HEADER VIRAL PROTEIN 11-MAY-21 7OI3 TITLE CRYO-EM STRUCTURE OF THE CETACEAN MORBILLIVIRUS NUCLEOPROTEIN-RNA TITLE 2 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: CETACEAN MORBILLIVIRUS NUCLEOPROTEIN; COMPND 3 CHAIN: E; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: POLY-A 6-MER; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MORBILLIVIRUS SP.; SOURCE 3 ORGANISM_TAXID: 2078987; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: MORBILLIVIRUS SP.; SOURCE 8 ORGANISM_TAXID: 2078987; SOURCE 9 EXPRESSION_SYSTEM: SYNTHETIC CONSTRUCT; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 32630 KEYWDS CETACEAN MORBILLIVIRUS; NUCLEOCAPSID; RNA VIRUS REPLICATION; CRYO- KEYWDS 2 ELECTRON MICROSCOPY; HELICAL RECONSTRUCTION; SINGLE PARTICLE KEYWDS 3 ANALYSIS, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR L.ZINZULA,F.BECK,S.KLUMPE,S.BOHN,G.PFEIFER,D.BOLLSCHWEILER,I.NAGY, AUTHOR 2 J.M.PLITZKO,W.BAUMEISTER REVDAT 2 10-JUL-24 7OI3 1 REMARK REVDAT 1 23-JUN-21 7OI3 0 JRNL AUTH L.ZINZULA,F.BECK,S.KLUMPE,S.BOHN,G.PFEIFER,D.BOLLSCHWEILER, JRNL AUTH 2 I.NAGY,J.M.PLITZKO,W.BAUMEISTER JRNL TITL CRYO-EM STRUCTURE OF THE CETACEAN MORBILLIVIRUS JRNL TITL 2 NUCLEOPROTEIN-RNA COMPLEX. JRNL REF J.STRUCT.BIOL. V. 213 07750 2021 JRNL REFN ESSN 1095-8657 JRNL PMID 34089875 JRNL DOI 10.1016/J.JSB.2021.107750 REMARK 2 REMARK 2 RESOLUTION. 4.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : SERIALEM, LATITUDE, CTFFIND, RELION, REMARK 3 RELION 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) : 4.000 REMARK 3 NUMBER OF PARTICLES : 31361 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 7OI3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-MAY-21. REMARK 100 THE DEPOSITION ID IS D_1292115174. 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 : HELICAL ARRAY REMARK 245 PARTICLE TYPE : HELICAL REMARK 245 NAME OF SAMPLE : CETACEAN MORBILLIVIRUS REMARK 245 NUCLEOPROTEIN-RNA COMPLEX; REMARK 245 CETACEAN MORBILLIVIRUS REMARK 245 NUCLEOPROTEIN; POLY-A 6-MER REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.80 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 : 3153 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3000.00 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) : 5500.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 22500 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: 30-MERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, 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 350 BIOMT1 2 0.546102 0.837719 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.837719 0.546102 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 10.00000 REMARK 350 BIOMT1 3 0.081069 0.996709 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.996709 0.081069 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 15.00000 REMARK 350 BIOMT1 4 -0.403545 0.914960 0.000000 0.00000 REMARK 350 BIOMT2 4 -0.914960 -0.403545 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 20.00000 REMARK 350 BIOMT1 5 -0.790690 0.612217 0.000000 0.00000 REMARK 350 BIOMT2 5 -0.612217 -0.790690 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 25.00000 REMARK 350 BIOMT1 6 -0.986856 0.161604 0.000000 0.00000 REMARK 350 BIOMT2 6 -0.161604 -0.986856 0.000000 0.00000 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 30.00000 REMARK 350 BIOMT1 7 -0.944663 -0.328042 0.000000 0.00000 REMARK 350 BIOMT2 7 0.328042 -0.944663 0.000000 0.00000 REMARK 350 BIOMT3 7 0.000000 0.000000 1.000000 35.00000 REMARK 350 BIOMT1 8 0.879233 -0.476392 0.000000 0.00000 REMARK 350 BIOMT2 8 0.476392 0.879233 0.000000 0.00000 REMARK 350 BIOMT3 8 0.000000 0.000000 1.000000 -5.00000 REMARK 350 BIOMT1 9 0.546102 -0.837719 0.000000 0.00000 REMARK 350 BIOMT2 9 0.837719 0.546102 0.000000 0.00000 REMARK 350 BIOMT3 9 0.000000 0.000000 1.000000 -10.00000 REMARK 350 BIOMT1 10 0.081069 -0.996709 0.000000 0.00000 REMARK 350 BIOMT2 10 0.996709 0.081069 0.000000 0.00000 REMARK 350 BIOMT3 10 0.000000 0.000000 1.000000 -15.00000 REMARK 350 BIOMT1 11 -0.403545 -0.914960 0.000000 0.00000 REMARK 350 BIOMT2 11 0.914960 -0.403545 0.000000 0.00000 REMARK 350 BIOMT3 11 0.000000 0.000000 1.000000 -20.00000 REMARK 350 BIOMT1 12 -0.790690 -0.612217 0.000000 0.00000 REMARK 350 BIOMT2 12 0.612217 -0.790690 0.000000 0.00000 REMARK 350 BIOMT3 12 0.000000 0.000000 1.000000 -25.00000 REMARK 350 BIOMT1 13 -0.986856 -0.161604 0.000000 0.00000 REMARK 350 BIOMT2 13 0.161604 -0.986856 0.000000 0.00000 REMARK 350 BIOMT3 13 0.000000 0.000000 1.000000 -30.00000 REMARK 350 BIOMT1 14 -0.944663 0.328042 0.000000 0.00000 REMARK 350 BIOMT2 14 -0.328042 -0.944663 0.000000 0.00000 REMARK 350 BIOMT3 14 0.000000 0.000000 1.000000 -35.00000 REMARK 350 BIOMT1 15 0.879233 0.476392 0.000000 0.00000 REMARK 350 BIOMT2 15 -0.476392 0.879233 0.000000 0.00000 REMARK 350 BIOMT3 15 0.000000 0.000000 1.000000 5.00000 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 E 0 REMARK 465 MET E 1 REMARK 465 GLU E 396 REMARK 465 ILE E 397 REMARK 465 ALA E 398 REMARK 465 ALA E 399 REMARK 465 GLN E 400 REMARK 465 ALA E 401 REMARK 465 ASN E 402 REMARK 465 ASP E 403 REMARK 465 ASP E 404 REMARK 465 ARG E 405 REMARK 465 VAL E 406 REMARK 465 GLU E 407 REMARK 465 HIS E 408 REMARK 465 HIS E 409 REMARK 465 HIS E 410 REMARK 465 HIS E 411 REMARK 465 HIS E 412 REMARK 465 HIS E 413 REMARK 465 HIS E 414 REMARK 465 HIS E 415 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 OG SER E 44 OG1 THR E 47 2.01 REMARK 500 O SER E 268 OG1 THR E 272 2.03 REMARK 500 OG SER E 334 OD1 ASP E 358 2.09 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 ASP E 93 31.69 -142.22 REMARK 500 GLU E 108 31.76 -98.04 REMARK 500 LYS E 180 16.02 -143.08 REMARK 500 THR E 187 55.51 -90.78 REMARK 500 ALA E 188 31.85 -140.90 REMARK 500 PHE E 209 52.28 -92.47 REMARK 500 THR E 243 108.68 -58.67 REMARK 500 GLU E 317 44.55 39.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-12918 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF THE CETACEAN MORBILLIVIRUS NUCLEOPROTEIN-RNA REMARK 900 COMPLEX DBREF1 7OI3 E 1 408 UNP A0A1I9RYK9_9MONO DBREF2 7OI3 E A0A1I9RYK9 1 408 DBREF 7OI3 B 1 6 PDB 7OI3 7OI3 1 6 SEQADV 7OI3 GLY E 0 UNP A0A1I9RYK EXPRESSION TAG SEQADV 7OI3 VAL E 406 UNP A0A1I9RYK ALA 406 CONFLICT SEQADV 7OI3 GLU E 407 UNP A0A1I9RYK ASN 407 CONFLICT SEQADV 7OI3 HIS E 408 UNP A0A1I9RYK ARG 408 CONFLICT SEQADV 7OI3 HIS E 409 UNP A0A1I9RYK EXPRESSION TAG SEQADV 7OI3 HIS E 410 UNP A0A1I9RYK EXPRESSION TAG SEQADV 7OI3 HIS E 411 UNP A0A1I9RYK EXPRESSION TAG SEQADV 7OI3 HIS E 412 UNP A0A1I9RYK EXPRESSION TAG SEQADV 7OI3 HIS E 413 UNP A0A1I9RYK EXPRESSION TAG SEQADV 7OI3 HIS E 414 UNP A0A1I9RYK EXPRESSION TAG SEQADV 7OI3 HIS E 415 UNP A0A1I9RYK EXPRESSION TAG SEQRES 1 E 416 GLY MET ALA THR LEU LEU ARG SER LEU ALA LEU PHE LYS SEQRES 2 E 416 ARG ASN LYS ASP ARG THR PRO LEU THR ALA GLY SER GLY SEQRES 3 E 416 GLY ALA ILE ARG GLY ILE LYS HIS VAL ILE VAL VAL PRO SEQRES 4 E 416 VAL PRO GLY ASP SER SER ILE VAL THR ARG SER ARG LEU SEQRES 5 E 416 LEU ASP ARG LEU VAL ARG LEU ALA GLY ASP PRO TYR ILE SEQRES 6 E 416 SER GLY PRO LYS LEU THR GLY VAL MET ILE SER ILE LEU SEQRES 7 E 416 SER LEU PHE VAL GLU SER PRO SER GLN LEU ILE GLN ARG SEQRES 8 E 416 ILE THR ASP ASP PRO ASP VAL SER ILE ARG LEU VAL GLU SEQRES 9 E 416 VAL ILE GLN SER GLU LYS SER LEU SER GLY LEU THR PHE SEQRES 10 E 416 ALA SER ARG GLY ALA ASN MET GLU ASP GLU ALA ASP ASP SEQRES 11 E 416 TYR PHE SER ILE GLN ALA GLY GLU GLU GLY ASP THR ARG SEQRES 12 E 416 GLY THR HIS TRP PHE GLU ASN LYS GLU ILE VAL GLU ILE SEQRES 13 E 416 GLU VAL GLN ASP PRO GLU GLU PHE ASN ILE LEU LEU ALA SEQRES 14 E 416 SER ILE LEU ALA GLN ILE TRP ILE LEU LEU ALA LYS ALA SEQRES 15 E 416 VAL THR ALA PRO ASP THR ALA ALA ASP SER GLU THR ARG SEQRES 16 E 416 ARG TRP ILE LYS TYR THR GLN GLN ARG ARG VAL VAL GLY SEQRES 17 E 416 GLU PHE ARG LEU ASP LYS GLY TRP LEU ASP ALA VAL ARG SEQRES 18 E 416 ASN ARG ILE ALA GLU ASP LEU SER LEU ARG ARG PHE MET SEQRES 19 E 416 VAL ALA LEU ILE LEU ASP ILE LYS ARG THR PRO GLY ASN SEQRES 20 E 416 LYS PRO ARG ILE ALA GLU MET ILE CYS ASP ILE ASP THR SEQRES 21 E 416 TYR ILE VAL GLU ALA GLY LEU ALA SER PHE ILE LEU THR SEQRES 22 E 416 ILE LYS PHE GLY ILE GLU THR MET TYR PRO ALA LEU GLY SEQRES 23 E 416 LEU HIS GLU PHE SER GLY GLU LEU THR THR VAL GLU SER SEQRES 24 E 416 LEU MET ASN LEU TYR GLN GLN MET GLY GLU THR ALA PRO SEQRES 25 E 416 TYR MET VAL ILE LEU GLU ASN SER ILE GLN ASN LYS PHE SEQRES 26 E 416 SER ALA GLY SER TYR PRO LEU LEU TRP SER TYR ALA MET SEQRES 27 E 416 GLY VAL GLY VAL GLU LEU GLU ASN SER MET GLY GLY LEU SEQRES 28 E 416 ASN PHE GLY ARG SER TYR PHE ASP PRO ALA TYR PHE ARG SEQRES 29 E 416 LEU GLY GLN GLU MET VAL ARG ARG SER ALA GLY LYS VAL SEQRES 30 E 416 SER SER SER LEU ALA ALA GLU LEU GLY ILE THR ALA GLU SEQRES 31 E 416 ASP ALA LYS LEU VAL SER GLU ILE ALA ALA GLN ALA ASN SEQRES 32 E 416 ASP ASP ARG VAL GLU HIS HIS HIS HIS HIS HIS HIS HIS SEQRES 1 B 6 A A A A A A HELIX 1 AA1 ALA E 2 ASP E 16 1 15 HELIX 2 AA2 ILE E 45 GLY E 60 1 16 HELIX 3 AA3 SER E 65 SER E 78 1 14 HELIX 4 AA4 SER E 83 THR E 92 1 10 HELIX 5 AA5 GLU E 124 SER E 132 1 9 HELIX 6 AA6 ASP E 140 THR E 144 5 5 HELIX 7 AA7 ASP E 159 ILE E 176 1 18 HELIX 8 AA8 LEU E 177 LYS E 180 5 4 HELIX 9 AA9 ALA E 188 GLN E 201 1 14 HELIX 10 AB1 VAL E 206 ARG E 210 5 5 HELIX 11 AB2 ASP E 212 ASP E 226 1 15 HELIX 12 AB3 LEU E 227 ARG E 242 1 16 HELIX 13 AB4 PRO E 248 VAL E 262 1 15 HELIX 14 AB5 LEU E 266 ILE E 277 1 12 HELIX 15 AB6 TYR E 281 LEU E 286 5 6 HELIX 16 AB7 PHE E 289 GLY E 307 1 19 HELIX 17 AB8 ALA E 310 VAL E 314 5 5 HELIX 18 AB9 ASN E 318 SER E 328 5 11 HELIX 19 AC1 TYR E 329 GLU E 344 1 16 HELIX 20 AC2 ASP E 358 SER E 372 1 15 HELIX 21 AC3 SER E 378 GLY E 385 1 8 HELIX 22 AC4 THR E 387 ALA E 391 5 5 SHEET 1 AA1 3 HIS E 33 PRO E 40 0 SHEET 2 AA1 3 VAL E 97 GLN E 106 1 O SER E 98 N HIS E 33 SHEET 3 AA1 3 LEU E 114 PHE E 116 -1 O THR E 115 N ILE E 105 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