HEADER VIRAL PROTEIN 02-DEC-22 8FD5 TITLE NUCLEOCAPSID MONOMER STRUCTURE FROM SARS-COV-2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOPROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: N,NUCLEOCAPSID PROTEIN,NC,PROTEIN N; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_TAXID: 2697049; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SARS-COV-2, N PROTEIN, COVID-19, RNA BINDING PROTEIN, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR M.CASASANTA,G.M.JONAID,L.KAYLOR,W.LUQIU,L.DICECCO,M.SOLARES,S.BERRY, AUTHOR 2 D.F.KELLY REVDAT 2 11-OCT-23 8FD5 1 JRNL REVDAT 1 11-JAN-23 8FD5 0 JRNL AUTH M.A.CASASANTA,G.M.JONAID,L.KAYLOR,W.Y.LUQIU,L.A.DICECCO, JRNL AUTH 2 M.J.SOLARES,S.BERRY,W.J.DEARNALEY,D.F.KELLY JRNL TITL STRUCTURAL INSIGHTS OF THE SARS-COV-2 NUCLEOCAPSID PROTEIN: JRNL TITL 2 IMPLICATIONS FOR THE INNER-WORKINGS OF RAPID ANTIGEN TESTS. JRNL REF MICROSC MICROANAL V. 29 649 2023 JRNL REFN ESSN 1435-8115 JRNL PMID 37749713 JRNL DOI 10.1093/MICMIC/OZAC036 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.A.CASASANTA,G.M.JONAID,L.KAYLOR,W.Y.LUQIU,M.J.SOLARES, REMARK 1 AUTH 2 M.L.SCHROEN,W.J.DEARNALEY,J.WILSON,M.J.DUKES,D.F.KELLY REMARK 1 TITL MICROCHIP-BASED STRUCTURE DETERMINATION OF LOW-MOLECULAR REMARK 1 TITL 2 WEIGHT PROTEINS USING CRYO-ELECTRON MICROSCOPY. REMARK 1 REF NANOSCALE V. 13 7285 2021 REMARK 1 REFN ESSN 2040-3372 REMARK 1 PMID 33889923 REMARK 1 DOI 10.1016/J.APSB.2020.04.009 REMARK 2 REMARK 2 RESOLUTION. 4.57 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, SERIALEM, RELION, PHENIX, REMARK 3 RELION, RELION, RELION, RELION, ISOLDE REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : 100.000 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) : 4.570 REMARK 3 NUMBER OF PARTICLES : 20000 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING ONLY REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 8FD5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-DEC-22. REMARK 100 THE DEPOSITION ID IS D_1000270416. 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 : A CHAIN CONTAINS THE FULL REMARK 245 -LENGTH N PROTEIN REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.10 REMARK 245 SAMPLE SUPPORT DETAILS : PROTEIN SAMPLES WERE ADDED TO REMARK 245 THE NI-NTA-COATED MICROCHIPS REMARK 245 AND INCUBATED FOR 1 MINUTE AT REMARK 245 ROOM TEMPERATURE PRIOR TO REMARK 245 VITRIFICATION. REMARK 245 SAMPLE VITRIFICATION DETAILS : A MARK III VITROBOT WAS USED TO REMARK 245 PLUNGE SAMPLES INTO LIQUID REMARK 245 ETHANE, OPERATING AT ROOM REMARK 245 TEMPERATURE AND 100% HUMIDITY REMARK 245 WITH 3 - 4 SECONDS BLOT TIME REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : RESIDUES 1-49 WERE FIT INTO THE REMARK 245 MAP SEPARATELY FROM RESIDUES 50 - 419. THE 2 FRAGMENTS WERE FIT REMARK 245 AS INDIVIDUAL RIGID BODIES, THEN REFINED AND REBUILT. THERE IS A REMARK 245 MISSING PEPTIDE LINKAGE BETWEEN RESIDUES 49 AND 50. REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 200 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS TALOS F200C REMARK 245 DETECTOR TYPE : DIRECT ELECTRON DE-12 (4K X REMARK 245 3K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 5000.00 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 : 45000 REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 200 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 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 ARG A 10 NE - CZ - NH1 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 149 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 149 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 203 NE - CZ - NH2 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 226 NE - CZ - NH2 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG A 259 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 262 NE - CZ - NH2 ANGL. DEV. = 4.0 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 PRO A 20 -167.12 -75.59 REMARK 500 THR A 49 -134.46 -104.10 REMARK 500 LYS A 61 10.32 -141.83 REMARK 500 PRO A 67 173.39 -53.14 REMARK 500 PRO A 117 172.86 -56.24 REMARK 500 PRO A 162 48.98 -88.47 REMARK 500 ALA A 173 175.92 -57.50 REMARK 500 LEU A 219 -137.79 55.01 REMARK 500 ALA A 220 -123.42 41.11 REMARK 500 TYR A 298 121.56 -34.10 REMARK 500 PRO A 326 0.24 -63.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 88 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-29002 RELATED DB: EMDB REMARK 900 NUCLEOCAPSID MONOMER STRUCTURE FROM SARS-COV-2 DBREF 8FD5 A 1 419 UNP P0DTC9 NCAP_SARS2 1 419 SEQRES 1 A 419 MET SER ASP ASN GLY PRO GLN ASN GLN ARG ASN ALA PRO SEQRES 2 A 419 ARG ILE THR PHE GLY GLY PRO SER ASP SER THR GLY SER SEQRES 3 A 419 ASN GLN ASN GLY GLU ARG SER GLY ALA ARG SER LYS GLN SEQRES 4 A 419 ARG ARG PRO GLN GLY LEU PRO ASN ASN THR ALA SER TRP SEQRES 5 A 419 PHE THR ALA LEU THR GLN HIS GLY LYS GLU ASP LEU LYS SEQRES 6 A 419 PHE PRO ARG GLY GLN GLY VAL PRO ILE ASN THR ASN SER SEQRES 7 A 419 SER PRO ASP ASP GLN ILE GLY TYR TYR ARG ARG ALA THR SEQRES 8 A 419 ARG ARG ILE ARG GLY GLY ASP GLY LYS MET LYS ASP LEU SEQRES 9 A 419 SER PRO ARG TRP TYR PHE TYR TYR LEU GLY THR GLY PRO SEQRES 10 A 419 GLU ALA GLY LEU PRO TYR GLY ALA ASN LYS ASP GLY ILE SEQRES 11 A 419 ILE TRP VAL ALA THR GLU GLY ALA LEU ASN THR PRO LYS SEQRES 12 A 419 ASP HIS ILE GLY THR ARG ASN PRO ALA ASN ASN ALA ALA SEQRES 13 A 419 ILE VAL LEU GLN LEU PRO GLN GLY THR THR LEU PRO LYS SEQRES 14 A 419 GLY PHE TYR ALA GLU GLY SER ARG GLY GLY SER GLN ALA SEQRES 15 A 419 SER SER ARG SER SER SER ARG SER ARG ASN SER SER ARG SEQRES 16 A 419 ASN SER THR PRO GLY SER SER ARG GLY THR SER PRO ALA SEQRES 17 A 419 ARG MET ALA GLY ASN GLY GLY ASP ALA ALA LEU ALA LEU SEQRES 18 A 419 LEU LEU LEU ASP ARG LEU ASN GLN LEU GLU SER LYS MET SEQRES 19 A 419 SER GLY LYS GLY GLN GLN GLN GLN GLY GLN THR VAL THR SEQRES 20 A 419 LYS LYS SER ALA ALA GLU ALA SER LYS LYS PRO ARG GLN SEQRES 21 A 419 LYS ARG THR ALA THR LYS ALA TYR ASN VAL THR GLN ALA SEQRES 22 A 419 PHE GLY ARG ARG GLY PRO GLU GLN THR GLN GLY ASN PHE SEQRES 23 A 419 GLY ASP GLN GLU LEU ILE ARG GLN GLY THR ASP TYR LYS SEQRES 24 A 419 HIS TRP PRO GLN ILE ALA GLN PHE ALA PRO SER ALA SER SEQRES 25 A 419 ALA PHE PHE GLY MET SER ARG ILE GLY MET GLU VAL THR SEQRES 26 A 419 PRO SER GLY THR TRP LEU THR TYR THR GLY ALA ILE LYS SEQRES 27 A 419 LEU ASP ASP LYS ASP PRO ASN PHE LYS ASP GLN VAL ILE SEQRES 28 A 419 LEU LEU ASN LYS HIS ILE ASP ALA TYR LYS THR PHE PRO SEQRES 29 A 419 PRO THR GLU PRO LYS LYS ASP LYS LYS LYS LYS ALA ASP SEQRES 30 A 419 GLU THR GLN ALA LEU PRO GLN ARG GLN LYS LYS GLN GLN SEQRES 31 A 419 THR VAL THR LEU LEU PRO ALA ALA ASP LEU ASP ASP PHE SEQRES 32 A 419 SER LYS GLN LEU GLN GLN SER MET SER SER ALA ASP SER SEQRES 33 A 419 THR GLN ALA HELIX 1 AA1 LYS A 100 LEU A 104 5 5 HELIX 2 AA2 LEU A 219 MET A 234 1 16 HELIX 3 AA3 ALA A 252 LYS A 257 5 6 HELIX 4 AA4 PRO A 258 ARG A 262 5 5 HELIX 5 AA5 ASN A 269 PHE A 274 1 6 HELIX 6 AA6 ASP A 288 GLY A 295 1 8 HELIX 7 AA7 HIS A 300 ALA A 305 1 6 HELIX 8 AA8 SER A 310 PHE A 315 1 6 HELIX 9 AA9 ASN A 345 ILE A 357 1 13 HELIX 10 AB1 ASP A 358 PHE A 363 5 6 HELIX 11 AB2 ALA A 398 SER A 416 1 19 SHEET 1 AA1 4 LEU A 56 THR A 57 0 SHEET 2 AA1 4 ARG A 107 TYR A 112 -1 O TRP A 108 N LEU A 56 SHEET 3 AA1 4 GLY A 85 ARG A 89 -1 N ARG A 88 O TYR A 109 SHEET 4 AA1 4 GLY A 129 ILE A 130 -1 O GLY A 129 N ARG A 89 SHEET 1 AA2 2 GLY A 321 GLU A 323 0 SHEET 2 AA2 2 TRP A 330 THR A 332 -1 O TRP A 330 N GLU A 323 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