HEADER VIRAL PROTEIN 14-FEB-22 7YWQ TITLE SOLUTION STRUCTURE OF HOMODIMERIC CAPSID PROTEIN (RESIDUES 17-95) OF TITLE 2 TICK-BORNE ENCEPHALITIS VIRUS (D16-TBEVC) COMPND MOL_ID: 1; COMPND 2 MOLECULE: GENOME POLYPROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TICK-BORNE ENCEPHALITIS VIRUS; SOURCE 3 ORGANISM_TAXID: 11084; SOURCE 4 STRAIN: NEUDOERFL; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: RIL; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS CAPSID PROTEIN, HOMODIMER, TICK-BORNE ENCEPHALITIS VIRUS, VIRAL KEYWDS 2 PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR R.NOVOTNY REVDAT 4 19-JUN-24 7YWQ 1 REMARK REVDAT 3 23-NOV-22 7YWQ 1 JRNL REVDAT 2 26-OCT-22 7YWQ 1 JRNL REVDAT 1 19-OCT-22 7YWQ 0 JRNL AUTH M.SELINGER,R.NOVOTNY,J.SYS,J.A.ROBY,H.TYKALOVA,G.S.RANJANI, JRNL AUTH 2 M.VANCOVA,K.JAKLOVA,F.KAUFMAN,M.E.BLOOM,Z.ZDRAHAL, JRNL AUTH 3 L.GRUBHOFFER,J.K.FORWOOD,R.HRABAL,M.RUMLOVA,J.STERBA JRNL TITL TICK-BORNE ENCEPHALITIS VIRUS CAPSID PROTEIN INDUCES JRNL TITL 2 TRANSLATIONAL SHUTOFF AS REVEALED BY ITS JRNL TITL 3 STRUCTURAL-BIOLOGICAL ANALYSIS. JRNL REF J.BIOL.CHEM. V. 298 02585 2022 JRNL REFN ESSN 1083-351X JRNL PMID 36223838 JRNL DOI 10.1016/J.JBC.2022.102585 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH 3.2 REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7YWQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-FEB-22. REMARK 100 THE DEPOSITION ID IS D_1292118234. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.4 MM [U-99% 13C; U-99% 15N] REMARK 210 D16-TBEVC, 50 MM NACL, 50 MM REMARK 210 SODIUM PHOSPHATE, 5 % GLYCEROL, REMARK 210 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCO; 3D HCACO; 3D HNCA; 3D REMARK 210 HNCACB; 3D CBCA(CO)NH; 3D HCCH- REMARK 210 TOCSY; 3D 1H-15N NOESY; 3D 1H- REMARK 210 13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 3.5, CCPNMR ANALYSIS REMARK 210 2.5.2, X-PLOR NIH 3.2, HADDOCK REMARK 210 2.2 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1000 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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: 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 52 -157.93 -160.98 REMARK 500 1 ALA A 53 85.99 81.76 REMARK 500 1 LEU A 67 -66.21 -105.57 REMARK 500 1 VAL B 30 32.65 -82.72 REMARK 500 1 THR B 52 -162.50 -170.09 REMARK 500 1 ALA B 53 109.55 76.48 REMARK 500 1 ARG B 54 82.77 -154.49 REMARK 500 2 ARG A 29 82.46 68.70 REMARK 500 2 THR A 52 -163.39 -165.18 REMARK 500 2 ALA A 53 97.31 83.82 REMARK 500 2 PRO A 66 100.80 -54.71 REMARK 500 2 LYS A 93 79.05 -105.32 REMARK 500 2 SER B 18 -65.33 -149.28 REMARK 500 2 ARG B 29 77.93 67.68 REMARK 500 2 THR B 52 -166.93 -164.37 REMARK 500 2 ALA B 53 95.74 75.69 REMARK 500 2 ARG B 54 33.64 -150.52 REMARK 500 2 PRO B 66 99.99 -60.24 REMARK 500 2 LYS B 93 59.82 -104.67 REMARK 500 3 SER A 18 -110.13 -104.60 REMARK 500 3 GLU A 20 -173.86 65.18 REMARK 500 3 VAL A 30 44.32 -87.02 REMARK 500 3 ALA A 53 -82.97 -151.88 REMARK 500 3 ARG A 54 50.43 39.31 REMARK 500 3 SER B 18 -149.15 -108.49 REMARK 500 3 LYS B 19 -165.10 -121.40 REMARK 500 3 GLU B 20 -163.15 62.65 REMARK 500 3 VAL B 30 36.00 -86.77 REMARK 500 3 ALA B 53 -100.16 -156.06 REMARK 500 3 LEU B 67 -85.37 -97.04 REMARK 500 4 SER A 18 61.94 -100.38 REMARK 500 4 GLU A 20 -168.03 63.95 REMARK 500 4 LYS A 24 -40.44 -171.60 REMARK 500 4 VAL A 30 30.29 -91.41 REMARK 500 4 GLN A 31 98.75 -66.38 REMARK 500 4 ARG A 54 84.96 63.58 REMARK 500 4 GLU B 20 -159.03 59.09 REMARK 500 4 VAL B 30 45.36 -80.21 REMARK 500 4 ARG B 54 75.87 65.84 REMARK 500 5 GLU A 20 155.09 69.10 REMARK 500 5 ALA A 53 -147.29 -162.25 REMARK 500 5 GLU B 20 -156.15 62.63 REMARK 500 5 ALA B 53 -148.27 -172.16 REMARK 500 5 LEU B 67 -82.28 -90.09 REMARK 500 6 GLU A 20 -148.90 54.09 REMARK 500 6 THR A 52 136.60 -171.31 REMARK 500 6 ALA A 53 99.06 -172.34 REMARK 500 6 PRO A 66 109.51 -58.57 REMARK 500 6 GLU B 20 -165.19 61.18 REMARK 500 6 ALA B 53 91.60 -162.46 REMARK 500 REMARK 500 THIS ENTRY HAS 176 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34709 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF HOMODIMERIC CAPSID PROTEIN (RESIDUES 17-95) REMARK 900 OF TICK-BORNE ENCEPHALITIS VIRUS (D16-TBEVC) DBREF 7YWQ A 17 95 UNP P14336 POLG_TBEVW 18 96 DBREF 7YWQ B 17 95 UNP P14336 POLG_TBEVW 18 96 SEQRES 1 A 79 VAL SER LYS GLU THR ALA THR LYS THR ARG GLN PRO ARG SEQRES 2 A 79 VAL GLN MET PRO ASN GLY LEU VAL LEU MET ARG MET MET SEQRES 3 A 79 GLY ILE LEU TRP HIS ALA VAL ALA GLY THR ALA ARG ASN SEQRES 4 A 79 PRO VAL LEU LYS ALA PHE TRP ASN SER VAL PRO LEU LYS SEQRES 5 A 79 GLN ALA THR ALA ALA LEU ARG LYS ILE LYS ARG THR VAL SEQRES 6 A 79 SER ALA LEU MET VAL GLY LEU GLN LYS ARG GLY LYS ARG SEQRES 7 A 79 ARG SEQRES 1 B 79 VAL SER LYS GLU THR ALA THR LYS THR ARG GLN PRO ARG SEQRES 2 B 79 VAL GLN MET PRO ASN GLY LEU VAL LEU MET ARG MET MET SEQRES 3 B 79 GLY ILE LEU TRP HIS ALA VAL ALA GLY THR ALA ARG ASN SEQRES 4 B 79 PRO VAL LEU LYS ALA PHE TRP ASN SER VAL PRO LEU LYS SEQRES 5 B 79 GLN ALA THR ALA ALA LEU ARG LYS ILE LYS ARG THR VAL SEQRES 6 B 79 SER ALA LEU MET VAL GLY LEU GLN LYS ARG GLY LYS ARG SEQRES 7 B 79 ARG HELIX 1 AA1 VAL A 17 THR A 23 1 7 HELIX 2 AA2 PRO A 33 ALA A 50 1 18 HELIX 3 AA3 ASN A 55 SER A 64 1 10 HELIX 4 AA4 LEU A 67 LYS A 90 1 24 HELIX 5 AA5 SER B 18 THR B 25 1 8 HELIX 6 AA6 PRO B 33 LEU B 38 1 6 HELIX 7 AA7 ARG B 40 ALA B 50 1 11 HELIX 8 AA8 ASN B 55 ASN B 63 1 9 HELIX 9 AA9 LEU B 67 ARG B 91 1 25 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