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- PDB-4v0q: Dengue Virus Full Length NS5 Complexed with SAH -

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Basic information

Entry
Database: PDB / ID: 4v0q
TitleDengue Virus Full Length NS5 Complexed with SAH
ComponentsNS5 POLYMERASE
KeywordsTRANSFERASE / METHYLTRANSFERASE / RNA-DEPENDENT RNA POLYMERASE
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / : / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / protein complex oligomerization ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / : / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / protein complex oligomerization / monoatomic ion channel activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / structural molecule activity / virion attachment to host cell / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
: / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B ...: / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / Vaccinia Virus protein VP39 / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / S-ADENOSYL-L-HOMOCYSTEINE / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesDENGUE VIRUS 3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZhao, Y. / Soh, S. / Zheng, J. / Phoo, W.W. / Swaminathan, K. / Cornvik, T.C. / Lim, S.P. / Shi, P.-Y. / Lescar, J. / Vasudevan, S.G. / Luo, D.
CitationJournal: Plos Pathog. / Year: 2015
Title: A Crystal Structure of the Dengue Virus Ns5 Protein Reveals a Novel Inter-Domain Interface Essential for Protein Flexibility and Virus Replication.
Authors: Zhao, Y. / Soh, T.S. / Zheng, J. / Chan, K.W.K. / Phoo, W.W. / Lee, C.C. / Tay, M.Y.F. / Swaminathan, K. / Cornvik, T.C. / Lim, S.P. / Shi, P. / Lescar, J. / Vasudevan, S.G. / Luo, D.
History
DepositionSep 18, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references
Revision 1.2Jun 20, 2018Group: Data collection / Structure summary / Category: diffrn_source / struct
Item: _diffrn_source.pdbx_synchrotron_beamline / _struct.title
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NS5 POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,79211
Polymers102,8311
Non-polymers96210
Water4,990277
1
A: NS5 POLYMERASE
hetero molecules

A: NS5 POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,58422
Polymers205,6612
Non-polymers1,92320
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
Buried area5300 Å2
ΔGint-17.1 kcal/mol
Surface area70920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.129, 151.445, 69.124
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2134-

HOH

21A-2135-

HOH

31A-2142-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein NS5 POLYMERASE


Mass: 102830.633 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 2494-3385
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DENGUE VIRUS 3 / Strain: SINGAPORE STRAIN / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): CODON PLUS / References: UniProt: Q6DLV0, UniProt: Q5UB51*PLUS

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Non-polymers , 5 types, 287 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 43.2 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Type: SLS / Wavelength: 1
DetectorDate: Feb 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→39.18 Å / Num. obs: 41247 / % possible obs: 91.8 % / Observed criterion σ(I): 2.6 / Redundancy: 3.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.5

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3P97 AND 2J7U

3p97

2j7u


Resolution: 2.3→39.184 Å / SU ML: 0.26 / σ(F): 1.35 / Phase error: 24.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2464 2075 5 %
Rwork0.1907 --
obs0.1935 41182 91.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→39.184 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6828 0 58 277 7163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047047
X-RAY DIFFRACTIONf_angle_d0.8039533
X-RAY DIFFRACTIONf_dihedral_angle_d14.0632643
X-RAY DIFFRACTIONf_chiral_restr0.0331021
X-RAY DIFFRACTIONf_plane_restr0.0031223
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.35350.3521390.2732415X-RAY DIFFRACTION87
2.3535-2.41240.28751210.25452433X-RAY DIFFRACTION87
2.4124-2.47760.31741220.2342432X-RAY DIFFRACTION86
2.4776-2.55050.34811310.23712614X-RAY DIFFRACTION92
2.5505-2.63280.25071530.22832626X-RAY DIFFRACTION94
2.6328-2.72680.31431490.22092660X-RAY DIFFRACTION94
2.7268-2.8360.24821400.21292652X-RAY DIFFRACTION94
2.836-2.9650.26511500.21942687X-RAY DIFFRACTION94
2.965-3.12130.2881330.20552668X-RAY DIFFRACTION94
3.1213-3.31670.2851290.19742685X-RAY DIFFRACTION93
3.3167-3.57270.2621200.17812553X-RAY DIFFRACTION89
3.5727-3.93190.21911360.16872645X-RAY DIFFRACTION92
3.9319-4.50010.1681390.14852694X-RAY DIFFRACTION93
4.5001-5.6670.22341450.16112670X-RAY DIFFRACTION92
5.667-39.18980.22091680.17622673X-RAY DIFFRACTION88
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7595-0.11640.0590.88580.17210.3901-0.00460.0333-0.0225-0.08370.04310.0708-0.01790.02740.00010.1417-0.0229-0.02290.1354-0.00340.111419.1812134.989218.4777
20.441-0.012-0.2140.41730.27150.282-0.0154-0.0146-0.03660.18260.04110.19250.1308-0.0596-0.02420.1536-0.03340.03870.1808-0.01730.298710.8371157.559238.7397
30.40080.25930.00270.2934-0.0938-0.0056-0.10460.10780.01870.00680.0740.11190.0222-0.06150.01230.2008-0.0265-0.02660.2355-0.00990.18126.251170.848330.2458
40.57310.12550.00370.44010.09960.2839-0.05320.01110.0151-0.0055-0.0510.020.0182-0.0062-0.00360.18120.0004-0.01280.1709-0.01220.176231.5467173.446135.7732
50.276-0.1340.3460.1915-0.0560.592-0.06070.0296-0.01140.0398-0.08610.0535-0.1302-0.3668-0.00020.40620.0293-0.01590.5129-0.02550.378826.4123182.66885.7367
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 6 THROUGH 263 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 264 THROUGH 321 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 322 THROUGH 403 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 404 THROUGH 722 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 723 THROUGH 883 )

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