK 465 GLU A 120 REMARK 465 LYS A 121 REMARK 465 ALA A 179 REMARK 465 PRO A 180 REMARK 465 ASP A 181 REMARK 465 THR A 182 REMARK 465 ALA A 183 REMARK 465 GLU A 184 REMARK 465 GLU A 185 REMARK 465 SER A 186 REMARK 465 GLU A 187 REMARK 465 ALA A 344 REMARK 465 LEU A 345 REMARK 465 GLN A 399 REMARK 465 ARG A 400 REMARK 465 HIS A 401 REMARK 465 GLU A 402 REMARK 465 THR A 403 REMARK 465 ASN A 404 REMARK 465 VAL A 405 REMARK 465 GLN A 406 REMARK 465 ALA A 407 REMARK 465 ARG A 408 REMARK 465 GLU A 409 REMARK 465 GLY A 410 REMARK 465 LYS A 411 REMARK 465 PHE A 412 REMARK 465 ASN A 413 REMARK 465 VAL A 414 REMARK 465 ALA A 415 REMARK 465 ALA A 416 REMARK 465 GLY A 417 REMARK 465 GLY A 418 REMARK 465 ILE A 419 REMARK 465 GLU A 420 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 TYR A 204 52.76 -90.64 REMARK 500 ASN A 367 32.64 -96.49 REMARK 500 GLN A 383 -4.62 68.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-55586 RELATED DB: EMDB REMARK 900 LOCAL REFINEMENT OF RNA-FREE ASSEMBLED LANGYA VIRUS N-CORE DBREF1 9T5K A 1 420 UNP A0AAX3C958_9MONO DBREF2 9T5K A A0AAX3C958 1 420 SEQADV 9T5K MET A -32 UNP A0AAX3C95 INITIATING METHIONINE SEQADV 9T5K HIS A -31 UNP A0AAX3C95 EXPRESSION TAG SEQADV 9T5K HIS A -30 UNP A0AAX3C95 EXPRESSION TAG SEQADV 9T5K HIS A -29 UNP A0AAX3C95 EXPRESSION TAG SEQADV 9T5K HIS A -28 UNP A0AAX3C95 EXPRESSION TAG SEQADV 9T5K HIS A -27 UNP A0AAX3C95 EXPRESSION TAG SEQADV 9T5K HIS A -26 UNP A0AAX3C95 EXPRESSION TAG SEQADV 9T5K GLY A -25 UNP A0AAX3C95 EXPRESSION TAG SEQADV 9T5K LYS A -24 UNP A0AAX3C95 EXPRESSION TAG SEQADV 9T5K PRO A -23 UNP A0AAX3C95 EXPRESSION TAG SEQADV 9T5K ILE A -22 UNP A0AAX3C95 EXPRESSION TAG SEQADV 9T5K PRO A -21 UNP A0AAX3C95 EXPRESSION TAG SEQADV 9T5K ASN A -20 UNP A0AAX3C95 EXPRESSION TAG SEQADV 9T5K PRO A -19 UNP A0AAX3C95 EXPRESSION TAG SEQADV 9T5K LEU A -18 UNP A0AAX3C95 EXPRESSION TAG SEQADV 9T5K LEU A -17 UNP A0AAX3C95 EXPRESSION TAG SEQADV 9T5K GLY A -16 UNP A0AAX3C95 EXPRESSION TAG SEQADV 9T5K LEU A -15 UNP A0AAX3C95 EXPRESSION TAG SEQADV 9T5K ASP A -14 UNP A0AAX3C95 EXPRESSION TAG SEQADV 9T5K SER A -13 UNP A0AAX3C95 EXPRESSION TAG SEQADV 9T5K THR A -12 UNP A0AAX3C95 EXPRESSION TAG SEQADV 9T5K GLU A -11 UNP A0AAX3C95 EXPRESSION TAG SEQADV 9T5K ASN A -10 UNP A0AAX3C95 EXPRESSION TAG SEQADV 9T5K LEU A -9 UNP A0AAX3C95 EXPRESSION TAG SEQADV 9T5K TYR A -8 UNP A0AAX3C95 EXPRESSION TAG SEQADV 9T5K PHE A -7 UNP A0AAX3C95 EXPRESSION TAG SEQADV 9T5K GLN A -6 UNP A0AAX3C95 EXPRESSION TAG SEQADV 9T5K GLY A -5 UNP A0AAX3C95 EXPRESSION TAG SEQADV 9T5K ILE A -4 UNP A0AAX3C95 EXPRESSION TAG SEQADV 9T5K ASP A -3 UNP A0AAX3C95 EXPRESSION TAG SEQADV 9T5K PRO A -2 UNP A0AAX3C95 EXPRESSION TAG SEQADV 9T5K PHE A -1 UNP A0AAX3C95 EXPRESSION TAG SEQADV 9T5K THR A 0 UNP A0AAX3C95 EXPRESSION TAG SEQRES 1 A 453 MET HIS HIS HIS HIS HIS HIS GLY LYS PRO ILE PRO ASN SEQRES 2 A 453 PRO LEU LEU GLY LEU ASP SER THR GLU ASN LEU TYR PHE SEQRES 3 A 453 GLN GLY ILE ASP PRO PHE THR MET PHE SER THR LEU LYS SEQRES 4 A 453 ASN GLU THR GLU LYS PHE ARG GLU TYR GLN ALA ASN LEU SEQRES 5 A 453 GLY ARG GLN GLY LYS PRO LEU ALA SER THR ALA THR LEU SEQRES 6 A 453 THR THR LYS ILE ILE VAL TYR ASN PRO SER ASN LYS SER SEQRES 7 A 453 PRO ALA LEU ARG TRP GLU ILE THR LYS PHE ALA MET ARG SEQRES 8 A 453 LEU ILE TRP SER PRO ALA ALA SER HIS SER VAL LYS VAL SEQRES 9 A 453 GLY ALA ALA LEU THR LEU LEU SER ALA HIS ALA GLU ASN SEQRES 10 A 453 PRO GLY ALA MET ILE ARG SER LEU VAL ASN ASP PRO ASP SEQRES 11 A 453 ILE GLU VAL VAL ILE THR ASP ILE SER GLU PHE ASP HIS SEQRES 12 A 453 GLY VAL PRO ARG LEU GLU ARG ARG GLY GLU LYS ALA GLU SEQRES 13 A 453 GLN GLN MET ASP SER TYR ARG ARG ILE LEU ASP ARG ALA SEQRES 14 A 453 PRO GLN GLU ASN LEU PHE TYR ASN PRO GLU VAL ASP ASP SEQRES 15 A 453 LEU GLU ILE LEU ASP SER GLY THR PHE LEU PHE ALA ILE SEQRES 16 A 453 ALA THR VAL LEU ALA GLN VAL TRP ILE LEU VAL ALA LYS SEQRES 17 A 453 ALA VAL THR ALA PRO ASP THR ALA GLU GLU SER GLU ASN SEQRES 18 A 453 LYS ARG TRP ALA LYS TYR VAL GLN GLN LYS ARG VAL ASN SEQRES 19 A 453 PRO ASP TYR LEU VAL SER ASN ARG TRP ILE THR ALA MET SEQRES 20 A 453 ARG SER LEU ILE SER ILE ASP LEU SER VAL ARG LYS TYR SEQRES 21 A 453 MET VAL GLU ILE LEU ILE GLU VAL LYS LYS SER GLY VAL SEQRES 22 A 453 ALA ARG GLY ARG LEU ASN GLU MET ILE ALA ASP ILE GLY SEQRES 23 A 453 ASN TYR ILE GLU GLU THR GLY MET ALA GLY PHE PHE LEU SEQRES 24 A 453 THR ILE LYS TYR GLY LEU GLU MET LYS PHE PRO VAL ILE SEQRES 25 A 453 VAL ILE ASN GLU PHE GLN ALA ASP LEU LEU THR LEU GLN SEQRES 26 A 453 THR LEU MET ARG THR TYR MET ASP LEU GLY PRO ARG ALA SEQRES 27 A 453 PRO TYR MET VAL LEU LEU GLU ASP SER ILE GLN THR LYS SEQRES 28 A 453 PHE ALA PRO GLY ASN TYR PRO LEU LEU TRP SER PHE ALA SEQRES 29 A 453 MET GLY VAL GLY THR THR LEU ASP ARG SER MET GLY ALA SEQRES 30 A 453 LEU ASN ILE ASN ARG SER TYR LEU GLU PRO ILE TYR PHE SEQRES 31 A 453 LYS LEU GLY GLN ASN ALA ALA ARG LYS ASN ALA GLY SER SEQRES 32 A 453 ILE ASP ARG LYS LEU ALA GLU GLU LEU GLY LEU THR GLN SEQRES 33 A 453 GLU GLN ALA ASN GLU ILE LYS GLU MET MET GLN GLU VAL SEQRES 34 A 453 THR THR GLN ARG HIS GLU THR ASN VAL GLN ALA ARG GLU SEQRES 35 A 453 GLY LYS PHE ASN VAL ALA ALA GLY GLY ILE GLU HELIX 1 AA1 THR A 4 ASN A 18 1 15 HELIX 2 AA2 SER A 45 TRP A 61 1 17 HELIX 3 AA3 SER A 66 SER A 79 1 14 HELIX 4 AA4 ASN A 84 VAL A 93 1 10 HELIX 5 AA5 GLN A 124 ALA A 136 1 13 HELIX 6 AA6 ASN A 144 ASP A 149 1 6 HELIX 7 AA7 ASP A 154 VAL A 177 1 24 HELIX 8 AA8 LYS A 189 GLN A 197 1 9 HELIX 9 AA9 ASN A 201 LEU A 205 5 5 HELIX 10 AB1 SER A 207 ASP A 221 1 15 HELIX 11 AB2 LEU A 222 LYS A 237 1 16 HELIX 12 AB3 GLY A 243 THR A 259 1 17 HELIX 13 AB4 MET A 261 LEU A 272 1 12 HELIX 14 AB5 PHE A 276 GLU A 283 5 8 HELIX 15 AB6 PHE A 284 MET A 299 1 16 HELIX 16 AB7 ASP A 300 PRO A 306 5 7 HELIX 17 AB8 TYR A 307 GLU A 312 1 6 HELIX 18 AB9 ASP A 313 ASN A 323 5 11 HELIX 19 AC1 TYR A 324 ASP A 339 1 16 HELIX 20 AC2 GLU A 353 ARG A 365 1 13 HELIX 21 AC3 ASP A 372 GLY A 380 1 9 HELIX 22 AC4 GLU A 384 THR A 397 1 14 SHEET 1 AA1 2 THR A 34 PRO A 41 0 SHEET 2 AA1 2 ILE A 98 ILE A 105 1 O THR A 103 N ASN A 40 SHEET 1 AA2 2 PHE A 108 ASP A 109 0 SHEET 2 AA2 2 VAL A 112 PRO A 113 -1 O VAL A 112 N ASP A 109 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 MASTER 199 0 0 22 4 0 0 6 3030 1 0 35 END