HEADER NUCLEAR PROTEIN/RNA 28-JAN-19 6JC3 TITLE THE CRYO-EM STRUCTURE OF NUCLEOPROTEIN-RNA COMPLEX OF NEWCASTLE TITLE 2 DISEASE VIRUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOCAPSID; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NUCLEOCAPSID PROTEIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: POLYU; COMPND 8 CHAIN: N; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AVIAN AVULAVIRUS 1; SOURCE 3 ORGANISM_TAXID: 11176; SOURCE 4 GENE: NP, N; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 10 ORGANISM_TAXID: 562 KEYWDS SELF-CAPPING HELICAL STRUCTURE COMPLEX, NUCLEAR PROTEIN, NUCLEAR KEYWDS 2 PROTEIN-RNA COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR X.SONG,H.SHAN,Y.ZHU,W.DING,S.OUYANG,Q.T.SHEN,Z.J.LIU REVDAT 4 27-MAR-24 6JC3 1 REMARK REVDAT 3 06-NOV-19 6JC3 1 CRYST1 REVDAT 2 14-AUG-19 6JC3 1 JRNL REVDAT 1 07-AUG-19 6JC3 0 JRNL AUTH X.SONG,H.SHAN,Y.ZHU,S.HU,L.XUE,Y.CHEN,W.DING,T.NIU,J.GU, JRNL AUTH 2 S.OUYANG,Q.T.SHEN,Z.J.LIU JRNL TITL SELF-CAPPING OF NUCLEOPROTEIN FILAMENTS PROTECTS THE JRNL TITL 2 NEWCASTLE DISEASE VIRUS GENOME. JRNL REF ELIFE V. 8 2019 JRNL REFN ESSN 2050-084X JRNL PMID 31290740 JRNL DOI 10.7554/ELIFE.45057 REMARK 2 REMARK 2 RESOLUTION. 4.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : SERIALEM, CTFFIND, 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) : 4.800 REMARK 3 NUMBER OF PARTICLES : 75290 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 6JC3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-FEB-19. REMARK 100 THE DEPOSITION ID IS D_1300010128. 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 : TERNARY COMPLEX OF REMARK 245 NUCLEOPROTEIN-RNA OF NEWCASTLE REMARK 245 DISEASE VIRUS REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : GLOW DISCHARGED 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K2 SUMMIT (4K X 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) : 4100.00 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, N 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 ASN A 19 REMARK 465 GLY A 20 REMARK 465 ALA A 21 REMARK 465 LEU A 22 REMARK 465 GLY A 23 REMARK 465 GLY A 24 REMARK 465 GLY A 25 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 CD2 LEU A 314 OD1 ASP A 316 1.51 REMARK 500 NE2 GLN A 319 N MET A 320 1.63 REMARK 500 CE2 PHE A 107 CA PHE A 114 1.90 REMARK 500 O PHE A 128 N ALA A 132 1.92 REMARK 500 O ASP A 318 OG SER A 321 2.00 REMARK 500 CG MET A 180 OE2 GLU A 184 2.00 REMARK 500 O GLN A 319 N PHE A 322 2.00 REMARK 500 O SER A 286 N SER A 288 2.01 REMARK 500 CG PHE A 107 O GLN A 113 2.06 REMARK 500 O GLY A 336 OG SER A 339 2.09 REMARK 500 CZ PHE A 107 CB PHE A 114 2.13 REMARK 500 CZ PHE A 107 CA PHE A 114 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 U N 37 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES 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 GLN A 82 -79.90 -90.29 REMARK 500 ALA A 97 -159.51 -93.12 REMARK 500 VAL A 101 -60.08 -96.37 REMARK 500 GLU A 103 93.56 -60.81 REMARK 500 ASP A 105 8.85 51.36 REMARK 500 ASN A 141 -2.47 57.47 REMARK 500 ASP A 152 45.74 -82.51 REMARK 500 ALA A 242 -159.53 -76.73 REMARK 500 THR A 245 -154.28 -164.52 REMARK 500 LEU A 264 30.62 -93.51 REMARK 500 LEU A 287 -10.75 -39.17 REMARK 500 LYS A 304 -73.98 -69.49 REMARK 500 PRO A 309 10.07 -65.55 REMARK 500 MET A 320 -32.38 -37.91 REMARK 500 PHE A 322 39.35 -78.63 REMARK 500 GLN A 329 -70.86 -65.36 REMARK 500 LYS A 343 67.61 -105.59 REMARK 500 PHE A 350 74.72 -111.88 REMARK 500 ALA A 369 78.77 -118.09 REMARK 500 GLN A 370 27.07 -74.96 REMARK 500 SER A 373 88.44 -60.52 REMARK 500 GLN A 397 6.05 -67.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-9793 RELATED DB: EMDB REMARK 900 THE CRYO-EM STRUCTURE OF NUCLEOPROTEIN-RNA COMPLEX OF NEWCASTLE REMARK 900 DISEASE VIRUS DBREF 6JC3 A 1 398 UNP D6R3F6 D6R3F6_9MONO 1 398 DBREF 6JC3 N 34 39 PDB 6JC3 6JC3 34 39 SEQRES 1 A 398 MET SER SER VAL PHE ASP GLU TYR GLU GLN LEU LEU ALA SEQRES 2 A 398 ALA GLN THR ARG PRO ASN GLY ALA LEU GLY GLY GLY GLU SEQRES 3 A 398 LYS GLY SER THR LEU LYS VAL GLU VAL PRO VAL PHE THR SEQRES 4 A 398 LEU ASN SER ASP ASP PRO GLU ASP ARG TRP ASN PHE ALA SEQRES 5 A 398 VAL PHE CYS LEU ARG ILE ALA VAL SER GLU ASP ALA ASN SEQRES 6 A 398 LYS PRO LEU ARG GLN GLY ALA LEU ILE SER LEU LEU CYS SEQRES 7 A 398 SER HIS SER GLN VAL MET ARG ASN HIS VAL ALA LEU ALA SEQRES 8 A 398 GLY LYS GLN ASN GLU ALA THR LEU ALA VAL LEU GLU ILE SEQRES 9 A 398 ASP GLY PHE THR ASN GLY VAL PRO GLN PHE ASN ASN ARG SEQRES 10 A 398 SER GLY VAL SER GLU GLU ARG ALA GLN ARG PHE MET MET SEQRES 11 A 398 ILE ALA GLY SER LEU PRO ARG ALA CYS SER ASN GLY THR SEQRES 12 A 398 PRO PHE VAL THR ALA GLY VAL GLU ASP ASP ALA PRO GLU SEQRES 13 A 398 ASP ILE THR ASP THR LEU GLU ARG ILE LEU SER ILE GLN SEQRES 14 A 398 ALA GLN VAL TRP VAL THR VAL ALA LYS ALA MET THR ALA SEQRES 15 A 398 TYR GLU THR ALA ASP GLU SER GLU THR ARG ARG ILE ASN SEQRES 16 A 398 LYS TYR MET GLN GLN GLY ARG VAL GLN LYS LYS TYR ILE SEQRES 17 A 398 LEU HIS PRO VAL CYS ARG SER ALA ILE GLN LEU THR ILE SEQRES 18 A 398 ARG GLN SER LEU ALA VAL ARG ILE PHE LEU VAL SER GLU SEQRES 19 A 398 LEU LYS ARG GLY ARG ASN THR ALA GLY GLY THR SER THR SEQRES 20 A 398 TYR TYR ASN LEU VAL GLY ASP VAL ASP SER TYR ILE ARG SEQRES 21 A 398 ASN THR GLY LEU THR ALA PHE PHE LEU THR LEU LYS TYR SEQRES 22 A 398 GLY ILE ASN THR LYS THR SER ALA LEU ALA LEU SER SER SEQRES 23 A 398 LEU SER GLY ASP ILE GLN LYS MET LYS GLN LEU MET ARG SEQRES 24 A 398 LEU TYR ARG MET LYS GLY ASP ASN ALA PRO TYR MET THR SEQRES 25 A 398 LEU LEU GLY ASP SER ASP GLN MET SER PHE ALA PRO ALA SEQRES 26 A 398 GLU TYR ALA GLN LEU TYR SER PHE ALA MET GLY MET ALA SEQRES 27 A 398 SER VAL LEU ASP LYS GLY THR GLY LYS TYR GLN PHE ALA SEQRES 28 A 398 ARG ASP PHE MET SER THR SER PHE TRP ARG LEU GLY VAL SEQRES 29 A 398 GLU TYR ALA GLN ALA GLN GLY SER SER ILE ASN GLU ASP SEQRES 30 A 398 MET ALA ALA GLU LEU LYS LEU THR PRO ALA ALA ARG ARG SEQRES 31 A 398 GLY LEU ALA ALA ALA ALA GLN ARG SEQRES 1 N 6 U U U U U U HELIX 1 AA1 SER A 3 GLN A 15 1 13 HELIX 2 AA2 ASP A 44 VAL A 60 1 17 HELIX 3 AA3 ASN A 65 SER A 79 1 15 HELIX 4 AA4 MET A 84 LYS A 93 1 10 HELIX 5 AA5 GLU A 123 GLY A 133 1 11 HELIX 6 AA6 THR A 147 GLU A 151 5 5 HELIX 7 AA7 ASP A 157 THR A 175 1 19 HELIX 8 AA8 ALA A 186 GLY A 201 1 16 HELIX 9 AA9 GLN A 204 ILE A 208 5 5 HELIX 10 AB1 HIS A 210 SER A 224 1 15 HELIX 11 AB2 SER A 224 THR A 241 1 18 HELIX 12 AB3 SER A 246 ARG A 260 1 15 HELIX 13 AB4 LEU A 264 TYR A 273 1 10 HELIX 14 AB5 THR A 279 ALA A 283 5 5 HELIX 15 AB6 LEU A 287 MET A 303 1 17 HELIX 16 AB7 ASN A 307 PRO A 309 5 3 HELIX 17 AB8 TYR A 310 GLY A 315 1 6 HELIX 18 AB9 ASP A 316 ALA A 323 5 8 HELIX 19 AC1 PRO A 324 GLU A 326 5 3 HELIX 20 AC2 TYR A 327 ASP A 342 1 16 HELIX 21 AC3 SER A 356 ALA A 369 1 14 HELIX 22 AC4 ASN A 375 LYS A 383 1 9 HELIX 23 AC5 THR A 385 GLN A 397 1 13 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