HEADER VIRAL PROTEIN 12-JUN-23 8PDQ TITLE 11-MER RING OF HMPV N-RNA BOUND TO THE C-TERMINAL REGION OF P COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOPROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTEIN N,NUCLEOCAPSID PROTEIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: PHOSPHOPROTEIN; COMPND 8 CHAIN: B; COMPND 9 SYNONYM: PROTEIN P; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: RNA; COMPND 13 CHAIN: E; COMPND 14 OTHER_DETAILS: E.COLI RNA, CO-PURIFIED WITH N. DUE TO MIXED SEQUENCE, COMPND 15 MODELLED AS POLY-C SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN METAPNEUMOVIRUS (STRAIN CAN97-83); SOURCE 3 ORGANISM_COMMON: HMPV; SOURCE 4 ORGANISM_TAXID: 694067; SOURCE 5 STRAIN: CAN97-83; SOURCE 6 GENE: N; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: ROSETTA2; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: POPINE; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: UMAN METAPNEUMOVIRUS (STRAIN CAN97-83); SOURCE 14 ORGANISM_COMMON: HMPV; SOURCE 15 ORGANISM_TAXID: 694067; SOURCE 16 MOL_ID: 3; SOURCE 17 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 18 ORGANISM_TAXID: 562; SOURCE 19 STRAIN: ROSETTA2 KEYWDS NUCLEOPROTEIN, VIRUS, NUCLEOCAPSID, RNA-BINDING, HMPV, PNEUMOVIRIDAE, KEYWDS 2 MONONEGAVIRALES, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR J.D.WHITEHEAD,H.DECOOL,C.LEYRAT,L.CARRIQUE,J.FIX,J.F.ELEOUET, AUTHOR 2 M.GALLOUX,M.RENNER REVDAT 2 20-MAR-24 8PDQ 1 COMPND SOURCE DBREF SEQADV REVDAT 1 06-DEC-23 8PDQ 0 JRNL AUTH J.D.WHITEHEAD,H.DECOOL,C.LEYRAT,L.CARRIQUE,J.FIX, JRNL AUTH 2 J.F.ELEOUET,M.GALLOUX,M.RENNER JRNL TITL STRUCTURE OF THE N-RNA/P INTERFACE INDICATES MODE OF L/P JRNL TITL 2 RECRUITMENT TO THE NUCLEOCAPSID OF HUMAN METAPNEUMOVIRUS. JRNL REF NAT COMMUN V. 14 7627 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 37993464 JRNL DOI 10.1038/S41467-023-43434-5 REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, SERIALEM, CRYOSPARC, PHENIX, REMARK 3 CRYOSPARC, CRYOSPARC, CRYOSPARC 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) : 3.100 REMARK 3 NUMBER OF PARTICLES : 243119 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 8PDQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1292131119. 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 : HUMAN METAPNEUMOVIRUS N-RNA REMARK 245 BOUND TO C-TERMINAL REGION OF P; REMARK 245 NUCLEOPROTEIN; HUMAN REMARK 245 METAPNEUMOVIRUS P C-TERMINAL REMARK 245 REGION; RNA REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.50 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 : GATAN K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2600.00 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) : 4420.00 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: 33-MERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: 33-MERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, E 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 0.841254 -0.540641 0.000000 146.87132 REMARK 350 BIOMT2 2 0.540641 0.841254 0.000000 -80.19781 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 0.415415 -0.909632 0.000000 313.78554 REMARK 350 BIOMT2 3 0.909632 0.415415 0.000000 -68.25987 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -0.142315 -0.989821 0.000000 447.74859 REMARK 350 BIOMT2 4 0.989821 -0.142315 0.000000 32.02361 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 5 -0.654861 -0.755750 0.000000 506.22813 REMARK 350 BIOMT2 5 0.755750 -0.654861 0.000000 188.81333 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 6 -0.959493 -0.281733 0.000000 470.65733 REMARK 350 BIOMT2 6 0.281733 -0.959493 0.000000 352.32966 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 7 -0.959493 0.281733 0.000000 352.32966 REMARK 350 BIOMT2 7 -0.281733 -0.959493 0.000000 470.65733 REMARK 350 BIOMT3 7 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 8 -0.654861 0.755750 0.000000 188.81333 REMARK 350 BIOMT2 8 -0.755750 -0.654861 0.000000 506.22813 REMARK 350 BIOMT3 8 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 9 -0.142315 0.989821 0.000000 32.02361 REMARK 350 BIOMT2 9 -0.989821 -0.142315 0.000000 447.74859 REMARK 350 BIOMT3 9 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 10 0.415415 0.909632 0.000000 -68.25987 REMARK 350 BIOMT2 10 -0.909632 0.415415 0.000000 313.78554 REMARK 350 BIOMT3 10 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 11 0.841254 0.540641 0.000000 -80.19781 REMARK 350 BIOMT2 11 -0.540641 0.841254 0.000000 146.87132 REMARK 350 BIOMT3 11 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 GLY A 144 REMARK 465 ASN A 145 REMARK 465 PHE A 366 REMARK 465 SER A 367 REMARK 465 SER A 368 REMARK 465 LEU A 369 REMARK 465 GLY A 370 REMARK 465 LEU A 371 REMARK 465 THR A 372 REMARK 465 ASP A 373 REMARK 465 GLU A 374 REMARK 465 GLU A 375 REMARK 465 LYS A 376 REMARK 465 GLU A 377 REMARK 465 ALA A 378 REMARK 465 ALA A 379 REMARK 465 GLU A 380 REMARK 465 HIS A 381 REMARK 465 PHE A 382 REMARK 465 LEU A 383 REMARK 465 ASN A 384 REMARK 465 VAL A 385 REMARK 465 SER A 386 REMARK 465 ASP A 387 REMARK 465 ASP A 388 REMARK 465 SER A 389 REMARK 465 GLN A 390 REMARK 465 ASN A 391 REMARK 465 ASP A 392 REMARK 465 TYR A 393 REMARK 465 GLU A 394 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 OH TYR A 338 OP2 C E 74 2.15 REMARK 500 OH TYR A 98 OE2 GLU A 125 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 LEU A 3 53.72 -90.67 REMARK 500 TYR A 59 40.36 -109.89 REMARK 500 GLU A 89 30.18 -95.41 REMARK 500 LEU A 191 51.76 -94.96 REMARK 500 MET A 337 34.87 -96.66 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-17618 RELATED DB: EMDB REMARK 900 11-MER RING OF HMPV N-RNA BOUND TO THE C-TERMINAL REGION OF P DBREF 8PDQ A 1 394 UNP Q6WBA1 NCAP_HMPVC 1 394 DBREF 8PDQ B 10 16 UNP Q8B9Q8 PHOSP_HMPVC 288 294 DBREF 8PDQ E 71 77 PDB 8PDQ 8PDQ 71 77 SEQADV 8PDQ ILE A 103 UNP Q6WBA1 VAL 103 VARIANT SEQADV 8PDQ HIS A 220 UNP Q6WBA1 TYR 220 VARIANT SEQRES 1 A 394 MET SER LEU GLN GLY ILE HIS LEU SER ASP LEU SER TYR SEQRES 2 A 394 LYS HIS ALA ILE LEU LYS GLU SER GLN TYR THR ILE LYS SEQRES 3 A 394 ARG ASP VAL GLY THR THR THR ALA VAL THR PRO SER SER SEQRES 4 A 394 LEU GLN GLN GLU ILE THR LEU LEU CYS GLY GLU ILE LEU SEQRES 5 A 394 TYR ALA LYS HIS ALA ASP TYR LYS TYR ALA ALA GLU ILE SEQRES 6 A 394 GLY ILE GLN TYR ILE SER THR ALA LEU GLY SER GLU ARG SEQRES 7 A 394 VAL GLN GLN ILE LEU ARG ASN SER GLY SER GLU VAL GLN SEQRES 8 A 394 VAL VAL LEU THR ARG THR TYR SER LEU GLY LYS ILE LYS SEQRES 9 A 394 ASN ASN LYS GLY GLU ASP LEU GLN MET LEU ASP ILE HIS SEQRES 10 A 394 GLY VAL GLU LYS SER TRP VAL GLU GLU ILE ASP LYS GLU SEQRES 11 A 394 ALA ARG LYS THR MET ALA THR LEU LEU LYS GLU SER SER SEQRES 12 A 394 GLY ASN ILE PRO GLN ASN GLN ARG PRO SER ALA PRO ASP SEQRES 13 A 394 THR PRO ILE ILE LEU LEU CYS VAL GLY ALA LEU ILE PHE SEQRES 14 A 394 THR LYS LEU ALA SER THR ILE GLU VAL GLY LEU GLU THR SEQRES 15 A 394 THR VAL ARG ARG ALA ASN ARG VAL LEU SER ASP ALA LEU SEQRES 16 A 394 LYS ARG TYR PRO ARG MET ASP ILE PRO LYS ILE ALA ARG SEQRES 17 A 394 SER PHE TYR ASP LEU PHE GLU GLN LYS VAL TYR HIS ARG SEQRES 18 A 394 SER LEU PHE ILE GLU TYR GLY LYS ALA LEU GLY SER SER SEQRES 19 A 394 SER THR GLY SER LYS ALA GLU SER LEU PHE VAL ASN ILE SEQRES 20 A 394 PHE MET GLN ALA TYR GLY ALA GLY GLN THR MET LEU ARG SEQRES 21 A 394 TRP GLY VAL ILE ALA ARG SER SER ASN ASN ILE MET LEU SEQRES 22 A 394 GLY HIS VAL SER VAL GLN ALA GLU LEU LYS GLN VAL THR SEQRES 23 A 394 GLU VAL TYR ASP LEU VAL ARG GLU MET GLY PRO GLU SER SEQRES 24 A 394 GLY LEU LEU HIS LEU ARG GLN SER PRO LYS ALA GLY LEU SEQRES 25 A 394 LEU SER LEU ALA ASN CYS PRO ASN PHE ALA SER VAL VAL SEQRES 26 A 394 LEU GLY ASN ALA SER GLY LEU GLY ILE ILE GLY MET TYR SEQRES 27 A 394 ARG GLY ARG VAL PRO ASN THR GLU LEU PHE SER ALA ALA SEQRES 28 A 394 GLU SER TYR ALA LYS SER LEU LYS GLU SER ASN LYS ILE SEQRES 29 A 394 ASN PHE SER SER LEU GLY LEU THR ASP GLU GLU LYS GLU SEQRES 30 A 394 ALA ALA GLU HIS PHE LEU ASN VAL SER ASP ASP SER GLN SEQRES 31 A 394 ASN ASP TYR GLU SEQRES 1 B 7 ASP ILE TYR GLN LEU ILE MET SEQRES 1 E 7 C C C C C C C HELIX 1 AA1 SER A 9 GLU A 20 1 12 HELIX 2 AA2 PRO A 37 SER A 39 5 3 HELIX 3 AA3 LEU A 40 ILE A 51 1 12 HELIX 4 AA4 TYR A 61 GLY A 75 1 15 HELIX 5 AA5 GLY A 75 SER A 86 1 12 HELIX 6 AA6 GLU A 120 SER A 142 1 23 HELIX 7 AA7 PRO A 147 ARG A 151 5 5 HELIX 8 AA8 ASP A 156 LYS A 171 1 16 HELIX 9 AA9 THR A 175 ASN A 188 1 14 HELIX 10 AB1 LEU A 191 TYR A 198 1 8 HELIX 11 AB2 ASP A 202 LYS A 217 1 16 HELIX 12 AB3 VAL A 218 SER A 233 1 16 HELIX 13 AB4 SER A 238 GLN A 250 1 13 HELIX 14 AB5 GLN A 256 SER A 268 1 13 HELIX 15 AB6 ASN A 270 GLY A 274 5 5 HELIX 16 AB7 HIS A 275 ALA A 280 1 6 HELIX 17 AB8 GLU A 281 GLY A 296 1 16 HELIX 18 AB9 PRO A 297 GLY A 300 5 4 HELIX 19 AC1 LEU A 301 GLN A 306 1 6 HELIX 20 AC2 CYS A 318 LEU A 332 1 15 HELIX 21 AC3 ASN A 344 SER A 361 1 18 HELIX 22 AC4 ASP B 10 LEU B 14 5 5 SHEET 1 AA1 2 THR A 32 VAL A 35 0 SHEET 2 AA1 2 GLN A 91 LEU A 94 1 O VAL A 93 N THR A 33 SHEET 1 AA2 2 ARG A 96 LYS A 104 0 SHEET 2 AA2 2 ASP A 110 ASP A 115 -1 O MET A 113 N TYR A 98 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