HEADER NUCLEAR PROTEIN/RNA 18-MAR-20 6M7D TITLE STRUCTURE OF NCLEOPROTEIN OF SENDAI VIRUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOPROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NUCLEOCAPSID PROTEIN,PROTEIN N; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3'); COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SENDAI VIRUS (STRAIN OHITA); SOURCE 3 ORGANISM_COMMON: SEV; SOURCE 4 ORGANISM_TAXID: 302272; SOURCE 5 STRAIN: OHITA; SOURCE 6 GENE: N, NP; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630 KEYWDS NUCLEOCAPSID, SENDAI VIRUS, NUCLEAR PROTEIN, NUCLEAR PROTEIN-RNA KEYWDS 2 COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR Q.SHEN,H.SHAN,N.ZHANG REVDAT 2 27-MAR-24 6M7D 1 REMARK REVDAT 1 24-MAR-21 6M7D 0 JRNL AUTH Q.SHEN,H.SHAN,N.ZHANG JRNL TITL STRUCTURE OF THE NUCLEOCAPSID OF SENDAI VIRUS AT 2.9 JRNL TITL 2 ANGSTROMS RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL 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) : 2.900 REMARK 3 NUMBER OF PARTICLES : 134042 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 6M7D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1300015863. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : HELICAL REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : FILAMENT REMARK 245 PARTICLE TYPE : HELICAL REMARK 245 NAME OF SAMPLE : CLEAVED DOUBLE-HEADED REMARK 245 NUCLEOCAPSID OF SENDAI VIRUS 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 K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : NULL REMARK 245 MAXIMUM DEFOCUS (NM) : NULL 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 1 REMARK 465 ALA A 2 REMARK 465 GLY A 415 REMARK 465 ALA A 416 REMARK 465 ILE A 417 REMARK 465 GLU A 418 REMARK 465 VAL A 419 REMARK 465 ALA A 420 REMARK 465 LEU A 421 REMARK 465 ASP A 422 REMARK 465 ASN A 423 REMARK 465 ALA A 424 REMARK 465 ASP A 425 REMARK 465 ILE A 426 REMARK 465 ASP A 427 REMARK 465 LEU A 428 REMARK 465 GLU A 429 REMARK 465 PRO A 430 REMARK 465 GLU A 431 REMARK 465 ALA A 432 REMARK 465 HIS A 433 REMARK 465 THR A 434 REMARK 465 ASP A 435 REMARK 465 GLN A 436 REMARK 465 ASP A 437 REMARK 465 ALA A 438 REMARK 465 ARG A 439 REMARK 465 GLY A 440 REMARK 465 TRP A 441 REMARK 465 GLY A 442 REMARK 465 GLY A 443 REMARK 465 ASP A 444 REMARK 465 SER A 445 REMARK 465 GLY A 446 REMARK 465 ASP A 447 REMARK 465 ARG A 448 REMARK 465 TRP A 449 REMARK 465 ALA A 450 REMARK 465 ARG A 451 REMARK 465 SER A 452 REMARK 465 MET A 453 REMARK 465 GLY A 454 REMARK 465 SER A 455 REMARK 465 GLY A 456 REMARK 465 HIS A 457 REMARK 465 PHE A 458 REMARK 465 ILE A 459 REMARK 465 THR A 460 REMARK 465 LEU A 461 REMARK 465 HIS A 462 REMARK 465 GLY A 463 REMARK 465 ALA A 464 REMARK 465 GLU A 465 REMARK 465 ARG A 466 REMARK 465 LEU A 467 REMARK 465 GLU A 468 REMARK 465 GLU A 469 REMARK 465 GLU A 470 REMARK 465 THR A 471 REMARK 465 ASN A 472 REMARK 465 ASP A 473 REMARK 465 GLU A 474 REMARK 465 ASP A 475 REMARK 465 VAL A 476 REMARK 465 SER A 477 REMARK 465 ASP A 478 REMARK 465 ILE A 479 REMARK 465 GLU A 480 REMARK 465 ARG A 481 REMARK 465 ARG A 482 REMARK 465 ILE A 483 REMARK 465 ALA A 484 REMARK 465 ARG A 485 REMARK 465 ARG A 486 REMARK 465 LEU A 487 REMARK 465 ALA A 488 REMARK 465 GLU A 489 REMARK 465 ARG A 490 REMARK 465 ARG A 491 REMARK 465 GLN A 492 REMARK 465 GLU A 493 REMARK 465 ASP A 494 REMARK 465 ALA A 495 REMARK 465 THR A 496 REMARK 465 THR A 497 REMARK 465 HIS A 498 REMARK 465 GLU A 499 REMARK 465 ASP A 500 REMARK 465 GLU A 501 REMARK 465 GLY A 502 REMARK 465 ARG A 503 REMARK 465 ASN A 504 REMARK 465 ASN A 505 REMARK 465 GLY A 506 REMARK 465 VAL A 507 REMARK 465 ASP A 508 REMARK 465 HIS A 509 REMARK 465 ASP A 510 REMARK 465 GLU A 511 REMARK 465 GLU A 512 REMARK 465 ASP A 513 REMARK 465 ASP A 514 REMARK 465 ALA A 515 REMARK 465 ALA A 516 REMARK 465 ALA A 517 REMARK 465 ALA A 518 REMARK 465 ALA A 519 REMARK 465 GLY A 520 REMARK 465 MET A 521 REMARK 465 GLY A 522 REMARK 465 GLY A 523 REMARK 465 ILE A 524 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 ALA A 346 O2' U B 4 2.16 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 ARG A 123 -131.91 55.46 REMARK 500 ASP A 246 76.51 -69.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-30129 RELATED DB: EMDB REMARK 900 STRUCTURE OF NCLEOPROTEIN OF SENDAI VIRUS DBREF 6M7D A 1 524 UNP O57286 NCAP_SENDO 1 524 DBREF 6M7D B 1 6 PDB 6M7D 6M7D 1 6 SEQRES 1 A 524 MET ALA GLY LEU LEU SER THR PHE ASP THR PHE SER SER SEQRES 2 A 524 ARG ARG SER GLU SER ILE ASN LYS SER GLY GLY GLY ALA SEQRES 3 A 524 VAL ILE PRO GLY GLN ARG SER THR VAL SER VAL PHE VAL SEQRES 4 A 524 LEU GLY PRO SER VAL THR ASP ASP ALA ASP LYS LEU SER SEQRES 5 A 524 ILE ALA THR THR PHE LEU ALA HIS SER LEU ASP THR ASP SEQRES 6 A 524 LYS GLN HIS SER GLN ARG GLY GLY PHE LEU VAL SER LEU SEQRES 7 A 524 LEU ALA MET ALA TYR SER SER PRO GLU LEU TYR LEU THR SEQRES 8 A 524 THR ASN GLY VAL ASN ALA ASP VAL LYS TYR VAL ILE TYR SEQRES 9 A 524 ASN ILE GLU LYS ASP PRO LYS ARG THR LYS THR ASP GLY SEQRES 10 A 524 PHE ILE VAL LYS THR ARG ASP MET GLU TYR GLU ARG THR SEQRES 11 A 524 THR GLU TRP LEU PHE GLY PRO MET VAL ASN LYS SER PRO SEQRES 12 A 524 LEU PHE GLN GLY GLN ARG ASP ALA ALA ASP PRO ASP THR SEQRES 13 A 524 LEU LEU GLN ILE TYR GLY TYR PRO ALA CYS LEU GLY ALA SEQRES 14 A 524 ILE ILE VAL GLN VAL TRP ILE VAL LEU VAL LYS ALA ILE SEQRES 15 A 524 THR SER SER ALA GLY LEU ARG LYS GLY PHE PHE ASN ARG SEQRES 16 A 524 LEU GLU ALA PHE ARG GLN ASP GLY THR VAL LYS GLY ALA SEQRES 17 A 524 LEU VAL PHE THR GLY GLU THR VAL GLU GLY ILE GLY SER SEQRES 18 A 524 VAL MET ARG SER GLN GLN SER LEU VAL SER LEU MET VAL SEQRES 19 A 524 GLU THR LEU VAL THR MET ASN THR ALA ARG SER ASP LEU SEQRES 20 A 524 THR THR LEU GLU LYS ASN ILE GLN ILE VAL GLY ASN TYR SEQRES 21 A 524 ILE ARG ASP ALA GLY LEU ALA SER PHE MET ASN THR ILE SEQRES 22 A 524 LYS TYR GLY VAL GLU THR LYS MET ALA ALA LEU THR LEU SEQRES 23 A 524 SER ASN LEU ARG PRO ASP ILE ASN LYS LEU ARG SER LEU SEQRES 24 A 524 ILE ASP THR TYR LEU SER LYS GLY PRO ARG ALA PRO PHE SEQRES 25 A 524 ILE CYS ILE LEU LYS ASP PRO VAL HIS GLY GLU PHE ALA SEQRES 26 A 524 PRO GLY ASN TYR PRO ALA LEU TRP SER TYR ALA MET GLY SEQRES 27 A 524 VAL ALA VAL VAL GLN ASN LYS ALA MET GLN GLN TYR VAL SEQRES 28 A 524 THR GLY ARG THR TYR LEU ASP MET GLU MET PHE LEU LEU SEQRES 29 A 524 GLY GLN ALA VAL ALA LYS ASP ALA GLU SER LYS ILE SER SEQRES 30 A 524 SER ALA LEU GLU ASP GLU LEU GLY VAL THR ASP THR ALA SEQRES 31 A 524 LYS GLU ARG LEU ARG HIS HIS LEU ALA ASN LEU SER GLY SEQRES 32 A 524 GLY ASP GLY ALA TYR HIS LYS PRO THR GLY GLY GLY ALA SEQRES 33 A 524 ILE GLU VAL ALA LEU ASP ASN ALA ASP ILE ASP LEU GLU SEQRES 34 A 524 PRO GLU ALA HIS THR ASP GLN ASP ALA ARG GLY TRP GLY SEQRES 35 A 524 GLY ASP SER GLY ASP ARG TRP ALA ARG SER MET GLY SER SEQRES 36 A 524 GLY HIS PHE ILE THR LEU HIS GLY ALA GLU ARG LEU GLU SEQRES 37 A 524 GLU GLU THR ASN ASP GLU ASP VAL SER ASP ILE GLU ARG SEQRES 38 A 524 ARG ILE ALA ARG ARG LEU ALA GLU ARG ARG GLN GLU ASP SEQRES 39 A 524 ALA THR THR HIS GLU ASP GLU GLY ARG ASN ASN GLY VAL SEQRES 40 A 524 ASP HIS ASP GLU GLU ASP ASP ALA ALA ALA ALA ALA GLY SEQRES 41 A 524 MET GLY GLY ILE SEQRES 1 B 6 U U U U U U HELIX 1 AA1 LEU A 5 THR A 10 1 6 HELIX 2 AA2 THR A 10 ASN A 20 1 11 HELIX 3 AA3 ASP A 46 ASP A 63 1 18 HELIX 4 AA4 GLN A 67 MET A 81 1 15 HELIX 5 AA5 SER A 85 GLY A 94 1 10 HELIX 6 AA6 GLU A 128 GLY A 136 1 9 HELIX 7 AA7 ASP A 153 TYR A 161 1 9 HELIX 8 AA8 GLY A 162 ILE A 182 1 21 HELIX 9 AA9 GLY A 187 GLY A 203 1 17 HELIX 10 AB1 LYS A 206 VAL A 210 5 5 HELIX 11 AB2 THR A 212 GLN A 226 1 15 HELIX 12 AB3 GLN A 226 MET A 240 1 15 HELIX 13 AB4 THR A 248 ARG A 262 1 15 HELIX 14 AB5 LEU A 266 VAL A 277 1 12 HELIX 15 AB6 MET A 281 LEU A 286 5 6 HELIX 16 AB7 LEU A 289 LYS A 306 1 18 HELIX 17 AB8 GLY A 307 ILE A 313 5 7 HELIX 18 AB9 ASP A 318 ASN A 328 5 11 HELIX 19 AC1 TYR A 329 ASN A 344 1 16 HELIX 20 AC2 LYS A 345 TYR A 350 5 6 HELIX 21 AC3 ASP A 358 ASP A 371 1 14 HELIX 22 AC4 LEU A 380 GLY A 385 1 6 HELIX 23 AC5 THR A 387 SER A 402 1 16 SHEET 1 AA1 4 SER A 33 LEU A 40 0 SHEET 2 AA1 4 VAL A 99 LYS A 108 1 O VAL A 102 N VAL A 35 SHEET 3 AA1 4 PHE A 118 THR A 122 -1 O ILE A 119 N GLU A 107 SHEET 4 AA1 4 MET A 125 TYR A 127 -1 O TYR A 127 N VAL A 120 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