HEADER VIRAL PROTEIN 15-MAR-16 5ISN TITLE NMR SOLUTION STRUCTURE OF MACRO DOMAIN FROM VENEZUELAN EQUINE TITLE 2 ENCEPHALITIS VIRUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: NON-STRUCTURAL POLYPROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: POLYPROTEIN NSP1234,P1234; COMPND 5 EC: 2.1.1.-,2.7.7.-,3.1.3.33,3.4.22.-,3.6.1.15,3.6.4.13,2.7.7.48; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VENEZUELAN EQUINE ENCEPHALITIS VIRUS (STRAIN SOURCE 3 P676); SOURCE 4 ORGANISM_COMMON: VEEV; SOURCE 5 ORGANISM_TAXID: 36385; SOURCE 6 STRAIN: P676; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_VARIANT: ROSETTA 2 (PLYSS) DL39 KEYWDS VIRAL MACRO DOMAIN, ADP-RIBOSE-BINDING MODULE, ALPHAVIRUS, NMR KEYWDS 2 SPECTROSCOPY, VENEZUELAN EQUINE ENCEPHALITIS VIRUS, TRANSFERASE, KEYWDS 3 VIRAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 21 AUTHOR G.I.MAKRYNITSA,D.NTONTI,K.D.MAROUSIS,A.C.TSIKA,N.PAPAGEORGIOU, AUTHOR 2 B.COUTARD,D.BENTROP,G.A.SPYROULIAS REVDAT 4 14-JUN-23 5ISN 1 REMARK DBREF REVDAT 3 08-MAY-19 5ISN 1 REMARK REVDAT 2 17-APR-19 5ISN 1 JRNL REVDAT 1 29-NOV-17 5ISN 0 JRNL AUTH G.I.MAKRYNITSA,D.NTONTI,K.D.MAROUSIS,M.BIRKOU,M.T.MATSOUKAS, JRNL AUTH 2 S.ASAMI,D.BENTROP,N.PAPAGEORGIOU,B.CANARD,B.COUTARD, JRNL AUTH 3 G.A.SPYROULIAS JRNL TITL CONFORMATIONAL PLASTICITY OF THE VEEV MACRO DOMAIN IS JRNL TITL 2 IMPORTANT FOR BINDING OF ADP-RIBOSE. JRNL REF J.STRUCT.BIOL. V. 206 119 2019 JRNL REFN ESSN 1095-8657 JRNL PMID 30825649 JRNL DOI 10.1016/J.JSB.2019.02.008 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH G.I.MAKRYNITSA,D.NTONTI,K.D.MAROUSIS,A.C.TSIKA,J.LICHIERE, REMARK 1 AUTH 2 N.PAPAGEORGIOU,B.COUTARD,D.BENTROP,G.A.SPYROULIAS REMARK 1 TITL NMR STUDY OF NON-STRUCTURAL PROTEINS--PART II: (1)H, (13)C, REMARK 1 TITL 2 (15)N BACKBONE AND SIDE-CHAIN RESONANCE ASSIGNMENT OF MACRO REMARK 1 TITL 3 DOMAIN FROM VENEZUELAN EQUINE ENCEPHALITIS VIRUS (VEEV). REMARK 1 REF BIOMOL NMR ASSIGN V. 9 247 2015 REMARK 1 REFN ESSN 1874-270X REMARK 1 PMID 25291978 REMARK 1 DOI 10.1007/S12104-014-9584-9 REMARK 1 REFERENCE 2 REMARK 1 AUTH E.MELEKIS,A.C.TSIKA,J.LICHIERE,C.T.CHASAPIS,I.MARGIOLAKI, REMARK 1 AUTH 2 N.PAPAGEORGIOU,B.COUTARD,D.BENTROP,G.A.SPYROULIAS REMARK 1 TITL NMR STUDY OF NON-STRUCTURAL PROTEINS--PART I: (1)H, (13)C, REMARK 1 TITL 2 (15)N BACKBONE AND SIDE-CHAIN RESONANCE ASSIGNMENT OF MACRO REMARK 1 TITL 3 DOMAIN FROM MAYARO VIRUS (MAYV). REMARK 1 REF BIOMOL NMR ASSIGN V. 9 191 2015 REMARK 1 REFN ESSN 1874-270X REMARK 1 PMID 25217003 REMARK 1 DOI 10.1007/S12104-014-9572-0 REMARK 1 REFERENCE 3 REMARK 1 AUTH H.MALET,B.COUTARD,S.JAMAL,H.DUTARTRE,N.PAPAGEORGIOU, REMARK 1 AUTH 2 M.NEUVONEN,T.AHOLA,N.FORRESTER,E.A.GOULD,D.LAFITTE,F.FERRON, REMARK 1 AUTH 3 J.LESCAR,A.E.GORBALENYA,X.DE LAMBALLERIE,B.CANARD REMARK 1 TITL THE CRYSTAL STRUCTURES OF CHIKUNGUNYA AND VENEZUELAN EQUINE REMARK 1 TITL 2 ENCEPHALITIS VIRUS NSP3 MACRO DOMAINS DEFINE A CONSERVED REMARK 1 TITL 3 ADENOSINE BINDING POCKET. REMARK 1 REF J. VIROL. V. 83 6534 2009 REMARK 1 REFN ESSN 1098-5514 REMARK 1 PMID 19386706 REMARK 1 DOI 10.1128/JVI.00189-09 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5ISN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000218831. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 20 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.4 MM [U-99% 15N] VEEV MACRO REMARK 210 DOMAIN, 90% H2O/10% D2O; 0.8 MM REMARK 210 [U-99% 13C; U-99% 15N] VEEV REMARK 210 MACRO DOMAIN, 90% H2O/10% D2O; REMARK 210 0.01 MM [U-15N]-LEU-ALA-VAL VEEV REMARK 210 MACRO DOMAIN, 90% H2O/10% D2O; REMARK 210 0.02 MM [U-14N]-LYS VEEV MACRO REMARK 210 DOMAIN, 90% H2O/10% D2O; 0.3 MM REMARK 210 VEEV MACRO DOMAIN, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-15N HSQC REMARK 210 TROSY; 3D HNCACB; 3D HNCACB REMARK 210 TROSY; 3D HN(CA)CO; 3D HN(CA)CO REMARK 210 TROSY; 3D HNHA; 3D HNCO; 3D REMARK 210 HN(CO)CA; 3D CBCA(CO)NH; 3D REMARK 210 HBHA(CO)NH; 3D HCCH-TOCSY; 2D 1H- REMARK 210 13C HSQC; 3D 1H-15N NOESY; 3D 1H- REMARK 210 13C NOESY ALIPHATIC; 3D 1H-13C REMARK 210 NOESY AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 3.2, CARA 1.5.5, XEASY, REMARK 210 DYANA REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 21 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 21 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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 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: 9250 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-21 REMARK 465 RES C SSSEQI REMARK 465 MET A -1 REMARK 465 LYS A 0 REMARK 465 HIS A 161 REMARK 465 HIS A 162 REMARK 465 HIS A 163 REMARK 465 HIS A 164 REMARK 465 HIS A 165 REMARK 465 HIS A 166 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 1 TYR A 142 CB - CG - CD2 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 TYR A 142 CB - CG - CD1 ANGL. DEV. = 3.7 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 1 PRO A 2 -141.81 -107.38 REMARK 500 1 THR A 15 38.37 -78.13 REMARK 500 1 GLU A 16 24.64 -77.99 REMARK 500 1 ALA A 23 -48.10 -153.71 REMARK 500 1 ASN A 24 -176.33 66.40 REMARK 500 1 LEU A 47 47.73 28.23 REMARK 500 1 GLU A 51 -171.27 -66.32 REMARK 500 1 LYS A 59 79.28 -110.03 REMARK 500 1 LYS A 118 -69.34 154.71 REMARK 500 1 THR A 134 0.77 -61.37 REMARK 500 1 ALA A 137 -109.66 -91.44 REMARK 500 1 ARG A 144 92.47 -68.45 REMARK 500 1 ASP A 145 -34.82 -165.13 REMARK 500 1 LYS A 146 -42.59 86.66 REMARK 500 2 THR A 15 49.35 -78.98 REMARK 500 2 GLU A 16 45.06 -89.06 REMARK 500 2 ALA A 23 -53.25 -153.62 REMARK 500 2 ASN A 24 -173.96 61.04 REMARK 500 2 PHE A 41 86.06 -166.36 REMARK 500 2 PHE A 45 54.37 32.95 REMARK 500 2 LEU A 47 6.98 -62.60 REMARK 500 2 ASN A 117 50.88 -151.17 REMARK 500 2 LYS A 118 -169.53 -164.35 REMARK 500 2 ASP A 119 91.66 49.11 REMARK 500 2 THR A 134 -8.40 -57.79 REMARK 500 2 ALA A 137 -125.37 -101.88 REMARK 500 2 ASP A 145 -48.33 -171.89 REMARK 500 2 LYS A 146 -52.37 98.16 REMARK 500 3 THR A 15 43.96 -80.40 REMARK 500 3 GLU A 16 32.95 -77.84 REMARK 500 3 ALA A 23 -50.25 -152.68 REMARK 500 3 ASN A 24 -176.36 56.29 REMARK 500 3 PHE A 45 49.69 -83.83 REMARK 500 3 LEU A 47 44.34 38.03 REMARK 500 3 PRO A 107 -166.36 -76.37 REMARK 500 3 LYS A 118 -69.33 67.90 REMARK 500 3 ASP A 136 60.52 -104.42 REMARK 500 3 ALA A 137 -124.76 -100.09 REMARK 500 3 ASP A 145 -29.14 -175.71 REMARK 500 3 LYS A 146 -51.17 80.97 REMARK 500 4 ALA A 23 -44.91 -149.42 REMARK 500 4 ASN A 24 -174.34 58.92 REMARK 500 4 PHE A 41 97.59 -168.05 REMARK 500 4 LEU A 47 46.23 34.02 REMARK 500 4 ILE A 113 -53.22 -142.28 REMARK 500 4 LYS A 118 -79.16 -75.04 REMARK 500 4 ARG A 120 -32.23 158.83 REMARK 500 4 ASP A 136 59.24 -107.94 REMARK 500 4 ALA A 137 -123.73 -95.97 REMARK 500 4 ASP A 145 -29.91 168.18 REMARK 500 REMARK 500 THIS ENTRY HAS 284 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 TYR A 142 CYS A 143 1 138.57 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 8 ARG A 144 0.08 SIDE CHAIN REMARK 500 12 ARG A 144 0.09 SIDE CHAIN REMARK 500 15 ARG A 144 0.08 SIDE CHAIN REMARK 500 17 ARG A 144 0.08 SIDE CHAIN REMARK 500 20 TYR A 101 0.11 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3GQE RELATED DB: PDB REMARK 900 RELATED ID: 25132 RELATED DB: BMRB DBREF 5ISN A 1 160 UNP P36328 POLN_EEVVP 1330 1489 SEQADV 5ISN MET A -1 UNP P36328 INITIATING METHIONINE SEQADV 5ISN LYS A 0 UNP P36328 EXPRESSION TAG SEQADV 5ISN HIS A 161 UNP P36328 EXPRESSION TAG SEQADV 5ISN HIS A 162 UNP P36328 EXPRESSION TAG SEQADV 5ISN HIS A 163 UNP P36328 EXPRESSION TAG SEQADV 5ISN HIS A 164 UNP P36328 EXPRESSION TAG SEQADV 5ISN HIS A 165 UNP P36328 EXPRESSION TAG SEQADV 5ISN HIS A 166 UNP P36328 EXPRESSION TAG SEQRES 1 A 168 MET LYS ALA PRO SER TYR HIS VAL VAL ARG GLY ASP ILE SEQRES 2 A 168 ALA THR ALA THR GLU GLY VAL ILE ILE ASN ALA ALA ASN SEQRES 3 A 168 SER LYS GLY GLN PRO GLY GLY GLY VAL CYS GLY ALA LEU SEQRES 4 A 168 TYR LYS LYS PHE PRO GLU SER PHE ASP LEU GLN PRO ILE SEQRES 5 A 168 GLU VAL GLY LYS ALA ARG LEU VAL LYS GLY ALA ALA LYS SEQRES 6 A 168 HIS ILE ILE HIS ALA VAL GLY PRO ASN PHE ASN LYS VAL SEQRES 7 A 168 SER GLU VAL GLU GLY ASP LYS GLN LEU ALA GLU ALA TYR SEQRES 8 A 168 GLU SER ILE ALA LYS ILE VAL ASN ASP ASN ASN TYR LYS SEQRES 9 A 168 SER VAL ALA ILE PRO LEU LEU SER THR GLY ILE PHE SER SEQRES 10 A 168 GLY ASN LYS ASP ARG LEU THR GLN SER LEU ASN HIS LEU SEQRES 11 A 168 LEU THR ALA LEU ASP THR THR ASP ALA ASP VAL ALA ILE SEQRES 12 A 168 TYR CYS ARG ASP LYS LYS TRP GLU MET THR LEU LYS GLU SEQRES 13 A 168 ALA VAL ALA ARG ARG GLU HIS HIS HIS HIS HIS HIS HELIX 1 AA1 ASP A 10 ALA A 14 5 5 HELIX 2 AA2 ASN A 24 GLY A 27 5 4 HELIX 3 AA3 GLY A 32 PHE A 41 1 10 HELIX 4 AA4 PRO A 42 PHE A 45 5 4 HELIX 5 AA5 ASN A 72 VAL A 76 5 5 HELIX 6 AA6 SER A 77 ASN A 99 1 23 HELIX 7 AA7 ARG A 120 THR A 134 1 15 HELIX 8 AA8 LYS A 146 ARG A 159 1 14 SHEET 1 AA1 2 TYR A 4 VAL A 7 0 SHEET 2 AA1 2 VAL A 139 TYR A 142 1 O VAL A 139 N HIS A 5 SHEET 1 AA2 3 ILE A 20 ALA A 22 0 SHEET 2 AA2 3 HIS A 64 ALA A 68 1 O ALA A 68 N ASN A 21 SHEET 3 AA2 3 ARG A 56 LYS A 59 -1 N VAL A 58 O ILE A 65 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 0.001000 0.000000 0.000000 0.00000 SCALE2 0.000000 0.001000 0.000000 0.00000 SCALE3 0.000000 0.000000 0.001000 0.00000 MODEL 1 MODEL 2 MODEL 3 MODEL 4 MODEL 5 MODEL 6 MODEL 7 MODEL 8 MODEL 9 MODEL 10 MODEL 11 MODEL 12 MODEL 13 MODEL 14 MODEL 15 MODEL 16 MODEL 17 MODEL 18 MODEL 19 MODEL 20 MODEL 21