HEADER VIRAL PROTEIN 19-DEC-23 8XID TITLE DGNNV PROTRUSION DOMAIN STRUCTURE AT NEUTRAL PH COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAPSID PROTEIN ALPHA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DRAGON GROUPER NERVOUS NECROSIS VIRUS; SOURCE 3 ORGANISM_TAXID: 292633; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS PROTRUSION DOMAIN, MONOMER, VIRAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR P.STERBOVA,D.L.TZOU,W.H.CHANG REVDAT 1 30-OCT-24 8XID 0 JRNL AUTH P.STERBOVA,C.H.WANG,K.J.D.CARILLO,Y.C.LOU,T.KATO,K.NAMBA, JRNL AUTH 2 D.M.TZOU,W.H.CHANG JRNL TITL MOLECULAR MECHANISM OF PH-INDUCED PROTRUSION CONFIGURATION JRNL TITL 2 SWITCHING IN PISCINE BETANODAVIRUS IMPLIES A NOVEL ANTIVIRAL JRNL TITL 3 STRATEGY. JRNL REF ACS INFECT DIS. V. 10 3304 2024 JRNL REFN ESSN 2373-8227 JRNL PMID 39087906 JRNL DOI 10.1021/ACSINFECDIS.4C00407 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8XID COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-DEC-23. REMARK 100 THE DEPOSITION ID IS D_1300043601. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 0.12 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1.0 MM [U-13C; U-15N] PROTRUSION REMARK 210 DOMAIN, 95% H2O/5% 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 REMARK 210 HNCACB; 3D HBHA(CO)NH; 3D HCCH- REMARK 210 TOCSY; 3D 1H-15N NOESY; 3D HN(CO) REMARK 210 CA REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CARA, X-PLOR NIH, TOPSPIN REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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: 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 TRP A 67 15.79 -153.63 REMARK 500 1 ALA A 80 -78.85 -129.58 REMARK 500 1 SER A 123 -161.92 -164.43 REMARK 500 2 THR A 6 -69.87 -99.14 REMARK 500 2 TRP A 67 25.54 -161.72 REMARK 500 2 ALA A 80 -73.88 -116.28 REMARK 500 2 SER A 123 -149.35 65.04 REMARK 500 3 ASN A 23 -9.55 -143.68 REMARK 500 3 TRP A 67 15.72 -144.40 REMARK 500 3 ALA A 80 -83.33 -111.86 REMARK 500 3 SER A 123 -126.93 65.98 REMARK 500 4 GLU A 4 99.22 75.68 REMARK 500 4 TRP A 67 24.30 -157.93 REMARK 500 4 ALA A 80 -81.39 -118.27 REMARK 500 4 SER A 123 -119.79 60.46 REMARK 500 5 GLU A 3 -115.67 67.21 REMARK 500 5 ASN A 23 -3.64 -144.66 REMARK 500 5 TRP A 67 15.09 -156.74 REMARK 500 5 ALA A 80 -85.31 -111.67 REMARK 500 6 TRP A 67 21.06 -155.64 REMARK 500 6 ALA A 80 -81.87 -108.54 REMARK 500 7 TRP A 67 15.90 -158.93 REMARK 500 7 ALA A 80 -82.55 -118.37 REMARK 500 8 TRP A 67 16.00 -156.05 REMARK 500 8 ALA A 80 -83.00 -109.65 REMARK 500 9 ALA A 80 -79.77 -126.51 REMARK 500 10 ALA A 80 -84.52 -109.62 REMARK 500 11 ALA A 7 72.85 68.69 REMARK 500 11 TRP A 67 15.50 -151.35 REMARK 500 11 ALA A 80 -74.00 -116.72 REMARK 500 11 ASP A 97 -169.76 -77.44 REMARK 500 12 ASN A 23 -2.10 -144.07 REMARK 500 12 TRP A 67 12.24 -149.50 REMARK 500 12 ALA A 80 -75.72 -116.30 REMARK 500 12 SER A 123 -55.33 -171.50 REMARK 500 13 ASN A 23 -3.32 -144.26 REMARK 500 13 TRP A 67 21.98 -159.39 REMARK 500 13 ALA A 80 -82.94 -122.81 REMARK 500 14 SER A 21 -162.92 -100.77 REMARK 500 14 TRP A 67 19.11 -153.13 REMARK 500 14 ALA A 80 -80.49 -121.22 REMARK 500 15 GLU A 3 -121.73 63.94 REMARK 500 15 GLU A 4 -68.29 -150.78 REMARK 500 15 ASN A 23 -1.05 -144.06 REMARK 500 15 TRP A 67 18.33 -154.23 REMARK 500 15 ALA A 80 -81.46 -115.65 REMARK 500 15 SER A 123 -107.34 62.73 REMARK 500 16 TRP A 67 15.39 -151.79 REMARK 500 16 ALA A 80 -79.80 -120.59 REMARK 500 16 ASP A 97 -168.26 -78.86 REMARK 500 REMARK 500 THIS ENTRY HAS 67 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36628 RELATED DB: BMRB REMARK 900 DGNNV PROTRUSION DOMAIN STRUCTURE AT NEUTRAL PH DBREF 8XID A 1 125 UNP Q9E6H7 Q9E6H7_9VIRU 214 338 SEQRES 1 A 125 THR PRO GLU GLU THR THR ALA PRO ILE MET THR GLN GLY SEQRES 2 A 125 SER LEU TYR ASN ASP SER LEU SER THR ASN ASP PHE LYS SEQRES 3 A 125 SER ILE LEU LEU GLY SER THR PRO LEU ASP ILE ALA PRO SEQRES 4 A 125 ASP GLY ALA VAL PHE GLN LEU ASP ARG PRO LEU SER ILE SEQRES 5 A 125 ASP TYR SER LEU GLY THR GLY ASP VAL ASP ARG ALA VAL SEQRES 6 A 125 TYR TRP HIS LEU LYS LYS PHE ALA GLY ASN ALA GLY THR SEQRES 7 A 125 PRO ALA GLY TRP PHE ARG TRP GLY ILE TRP ASP ASN PHE SEQRES 8 A 125 ASN LYS THR PHE THR ASP GLY VAL ALA TYR TYR SER ASP SEQRES 9 A 125 GLU GLN PRO ARG GLN ILE LEU LEU PRO VAL GLY THR VAL SEQRES 10 A 125 CYS THR ARG VAL ASP SER GLU ASN HELIX 1 AA1 ASP A 18 LEU A 20 5 3 HELIX 2 AA2 LYS A 26 GLY A 31 1 6 HELIX 3 AA3 SER A 32 ILE A 37 1 6 SHEET 1 AA1 6 PRO A 8 THR A 11 0 SHEET 2 AA1 6 THR A 116 VAL A 121 -1 O CYS A 118 N ILE A 9 SHEET 3 AA1 6 VAL A 43 SER A 55 -1 N VAL A 43 O VAL A 121 SHEET 4 AA1 6 VAL A 61 ALA A 73 -1 O TYR A 66 N LEU A 50 SHEET 5 AA1 6 GLY A 81 ASP A 89 -1 O TRP A 82 N PHE A 72 SHEET 6 AA1 6 ASP A 24 PHE A 25 -1 N PHE A 25 O PHE A 83 SHEET 1 AA2 6 PRO A 8 THR A 11 0 SHEET 2 AA2 6 THR A 116 VAL A 121 -1 O CYS A 118 N ILE A 9 SHEET 3 AA2 6 VAL A 43 SER A 55 -1 N VAL A 43 O VAL A 121 SHEET 4 AA2 6 VAL A 61 ALA A 73 -1 O TYR A 66 N LEU A 50 SHEET 5 AA2 6 GLY A 81 ASP A 89 -1 O TRP A 82 N PHE A 72 SHEET 6 AA2 6 THR A 94 ASP A 97 -1 O THR A 94 N ASP A 89 SHEET 1 AA3 2 LEU A 15 TYR A 16 0 SHEET 2 AA3 2 ILE A 110 LEU A 112 -1 O LEU A 111 N LEU A 15 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