HEADER VIRAL PROTEIN/RNA 22-MAY-25 9V47 TITLE COUPLING OF POLYMERASE-NUCLEOPROTEIN-RNA IN AN INFLUENZA VIRUS MINI TITLE 2 RIBONUCLEOPROTEIN COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOPROTEIN; COMPND 3 CHAIN: B; COMPND 4 SYNONYM: NUCLEOCAPSID PROTEIN,PROTEIN N; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'); COMPND 8 CHAIN: C; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: INFLUENZA A VIRUS (A/VICTORIA/3/1975(H3N2)); SOURCE 3 ORGANISM_TAXID: 392809; SOURCE 4 GENE: NP; SOURCE 5 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: INFLUENZA A VIRUS (A/VICTORIA/3/1975(H3N2)); SOURCE 9 ORGANISM_TAXID: 392809; SOURCE 10 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS INFLUENZA VIRUS, RIBONUCLEOPROTEIN COMPLEX, POLYMERASE, CRYO-EM, KEYWDS 2 VIRAL PROTEIN/RNA, VIRAL PROTEIN-RNA COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR H.KANG,Y.YANG,Y.LIU,M.LI,L.ZHANG,Y.LIN,Z.RAO,Z.LOU REVDAT 2 26-NOV-25 9V47 1 JRNL REVDAT 1 08-OCT-25 9V47 0 JRNL AUTH H.KANG,Y.YANG,Y.LIU,M.LI,L.ZHANG,Y.LIN,L.WITTE,K.Y.CHEN, JRNL AUTH 2 W.SONG,Z.XU,X.HE,L.W.GUDDAT,Y.GUO,L.YAN,Y.GAO,E.FODOR,Z.RAO, JRNL AUTH 3 Z.LOU JRNL TITL COUPLING OF POLYMERASE-NUCLEOPROTEIN-RNA IN AN INFLUENZA JRNL TITL 2 VIRUS MINI RIBONUCLEOPROTEIN COMPLEX. JRNL REF NAT COMMUN V. 16 9741 2025 JRNL REFN ESSN 2041-1723 JRNL PMID 41188214 JRNL DOI 10.1038/S41467-025-64741-Z REMARK 2 REMARK 2 RESOLUTION. 4.52 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) : 4.520 REMARK 3 NUMBER OF PARTICLES : 265200 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 9V47 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 27-MAY-25. REMARK 100 THE DEPOSITION ID IS D_1300059758. 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 : NP+1_NP+2_RNA_STATE IN 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 : 8.00 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) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 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) : 6000.00 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C 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 B 1 REMARK 465 ALA B 2 REMARK 465 SER B 3 REMARK 465 GLN B 4 REMARK 465 GLY B 5 REMARK 465 THR B 6 REMARK 465 LYS B 7 REMARK 465 ARG B 8 REMARK 465 SER B 9 REMARK 465 TYR B 10 REMARK 465 GLU B 11 REMARK 465 GLN B 12 REMARK 465 MET B 13 REMARK 465 GLU B 14 REMARK 465 THR B 15 REMARK 465 ASP B 16 REMARK 465 GLY B 17 REMARK 465 GLU B 18 REMARK 465 ARG B 19 REMARK 465 GLN B 20 REMARK 465 SER B 392 REMARK 465 GLY B 393 REMARK 465 GLY B 394 REMARK 465 ASN B 395 REMARK 465 THR B 396 REMARK 465 ASN B 397 REMARK 465 GLN B 398 REMARK 465 GLN B 399 REMARK 465 ARG B 400 REMARK 465 ALA B 401 REMARK 465 SER B 402 REMARK 465 ALA B 403 REMARK 465 GLY B 404 REMARK 465 TYR B 487 REMARK 465 PHE B 488 REMARK 465 PHE B 489 REMARK 465 GLY B 490 REMARK 465 ASP B 491 REMARK 465 ASN B 492 REMARK 465 ALA B 493 REMARK 465 GLU B 494 REMARK 465 GLU B 495 REMARK 465 TYR B 496 REMARK 465 ASP B 497 REMARK 465 ASN B 498 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 GLY B 94 O REMARK 470 GLY B 126 O 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 B 55 32.03 -95.71 REMARK 500 GLU B 73 -157.85 -97.40 REMARK 500 ARG B 74 173.35 -59.69 REMARK 500 HIS B 82 75.79 69.67 REMARK 500 PRO B 83 172.33 -54.87 REMARK 500 GLU B 115 -38.57 -36.10 REMARK 500 TYR B 148 -168.27 -168.89 REMARK 500 ARG B 156 -66.15 -99.05 REMARK 500 LYS B 184 152.98 -49.34 REMARK 500 ASN B 202 36.62 -91.22 REMARK 500 TRP B 207 35.29 -141.85 REMARK 500 THR B 360 149.90 -177.16 REMARK 500 ARG B 361 -165.25 -113.85 REMARK 500 LEU B 418 135.05 -39.54 REMARK 500 THR B 430 55.36 34.61 REMARK 500 ASN B 432 15.60 51.76 REMARK 500 THR B 433 -70.10 -63.99 REMARK 500 GLU B 434 168.55 179.10 REMARK 500 SER B 438 -161.75 169.71 REMARK 500 LYS B 470 4.93 -69.75 REMARK 500 VAL B 476 107.71 -52.42 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-64769 RELATED DB: EMDB REMARK 900 COUPLING OF POLYMERASE-NUCLEOPROTEIN-RNA IN AN INFLUENZA VIRUS MINI REMARK 900 RIBONUCLEOPROTEIN COMPLEX DBREF 9V47 B 1 498 UNP Q9WLG4 Q9WLG4_I75A3 1 498 DBREF 9V47 C 1001 1010 PDB 9V47 9V47 1001 1010 SEQRES 1 B 498 MET ALA SER GLN GLY THR LYS ARG SER TYR GLU GLN MET SEQRES 2 B 498 GLU THR ASP GLY GLU ARG GLN ASN ALA THR GLU ILE ARG SEQRES 3 B 498 ALA SER VAL GLY LYS MET ILE ASN GLY ILE GLY ARG PHE SEQRES 4 B 498 TYR ILE GLN MET CYS THR GLU LEU LYS LEU SER ASP TYR SEQRES 5 B 498 GLU GLY ARG LEU ILE GLN ASN SER LEU THR ILE GLU ARG SEQRES 6 B 498 MET VAL LEU SER ALA PHE ASP GLU ARG ARG ASN ARG TYR SEQRES 7 B 498 LEU GLU GLU HIS PRO SER ALA GLY LYS ASP PRO LYS LYS SEQRES 8 B 498 THR GLY GLY PRO ILE TYR LYS ARG VAL ASP GLY LYS TRP SEQRES 9 B 498 MET ARG GLU LEU VAL LEU TYR ASP LYS GLU GLU ILE ARG SEQRES 10 B 498 ARG ILE TRP ARG GLN ALA ASN ASN GLY ASP ASP ALA THR SEQRES 11 B 498 ALA GLY LEU THR HIS MET MET ILE TRP HIS SER ASN LEU SEQRES 12 B 498 ASN ASP THR THR TYR GLN ARG THR ARG ALA LEU VAL ARG SEQRES 13 B 498 THR GLY MET ASP PRO ARG MET CYS SER LEU MET GLN GLY SEQRES 14 B 498 SER THR LEU PRO ARG ARG SER GLY ALA ALA GLY ALA ALA SEQRES 15 B 498 VAL LYS GLY VAL GLY THR MET VAL MET GLU LEU ILE ARG SEQRES 16 B 498 MET ILE LYS ARG GLY ILE ASN ASP ARG ASN PHE TRP ARG SEQRES 17 B 498 GLY GLU ASN GLY ARG LYS THR ARG SER ALA TYR GLU ARG SEQRES 18 B 498 MET CYS ASN ILE LEU LYS GLY LYS PHE GLN THR ALA ALA SEQRES 19 B 498 GLN ARG ALA MET MET ASP GLN VAL ARG GLU SER ARG ASN SEQRES 20 B 498 PRO GLY ASN ALA GLU ILE GLU ASP LEU ILE PHE SER ALA SEQRES 21 B 498 ARG SER ALA LEU ILE LEU ARG GLY SER VAL ALA HIS LYS SEQRES 22 B 498 SER CYS LEU PRO ALA CYS VAL TYR GLY PRO ALA VAL ALA SEQRES 23 B 498 SER GLY TYR ASP PHE GLU LYS GLU GLY TYR SER LEU VAL SEQRES 24 B 498 GLY ILE ASP PRO PHE LYS LEU LEU GLN ASN SER GLN VAL SEQRES 25 B 498 TYR SER LEU ILE ARG PRO ASN GLU ASN PRO ALA HIS LYS SEQRES 26 B 498 SER GLN LEU VAL TRP MET ALA CYS HIS SER ALA ALA PHE SEQRES 27 B 498 GLU ASP LEU ARG LEU LEU SER PHE ILE ARG GLY THR LYS SEQRES 28 B 498 VAL SER PRO ARG GLY LYS LEU SER THR ARG GLY VAL GLN SEQRES 29 B 498 ILE ALA SER ASN GLU ASN MET ASP THR MET GLU SER SER SEQRES 30 B 498 THR LEU GLU LEU ARG SER ARG TYR TRP ALA ILE ARG THR SEQRES 31 B 498 ARG SER GLY GLY ASN THR ASN GLN GLN ARG ALA SER ALA SEQRES 32 B 498 GLY GLN ILE SER VAL GLN PRO ALA PHE SER VAL GLN ARG SEQRES 33 B 498 ASN LEU PRO PHE ASP LYS SER THR ILE MET ALA ALA PHE SEQRES 34 B 498 THR GLY ASN THR GLU GLY ARG THR SER ASP MET ARG ALA SEQRES 35 B 498 GLU ILE ILE ARG MET MET GLU GLY ALA LYS PRO GLU GLU SEQRES 36 B 498 VAL SER PHE ARG GLY ARG GLY VAL PHE GLU LEU SER ASP SEQRES 37 B 498 GLU LYS ALA THR ASN PRO VAL VAL PRO SER PHE ASP MET SEQRES 38 B 498 SER ASN GLU GLY SER TYR PHE PHE GLY ASP ASN ALA GLU SEQRES 39 B 498 GLU TYR ASP ASN SEQRES 1 C 10 A A A A A A A A A A HELIX 1 AA1 ASN B 21 LYS B 48 1 28 HELIX 2 AA2 SER B 50 ARG B 55 1 6 HELIX 3 AA3 LEU B 56 ALA B 70 1 15 HELIX 4 AA4 LYS B 113 ASN B 124 1 12 HELIX 5 AA5 ALA B 129 TYR B 148 1 20 HELIX 6 AA6 THR B 151 THR B 157 1 7 HELIX 7 AA7 ARG B 162 LEU B 166 5 5 HELIX 8 AA8 ALA B 179 LYS B 184 1 6 HELIX 9 AA9 GLY B 185 ASN B 202 1 18 HELIX 10 AB1 GLY B 212 LYS B 229 1 18 HELIX 11 AB2 THR B 232 SER B 245 1 14 HELIX 12 AB3 GLY B 249 LEU B 264 1 16 HELIX 13 AB4 PRO B 277 ALA B 286 1 10 HELIX 14 AB5 ASP B 290 GLY B 295 1 6 HELIX 15 AB6 ILE B 301 ASN B 309 1 9 HELIX 16 AB7 ASN B 321 SER B 335 1 15 HELIX 17 AB8 ASP B 340 GLY B 349 1 10 HELIX 18 AB9 PRO B 354 LEU B 358 5 5 HELIX 19 AC1 LYS B 422 THR B 430 1 9 HELIX 20 AC2 SER B 438 MET B 448 1 11 SHEET 1 AA1 2 LYS B 91 THR B 92 0 SHEET 2 AA1 2 TYR B 111 ASP B 112 -1 O TYR B 111 N THR B 92 SHEET 1 AA2 2 ILE B 96 VAL B 100 0 SHEET 2 AA2 2 LYS B 103 GLU B 107 -1 O LYS B 103 N VAL B 100 SHEET 1 AA3 2 TYR B 313 SER B 314 0 SHEET 2 AA3 2 SER B 377 THR B 378 -1 O SER B 377 N SER B 314 SHEET 1 AA4 2 TYR B 385 ALA B 387 0 SHEET 2 AA4 2 VAL B 463 GLU B 465 -1 O PHE B 464 N TRP B 386 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 TER 3572 SER B 486 TER 3793 A C1010 MASTER 198 0 0 20 8 0 0 6 3791 2 0 40 END