HEADER VIRAL PROTEIN 31-MAR-20 6YI3 TITLE THE N-TERMINAL RNA-BINDING DOMAIN OF THE SARS-COV-2 NUCLEOCAPSID TITLE 2 PHOSPHOPROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOPROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NUCLEOCAPSID PROTEIN,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_COMMON: 2019-NCOV; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COVID-19, RNA-BINDING DOMAIN, SARS, MERS, VIRAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 40 AUTHOR V.VEVERKA,E.BOURA REVDAT 4 14-JUN-23 6YI3 1 REMARK REVDAT 3 30-DEC-20 6YI3 1 JRNL REVDAT 2 06-MAY-20 6YI3 1 COMPND SOURCE DBREF SEQADV REVDAT 1 08-APR-20 6YI3 0 JRNL AUTH D.C.DINESH,D.CHALUPSKA,J.SILHAN,E.KOUTNA,R.NENCKA,V.VEVERKA, JRNL AUTH 2 E.BOURA JRNL TITL STRUCTURAL BASIS OF RNA RECOGNITION BY THE SARS-COV-2 JRNL TITL 2 NUCLEOCAPSID PHOSPHOPROTEIN. JRNL REF PLOS PATHOG. V. 16 09100 2020 JRNL REFN ESSN 1553-7374 JRNL PMID 33264373 JRNL DOI 10.1371/JOURNAL.PPAT.1009100 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA, YASARA REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), YASARA REMARK 3 (YASARA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6YI3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1292107666. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 125 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1 MM [U-13C; U-15N] N-NTD, 25 MM REMARK 210 SODIUM PHOSPHATE, 50 MM SODIUM REMARK 210 CHLORIDE, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCO; 3D HNCACB; 3D CBCA(CO) REMARK 210 NH; 3D 1H-15N NOESY; 3D 1H-13C REMARK 210 NOESY; 3D HCCH-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 850 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, SPARKY REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 40 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 3 ARG A 109 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 4 ARG A 109 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 5 ARG A 49 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 8 ARG A 49 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 11 ARG A 49 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 11 ARG A 109 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 13 ARG A 109 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 14 ARG A 109 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 15 ARG A 109 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 16 ARG A 109 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 19 ARG A 48 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 20 ARG A 49 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 20 ARG A 109 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 21 ARG A 109 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 23 ARG A 49 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 23 ARG A 109 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 25 ARG A 109 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 26 ARG A 109 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 27 ARG A 109 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 28 ARG A 109 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 33 ARG A 109 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 35 ARG A 109 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 39 ARG A 67 NE - CZ - NH1 ANGL. DEV. = 3.2 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 1 THR A 9 77.09 35.11 REMARK 500 1 ASP A 23 -62.84 -95.81 REMARK 500 1 LEU A 24 136.04 173.76 REMARK 500 1 LYS A 103 58.69 -142.29 REMARK 500 2 ASN A 7 -61.93 -144.69 REMARK 500 2 LEU A 24 143.30 179.10 REMARK 500 2 ASP A 63 -140.13 54.45 REMARK 500 2 LEU A 64 173.84 61.11 REMARK 500 2 LYS A 103 57.93 -154.42 REMARK 500 3 LEU A 24 145.77 174.60 REMARK 500 3 ASP A 63 24.02 44.88 REMARK 500 4 ASN A 7 -153.63 -141.70 REMARK 500 4 ASN A 8 44.18 -97.59 REMARK 500 4 LEU A 24 142.55 179.62 REMARK 500 4 LEU A 64 -70.70 -121.22 REMARK 500 4 LYS A 103 57.55 -148.97 REMARK 500 5 ASN A 7 -8.69 -143.92 REMARK 500 5 LEU A 24 141.94 165.28 REMARK 500 5 LEU A 64 -53.58 -125.02 REMARK 500 5 LYS A 103 55.15 -152.08 REMARK 500 6 ALA A 2 154.21 61.92 REMARK 500 6 ASN A 7 -144.82 -144.02 REMARK 500 6 LEU A 24 137.37 167.52 REMARK 500 6 ASP A 63 -145.53 53.26 REMARK 500 6 LEU A 64 173.93 67.17 REMARK 500 6 LYS A 103 56.67 -152.80 REMARK 500 7 ASN A 8 41.09 -108.18 REMARK 500 7 LEU A 24 142.79 -177.79 REMARK 500 7 LYS A 62 -72.99 -123.23 REMARK 500 7 LEU A 64 -63.57 -124.74 REMARK 500 7 LYS A 103 54.88 -143.91 REMARK 500 7 SER A 136 -166.83 -122.07 REMARK 500 8 LEU A 24 144.55 173.71 REMARK 500 8 ARG A 137 93.05 60.30 REMARK 500 9 ASN A 8 -98.28 -158.59 REMARK 500 9 THR A 9 73.19 39.87 REMARK 500 9 LEU A 24 137.38 165.69 REMARK 500 9 LYS A 62 -57.95 -136.88 REMARK 500 9 ASP A 63 64.04 34.47 REMARK 500 9 LYS A 103 56.84 -146.83 REMARK 500 10 THR A 9 97.41 -17.75 REMARK 500 10 LEU A 24 140.70 179.44 REMARK 500 10 LEU A 64 -94.27 -121.20 REMARK 500 11 ASN A 7 -142.38 -115.72 REMARK 500 11 ASN A 8 50.49 -103.91 REMARK 500 11 LEU A 24 144.80 172.62 REMARK 500 11 MET A 61 -163.21 -127.34 REMARK 500 11 LYS A 62 -57.82 -126.14 REMARK 500 11 LYS A 103 56.82 -151.78 REMARK 500 12 ASN A 7 -60.60 -123.08 REMARK 500 REMARK 500 THIS ENTRY HAS 199 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34511 RELATED DB: BMRB REMARK 900 THE N-TERMINAL RNA-BINDING DOMAIN OF THE SARS-COV-2 NUCLEOCAPSID REMARK 900 PHOSPHOPROTEIN DBREF 6YI3 A 4 140 UNP P0DTC9 NCAP_SARS2 44 180 SEQADV 6YI3 GLY A 1 UNP P0DTC9 EXPRESSION TAG SEQADV 6YI3 ALA A 2 UNP P0DTC9 EXPRESSION TAG SEQADV 6YI3 MET A 3 UNP P0DTC9 EXPRESSION TAG SEQRES 1 A 140 GLY ALA MET GLY LEU PRO ASN ASN THR ALA SER TRP PHE SEQRES 2 A 140 THR ALA LEU THR GLN HIS GLY LYS GLU ASP LEU LYS PHE SEQRES 3 A 140 PRO ARG GLY GLN GLY VAL PRO ILE ASN THR ASN SER SER SEQRES 4 A 140 PRO ASP ASP GLN ILE GLY TYR TYR ARG ARG ALA THR ARG SEQRES 5 A 140 ARG ILE ARG GLY GLY ASP GLY LYS MET LYS ASP LEU SER SEQRES 6 A 140 PRO ARG TRP TYR PHE TYR TYR LEU GLY THR GLY PRO GLU SEQRES 7 A 140 ALA GLY LEU PRO TYR GLY ALA ASN LYS ASP GLY ILE ILE SEQRES 8 A 140 TRP VAL ALA THR GLU GLY ALA LEU ASN THR PRO LYS ASP SEQRES 9 A 140 HIS ILE GLY THR ARG ASN PRO ALA ASN ASN ALA ALA ILE SEQRES 10 A 140 VAL LEU GLN LEU PRO GLN GLY THR THR LEU PRO LYS GLY SEQRES 11 A 140 PHE TYR ALA GLU GLY SER ARG GLY GLY SER HELIX 1 AA1 SER A 39 GLN A 43 5 5 HELIX 2 AA2 LYS A 103 GLY A 107 5 5 SHEET 1 AA1 5 ILE A 90 VAL A 93 0 SHEET 2 AA1 5 GLY A 45 ALA A 50 -1 N GLY A 45 O VAL A 93 SHEET 3 AA1 5 ARG A 67 TYR A 72 -1 O TYR A 69 N ARG A 48 SHEET 4 AA1 5 LEU A 16 GLN A 18 -1 N LEU A 16 O TRP A 68 SHEET 5 AA1 5 PHE A 131 ALA A 133 -1 O TYR A 132 N THR A 17 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 MODEL 1