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- PDB-7vmv: Crystal structure of Dengue NS2B-NS3 Protease after secondary cleavage -

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Basic information

Entry
Database: PDB / ID: 7vmv
TitleCrystal structure of Dengue NS2B-NS3 Protease after secondary cleavage
Components(Core protein) x 2
KeywordsVIRAL PROTEIN / NS3 Protease
Function / homology
Function and homology information


: / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / 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 / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / channel activity / monoatomic ion transmembrane transport ...: / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / 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 / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane
Similarity search - Function
Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A ...Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / 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. / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus capsid protein C / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / 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 / 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 / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesDengue virus 4
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.351 Å
AuthorsQuek, J.P.
Funding support Singapore, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore)NRF2016NRF-CRP001-063 Singapore
CitationJournal: Viruses / Year: 2022
Title: Dynamic Interactions of Post Cleaved NS2B Cofactor and NS3 Protease Identified by Integrative Structural Approaches.
Authors: Quek, J.P. / Ser, Z. / Chew, B.L.A. / Li, X. / Wang, L. / Sobota, R.M. / Luo, D. / Phoo, W.W.
History
DepositionOct 9, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Core protein
B: Core protein
C: Core protein
D: Core protein
E: Core protein
F: Core protein
G: Core protein
H: Core protein


Theoretical massNumber of molelcules
Total (without water)116,1148
Polymers116,1148
Non-polymers00
Water00
1
A: Core protein
B: Core protein


Theoretical massNumber of molelcules
Total (without water)29,0282
Polymers29,0282
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-20 kcal/mol
Surface area12520 Å2
MethodPISA
2
C: Core protein
D: Core protein


Theoretical massNumber of molelcules
Total (without water)29,0282
Polymers29,0282
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-22 kcal/mol
Surface area10890 Å2
MethodPISA
3
E: Core protein
F: Core protein


Theoretical massNumber of molelcules
Total (without water)29,0282
Polymers29,0282
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-20 kcal/mol
Surface area11120 Å2
MethodPISA
4
G: Core protein
H: Core protein


Theoretical massNumber of molelcules
Total (without water)29,0282
Polymers29,0282
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-22 kcal/mol
Surface area12520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)259.984, 259.984, 259.984
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number196
Space group name H-MF23
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 49 through 54 or (resid 55...
21(chain C and (resid 49 through 66 or (resid 67...
31(chain E and (resid 49 through 76 or resid 78...
41(chain G and (resid 49 through 54 or (resid 55...
12(chain B and ((resid 18 and (name N or name...
22(chain D and ((resid 18 and (name N or name...
32(chain F and (resid 18 through 23 or (resid 24...
42(chain H and ((resid 18 and (name N or name...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ALAALAGLUGLU(chain A and (resid 49 through 54 or (resid 55...AA49 - 5429 - 34
121LYSLYSALAALA(chain A and (resid 49 through 54 or (resid 55...AA55 - 5735 - 37
131METMETLYSLYS(chain A and (resid 49 through 54 or (resid 55...AA46 - 9926 - 79
141METMETLYSLYS(chain A and (resid 49 through 54 or (resid 55...AA46 - 9926 - 79
151METMETLYSLYS(chain A and (resid 49 through 54 or (resid 55...AA46 - 9926 - 79
161METMETLYSLYS(chain A and (resid 49 through 54 or (resid 55...AA46 - 9926 - 79
211ALAALAASPASP(chain C and (resid 49 through 66 or (resid 67...CC49 - 6629 - 46
221ILEILEILEILE(chain C and (resid 49 through 66 or (resid 67...CC6747
231ALAALALYSLYS(chain C and (resid 49 through 66 or (resid 67...CC49 - 9929 - 79
241ALAALALYSLYS(chain C and (resid 49 through 66 or (resid 67...CC49 - 9929 - 79
251ALAALALYSLYS(chain C and (resid 49 through 66 or (resid 67...CC49 - 9929 - 79
261ALAALALYSLYS(chain C and (resid 49 through 66 or (resid 67...CC49 - 9929 - 79
311ALAALAVALVAL(chain E and (resid 49 through 76 or resid 78...EE49 - 7629 - 56
321GLNGLNGLUGLU(chain E and (resid 49 through 76 or resid 78...EE78 - 8058 - 60
331ASPASPASPASP(chain E and (resid 49 through 76 or resid 78...EE8161
341SERSERLYSLYS(chain E and (resid 49 through 76 or resid 78...EE48 - 9928 - 79
351SERSERLYSLYS(chain E and (resid 49 through 76 or resid 78...EE48 - 9928 - 79
361SERSERLYSLYS(chain E and (resid 49 through 76 or resid 78...EE48 - 9928 - 79
371SERSERLYSLYS(chain E and (resid 49 through 76 or resid 78...EE48 - 9928 - 79
411ALAALAGLUGLU(chain G and (resid 49 through 54 or (resid 55...GG49 - 5429 - 34
421LYSLYSALAALA(chain G and (resid 49 through 54 or (resid 55...GG55 - 5735 - 37
431GLYGLYLYSLYS(chain G and (resid 49 through 54 or (resid 55...GG47 - 9927 - 79
441GLYGLYLYSLYS(chain G and (resid 49 through 54 or (resid 55...GG47 - 9927 - 79
451GLYGLYLYSLYS(chain G and (resid 49 through 54 or (resid 55...GG47 - 9927 - 79
461GLYGLYLYSLYS(chain G and (resid 49 through 54 or (resid 55...GG47 - 9927 - 79
112LEULEULEULEU(chain B and ((resid 18 and (name N or name...BB1818
122LEULEUGLUGLU(chain B and ((resid 18 and (name N or name...BB18 - 18018 - 180
132LEULEUGLUGLU(chain B and ((resid 18 and (name N or name...BB18 - 18018 - 180
142LEULEUGLUGLU(chain B and ((resid 18 and (name N or name...BB18 - 18018 - 180
152LEULEUGLUGLU(chain B and ((resid 18 and (name N or name...BB18 - 18018 - 180
212LEULEULEULEU(chain D and ((resid 18 and (name N or name...DD1818
222THRTHRGLUGLU(chain D and ((resid 18 and (name N or name...DD17 - 16917 - 169
232THRTHRGLUGLU(chain D and ((resid 18 and (name N or name...DD17 - 16917 - 169
242THRTHRGLUGLU(chain D and ((resid 18 and (name N or name...DD17 - 16917 - 169
252THRTHRGLUGLU(chain D and ((resid 18 and (name N or name...DD17 - 16917 - 169
312LEULEUTYRTYR(chain F and (resid 18 through 23 or (resid 24...FF18 - 2318 - 23
322ARGARGARGARG(chain F and (resid 18 through 23 or (resid 24...FF2424
332THRTHRILEILE(chain F and (resid 18 through 23 or (resid 24...FF17 - 17117 - 171
342THRTHRILEILE(chain F and (resid 18 through 23 or (resid 24...FF17 - 17117 - 171
352THRTHRILEILE(chain F and (resid 18 through 23 or (resid 24...FF17 - 17117 - 171
362THRTHRILEILE(chain F and (resid 18 through 23 or (resid 24...FF17 - 17117 - 171
412LEULEULEULEU(chain H and ((resid 18 and (name N or name...HH1818
422ALAALAGLUGLU(chain H and ((resid 18 and (name N or name...HH3 - 1733 - 173
432ALAALAGLUGLU(chain H and ((resid 18 and (name N or name...HH3 - 1733 - 173
442ALAALAGLUGLU(chain H and ((resid 18 and (name N or name...HH3 - 1733 - 173
452ALAALAGLUGLU(chain H and ((resid 18 and (name N or name...HH3 - 1733 - 173

NCS ensembles :
ID
1
2

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Components

#1: Protein
Core protein / Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 ...Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 catalytic subunit / Genome polyprotein / Matrix protein / Non-structural protein 1 / Non-structural protein 2A / Non-structural protein 2B / Non-structural protein 3 / Non-structural protein 4A / Non-structural protein 4B / Peptide 2k / Peptide pr / Protein prM / RNA-directed RNA polymerase NS5 / Serine protease NS3 / Serine protease subunit NS2B / Small envelope protein M


Mass: 9407.243 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus 4 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0M4C4I5, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase
#2: Protein
Core protein / Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 ...Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 catalytic subunit / Genome polyprotein / Matrix protein / Non-structural protein 1 / Non-structural protein 2A / Non-structural protein 2B / Non-structural protein 3 / Non-structural protein 4A / Non-structural protein 4B / Peptide 2k / Peptide pr / Protein prM / RNA-directed RNA polymerase NS5 / Serine protease NS3 / Serine protease subunit NS2B / Small envelope protein M


Mass: 19621.170 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus 4 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5I3B6, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.15 Å3/Da / Density % sol: 60.99 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 1.7 M Sodium malonate, pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: k,h,-l / Fraction: 0.04
ReflectionResolution: 3.351→43.33 Å / Num. obs: 20533 / % possible obs: 97.65 % / Redundancy: 1.8 % / CC1/2: 0.998 / Net I/σ(I): 10
Reflection shellResolution: 3.351→3.471 Å / Num. unique obs: 2084 / CC1/2: 0.512

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VBC

2vbc


Resolution: 3.351→43.33 Å / Cross valid method: THROUGHOUT / σ(F): 585.55 / Phase error: 28.92 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2628 988 -
Rwork0.2258 19517 -
obs-20504 97.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 267.75 Å2 / Biso mean: 138.6228 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.351→43.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6021 0 0 0 6021
Num. residues----852
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A736X-RAY DIFFRACTION15.827TORSIONAL
12C736X-RAY DIFFRACTION15.827TORSIONAL
13E736X-RAY DIFFRACTION15.827TORSIONAL
14G736X-RAY DIFFRACTION15.827TORSIONAL
21B2384X-RAY DIFFRACTION15.827TORSIONAL
22D2384X-RAY DIFFRACTION15.827TORSIONAL
23F2384X-RAY DIFFRACTION15.827TORSIONAL
24H2384X-RAY DIFFRACTION15.827TORSIONAL
LS refinement shellResolution: 3.3511→3.471 Å / Rfactor Rfree error: 0 /
RfactorNum. reflection
Rfree0.3576 121
Rwork0.3606 2079
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)
10.14860.04130.12156.9749-0.0713-0.0783-0.14070.22750.45450.28790.5272-1.00950.08550.1946-0.40380.99770.0931-0.09651.2113-0.06381.122818.763144.262577.1836
24.8342-1.19421.84025.77132.43526.83090.34250.3880.2853-0.3323-0.018-0.58030.32220.8381-0.33360.56710.12920.06810.80470.12740.770215.067155.527876.4436
35.14184.6155-3.8065.6697-3.17312.24690.56980.43390.78880.55130.08090.87590.08870.2836-0.58741.5011-0.3591-0.0791.6482-0.0391.336733.1151-11.215743.8934
48.05310.3445-1.12955.45291.87354.7407-0.08191.8780.3347-0.9164-0.14690.94860.2556-1.02030.25610.9975-0.1407-0.22061.3236-0.04640.827541.7839-1.004438.3146
53.0018-5.3692-0.92857.7464-0.9221.385-0.13660.1297-0.7347-0.1039-0.12060.76730.1621-0.1330.190.8759-0.0098-0.16661.1365-0.11171.247422.6217.189279.0085
67.6545-2.45362.38183.37140.32875.7708-0.3967-0.8658-0.36380.2024-0.02751.36270.2611-1.29470.37270.7074-0.05080.18960.9572-0.12451.19728.3184.153777.8788
75.50557.3311-1.99778.4797-4.32171.7186-0.1074-0.8958-0.2701-0.1445-0.2559-0.2825-0.27630.55370.3561.0481-0.0960.09351.2022-0.18751.185125.0792-31.447658.1298
85.89741.5786-0.89165.67390.29892.98460.1327-0.378-0.227-0.2043-0.1538-0.8692-0.41810.77950.02830.77410.01310.1330.96890.02310.781415.5028-42.382464.9787
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 46 through 99)A46 - 99
2X-RAY DIFFRACTION2(chain 'B' and resid 18 through 180)B18 - 180
3X-RAY DIFFRACTION3(chain 'C' and resid 49 through 99)C49 - 99
4X-RAY DIFFRACTION4(chain 'D' and resid 17 through 169)D17 - 169
5X-RAY DIFFRACTION5(chain 'E' and resid 48 through 99)E48 - 99
6X-RAY DIFFRACTION6(chain 'F' and resid 17 through 171)F17 - 171
7X-RAY DIFFRACTION7(chain 'G' and resid 47 through 99)G47 - 99
8X-RAY DIFFRACTION8(chain 'H' and resid 3 through 173)H3 - 173

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