HEADER VIRAL PROTEIN, RNA BINDING PROTEIN 02-SEP-08 2K87 TITLE NMR STRUCTURE OF A PUTATIVE RNA BINDING PROTEIN (SARS1) FROM SARS TITLE 2 CORONAVIRUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: NON-STRUCTURAL PROTEIN 3 OF REPLICASE POLYPROTEIN 1A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: NAB DOMAIN OF THE SARS CORONAVIRUS NSP3, RESIDUES 1884- COMPND 5 1999; COMPND 6 SYNONYM: NSP3, PAPAIN-LIKE PROTEINASE, PL-PRO, PL2-PRO; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SARS CORONAVIRUS; SOURCE 3 ORGANISM_COMMON: SARS-COV; SOURCE 4 ORGANISM_TAXID: 227859; SOURCE 5 GENE: 1A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET25B KEYWDS STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, KEYWDS 2 PROTEIN STRUCTURE INITIATIVE, PSI-2, VIRAL PROTEIN, RNA BINDING KEYWDS 3 PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 MDLTYP MINIMIZED AVERAGE AUTHOR P.SERRANO,K.WUTHRICH,M.A.JOHNSON,A.CHATTERJEE,I.WILSON,B.F.PEDRINI, AUTHOR 2 JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 9 08-MAY-24 2K87 1 REMARK REVDAT 8 14-JUN-23 2K87 1 REMARK REVDAT 7 01-FEB-23 2K87 1 SEQADV REVDAT 6 19-FEB-20 2K87 1 REMARK REVDAT 5 11-AUG-10 2K87 1 REMARK REVDAT 4 28-JUL-10 2K87 1 TITLE KEYWDS REVDAT 3 02-FEB-10 2K87 1 JRNL REVDAT 2 24-FEB-09 2K87 1 VERSN REVDAT 1 16-SEP-08 2K87 0 JRNL AUTH P.SERRANO,M.A.JOHNSON,A.CHATTERJEE,B.W.NEUMAN,J.S.JOSEPH, JRNL AUTH 2 M.J.BUCHMEIER,P.KUHN,K.WUTHRICH JRNL TITL NUCLEAR MAGNETIC RESONANCE STRUCTURE OF THE NUCLEIC JRNL TITL 2 ACID-BINDING DOMAIN OF SEVERE ACUTE RESPIRATORY SYNDROME JRNL TITL 3 CORONAVIRUS NONSTRUCTURAL PROTEIN 3. JRNL REF J.VIROL. V. 83 12998 2009 JRNL REFN ISSN 0022-538X JRNL PMID 19828617 JRNL DOI 10.1128/JVI.01253-09 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 1.X, OPAL 1 REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), REMARK 3 LUGINBUHL, GUNTERT, BILLETER AND WUTHRICH (OPAL) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2K87 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-SEP-08. REMARK 100 THE DEPOSITION ID IS D_1000100798. 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 : 0.2 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.4 MM [U-99% 13C; U-99% 15N] REMARK 210 SARS-COV NSP3E, 2 MM SODIUM REMARK 210 AZIDE, 50 MM SODIUM PHOSPHATE, REMARK 210 50 MM SODIUM CHLORIDE, 10 % D2O, REMARK 210 0.1 MM DSS, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D CBCA(CO)NH; 3D HNCO; 3D HNCA; REMARK 210 3D HNCACB; 3D 1H-15N NOESY; 3D REMARK 210 1H-13C NOESY; 3D HCCH-TOCSY; 3D REMARK 210 H(CCO)NH REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ; 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CARA 1.5, OPAL 1, TOPSPIN 1.3, REMARK 210 CANDID REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 80 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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 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: CLOSE CONTACTS 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 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 2 ARG A 68 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 6 LEU A 58 CB - CG - CD2 ANGL. DEV. = 10.6 DEGREES REMARK 500 7 LEU A 105 CB - CG - CD1 ANGL. DEV. = 11.0 DEGREES REMARK 500 10 ASP A 8 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 10 ASP A 8 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 10 TYR A 70 CB - CG - CD2 ANGL. DEV. = -4.2 DEGREES REMARK 500 12 TYR A 70 CB - CG - CD2 ANGL. DEV. = -4.6 DEGREES REMARK 500 13 ARG A 68 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 14 CYS A 27 CA - CB - SG ANGL. DEV. = 7.0 DEGREES REMARK 500 15 TYR A 70 CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES REMARK 500 16 VAL A 63 CA - CB - CG1 ANGL. DEV. = 10.0 DEGREES REMARK 500 20 TYR A 2 CB - CG - CD1 ANGL. DEV. = -3.8 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 GLU A 4 50.58 37.23 REMARK 500 1 ASP A 8 34.45 27.91 REMARK 500 1 ASN A 17 4.66 49.14 REMARK 500 1 ASP A 21 -147.17 -134.79 REMARK 500 1 PHE A 55 153.03 -49.38 REMARK 500 1 LEU A 80 -165.67 -78.69 REMARK 500 1 ASP A 115 13.31 -61.75 REMARK 500 2 ILE A 7 88.13 -68.79 REMARK 500 2 ASP A 8 28.54 40.70 REMARK 500 2 ASN A 17 -14.68 69.20 REMARK 500 2 ASN A 22 21.32 -67.99 REMARK 500 2 LEU A 80 -156.22 -83.61 REMARK 500 2 HIS A 82 14.96 -144.93 REMARK 500 2 THR A 111 -151.32 55.72 REMARK 500 2 LYS A 112 126.99 57.89 REMARK 500 2 VAL A 114 93.18 85.55 REMARK 500 2 ASP A 115 -70.85 -100.73 REMARK 500 3 GLU A 4 95.08 63.72 REMARK 500 3 GLN A 5 128.28 66.78 REMARK 500 3 ILE A 7 98.36 -46.89 REMARK 500 3 ASP A 8 27.12 33.26 REMARK 500 3 CYS A 27 156.46 175.41 REMARK 500 3 PHE A 55 153.91 -47.02 REMARK 500 3 TYR A 67 -17.12 -45.52 REMARK 500 3 LEU A 80 -154.54 -93.28 REMARK 500 3 HIS A 82 23.95 -144.18 REMARK 500 3 ASN A 90 40.28 148.26 REMARK 500 3 VAL A 114 18.18 48.10 REMARK 500 4 ILE A 7 83.09 -69.24 REMARK 500 4 ASP A 8 23.52 37.74 REMARK 500 4 ASN A 17 -23.41 74.69 REMARK 500 4 ASP A 21 -160.78 -114.76 REMARK 500 4 ASP A 57 122.23 -177.61 REMARK 500 4 LEU A 58 57.50 -147.79 REMARK 500 4 LEU A 80 -157.83 -113.97 REMARK 500 4 LYS A 112 140.60 57.17 REMARK 500 5 GLN A 5 128.31 53.74 REMARK 500 5 ILE A 7 90.62 -67.61 REMARK 500 5 ASP A 8 42.86 24.77 REMARK 500 5 ASN A 22 -3.25 -54.40 REMARK 500 5 ASN A 29 99.94 -67.28 REMARK 500 5 ASP A 57 123.32 -170.16 REMARK 500 5 LEU A 58 51.69 -150.45 REMARK 500 5 ARG A 68 -17.02 -49.40 REMARK 500 5 TYR A 70 66.95 -68.77 REMARK 500 5 LEU A 80 -164.21 -105.99 REMARK 500 5 LYS A 112 104.60 -35.38 REMARK 500 6 THR A 3 18.43 -154.60 REMARK 500 6 GLU A 4 -168.83 60.63 REMARK 500 6 ASP A 8 17.52 50.61 REMARK 500 REMARK 500 THIS ENTRY HAS 178 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASP A 8 LEU A 9 7 -138.47 REMARK 500 MET A 1 TYR A 2 13 148.70 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 2 TYR A 67 0.09 SIDE CHAIN REMARK 500 2 ARG A 68 0.09 SIDE CHAIN REMARK 500 3 PHE A 42 0.08 SIDE CHAIN REMARK 500 3 ARG A 48 0.10 SIDE CHAIN REMARK 500 4 ARG A 48 0.10 SIDE CHAIN REMARK 500 7 PHE A 42 0.11 SIDE CHAIN REMARK 500 8 ARG A 68 0.08 SIDE CHAIN REMARK 500 11 PHE A 42 0.13 SIDE CHAIN REMARK 500 12 PHE A 42 0.08 SIDE CHAIN REMARK 500 13 PHE A 42 0.08 SIDE CHAIN REMARK 500 14 PHE A 42 0.11 SIDE CHAIN REMARK 500 16 TYR A 2 0.08 SIDE CHAIN REMARK 500 16 PHE A 42 0.08 SIDE CHAIN REMARK 500 19 ARG A 48 0.14 SIDE CHAIN REMARK 500 20 ARG A 68 0.13 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 15723 RELATED DB: BMRB REMARK 900 CHEMICAL SHIFT ASSIGNMENTS REMARK 900 RELATED ID: 396981 RELATED DB: TARGETDB DBREF 2K87 A 2 116 UNP P0C6U8 R1A_CVHSA 1884 1998 SEQADV 2K87 MET A 1 UNP P0C6U8 EXPRESSION TAG SEQRES 1 A 116 MET TYR THR GLU GLN PRO ILE ASP LEU VAL PRO THR GLN SEQRES 2 A 116 PRO LEU PRO ASN ALA SER PHE ASP ASN PHE LYS LEU THR SEQRES 3 A 116 CYS SER ASN THR LYS PHE ALA ASP ASP LEU ASN GLN MET SEQRES 4 A 116 THR GLY PHE THR LYS PRO ALA SER ARG GLU LEU SER VAL SEQRES 5 A 116 THR PHE PHE PRO ASP LEU ASN GLY ASP VAL VAL ALA ILE SEQRES 6 A 116 ASP TYR ARG HIS TYR SER ALA SER PHE LYS LYS GLY ALA SEQRES 7 A 116 LYS LEU LEU HIS LYS PRO ILE VAL TRP HIS ILE ASN GLN SEQRES 8 A 116 ALA THR THR LYS THR THR PHE LYS PRO ASN THR TRP CYS SEQRES 9 A 116 LEU ARG CYS LEU TRP SER THR LYS PRO VAL ASP THR HELIX 1 1 ASN A 29 THR A 40 1 12 HELIX 2 2 ARG A 68 TYR A 70 5 3 HELIX 3 3 SER A 71 LYS A 75 5 5 HELIX 4 4 THR A 94 TRP A 109 1 16 SHEET 1 A 2 VAL A 10 PRO A 11 0 SHEET 2 A 2 ALA A 78 LYS A 79 -1 O LYS A 79 N VAL A 10 SHEET 1 B 4 PHE A 23 CYS A 27 0 SHEET 2 B 4 ARG A 48 PHE A 54 1 O LEU A 50 N LYS A 24 SHEET 3 B 4 VAL A 62 ASP A 66 1 O VAL A 62 N SER A 51 SHEET 4 B 4 TRP A 87 HIS A 88 1 O HIS A 88 N ILE A 65 CISPEP 1 LYS A 44 PRO A 45 1 6.38 CISPEP 2 PHE A 55 PRO A 56 1 -11.93 CISPEP 3 LYS A 44 PRO A 45 2 -0.31 CISPEP 4 PHE A 55 PRO A 56 2 -12.90 CISPEP 5 LYS A 44 PRO A 45 3 -3.16 CISPEP 6 PHE A 55 PRO A 56 3 1.43 CISPEP 7 LYS A 44 PRO A 45 4 2.45 CISPEP 8 PHE A 55 PRO A 56 4 -20.02 CISPEP 9 LYS A 44 PRO A 45 5 -6.64 CISPEP 10 PHE A 55 PRO A 56 5 -19.49 CISPEP 11 LYS A 44 PRO A 45 6 -3.79 CISPEP 12 PHE A 55 PRO A 56 6 -3.43 CISPEP 13 LYS A 44 PRO A 45 7 -4.32 CISPEP 14 PHE A 55 PRO A 56 7 -20.93 CISPEP 15 LYS A 44 PRO A 45 8 -3.16 CISPEP 16 PHE A 55 PRO A 56 8 -19.17 CISPEP 17 LYS A 44 PRO A 45 9 -2.68 CISPEP 18 PHE A 55 PRO A 56 9 -18.25 CISPEP 19 LYS A 44 PRO A 45 10 -1.95 CISPEP 20 PHE A 55 PRO A 56 10 -22.46 CISPEP 21 LYS A 44 PRO A 45 11 -0.28 CISPEP 22 PHE A 55 PRO A 56 11 -9.70 CISPEP 23 LYS A 44 PRO A 45 12 -6.03 CISPEP 24 PHE A 55 PRO A 56 12 -22.26 CISPEP 25 LYS A 44 PRO A 45 13 -7.25 CISPEP 26 PHE A 55 PRO A 56 13 -26.67 CISPEP 27 LYS A 44 PRO A 45 14 -9.33 CISPEP 28 PHE A 55 PRO A 56 14 -3.31 CISPEP 29 LYS A 44 PRO A 45 15 -1.26 CISPEP 30 PHE A 55 PRO A 56 15 -21.37 CISPEP 31 LYS A 44 PRO A 45 16 1.07 CISPEP 32 PHE A 55 PRO A 56 16 -17.61 CISPEP 33 LYS A 44 PRO A 45 17 -7.75 CISPEP 34 PHE A 55 PRO A 56 17 -13.80 CISPEP 35 LYS A 44 PRO A 45 18 -6.57 CISPEP 36 PHE A 55 PRO A 56 18 -9.51 CISPEP 37 LYS A 44 PRO A 45 19 -3.54 CISPEP 38 PHE A 55 PRO A 56 19 -15.00 CISPEP 39 LYS A 44 PRO A 45 20 -6.82 CISPEP 40 PHE A 55 PRO A 56 20 -19.80 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