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- PDB-4x42: Crystal structure of DEN4 ED3 mutant with epitope two residues su... -

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Basic information

Entry
Database: PDB / ID: 4x42
TitleCrystal structure of DEN4 ED3 mutant with epitope two residues substituted from DEN3 ED3
ComponentsEnvelope protein E
KeywordsSTRUCTURAL PROTEIN / IMMUNE SYSTEM / Sero-specificity / Epitope graft mutants / ELISA
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 / virion attachment to host cell / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
Immunoglobulin-like - #350 / : / 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 ...Immunoglobulin-like - #350 / : / 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 / 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 / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Biological speciesDengue virus type 4
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsKulkarni, M.R. / Islam, M.M. / Numoto, N. / Elahi, M.M. / Ito, N. / Kuroda, Y.
CitationJournal: Biochim.Biophys.Acta / Year: 2015
Title: Structural and biophysical analysis of sero-specific immune responses using epitope grafted Dengue ED3 mutants.
Authors: Kulkarni, M.R. / Islam, M.M. / Numoto, N. / Elahi, M. / Mahib, M.R. / Ito, N. / Kuroda, Y.
History
DepositionDec 2, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Envelope protein E
E: Envelope protein E
F: Envelope protein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,52910
Polymers69,1456
Non-polymers3844
Water19811
1
A: Envelope protein E
B: Envelope protein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3375
Polymers23,0482
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-44 kcal/mol
Surface area11280 Å2
MethodPISA
2
C: Envelope protein E
D: Envelope protein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1443
Polymers23,0482
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-15 kcal/mol
Surface area11270 Å2
MethodPISA
3
E: Envelope protein E


Theoretical massNumber of molelcules
Total (without water)11,5241
Polymers11,5241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5970 Å2
MethodPISA
4
F: Envelope protein E


Theoretical massNumber of molelcules
Total (without water)11,5241
Polymers11,5241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.585, 124.585, 86.132
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22D
13A
23C
14A
24E
15A
25F
16B
26D
17B
27C
18B
28E
19B
29F
110D
210C
111D
211E
112D
212F
113C
213E
114C
214F
115E
215F

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERARGARGAA577 - 6725 - 100
21SERSERARGARGBB577 - 6725 - 100
12SERSERGLYGLYAA577 - 6745 - 102
22SERSERGLYGLYDD577 - 6745 - 102
13SERSERARGARGAA577 - 6725 - 100
23SERSERARGARGCC577 - 6725 - 100
14TYRTYRARGARGAA578 - 6726 - 100
24TYRTYRARGARGEE578 - 6726 - 100
15SERSERARGARGAA577 - 6725 - 100
25SERSERARGARGFF577 - 6725 - 100
16SERSERARGARGBB574 - 6722 - 100
26SERSERARGARGDD574 - 6722 - 100
17SERSERARGARGBB577 - 6725 - 100
27SERSERARGARGCC577 - 6725 - 100
18TYRTYRARGARGBB578 - 6726 - 100
28TYRTYRARGARGEE578 - 6726 - 100
19SERSERLYSLYSBB574 - 6732 - 101
29SERSERLYSLYSFF574 - 6732 - 101
110SERSERARGARGDD577 - 6725 - 100
210SERSERARGARGCC577 - 6725 - 100
111TYRTYRARGARGDD578 - 6726 - 100
211TYRTYRARGARGEE578 - 6726 - 100
112SERSERARGARGDD574 - 6722 - 100
212SERSERARGARGFF574 - 6722 - 100
113TYRTYRARGARGCC578 - 6726 - 100
213TYRTYRARGARGEE578 - 6726 - 100
114SERSERARGARGCC577 - 6725 - 100
214SERSERARGARGFF577 - 6725 - 100
115TYRTYRARGARGEE578 - 6726 - 100
215TYRTYRARGARGFF578 - 6726 - 100

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Envelope protein E /


Mass: 11524.199 Da / Num. of mol.: 6 / Fragment: domain III (ED3), UNP residues 575-679 / Mutation: N663D, S664K, T667K, H669N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus type 4 / Strain: Dominica/814669/1981 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 (DE3 pLysS) / References: UniProt: P09866
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

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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: 2.79 Å3/Da / Density % sol: 55.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG 3350, Ammonium sulphate, Tris-HCL, Dioxane

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.78→50 Å / Num. obs: 19294 / % possible obs: 100 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 37.8
Reflection shellResolution: 2.78→2.83 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.872 / Mean I/σ(I) obs: 5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
Cootmodel building
HKL-2000data processing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WE1

3we1


Resolution: 2.78→40.03 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.889 / SU B: 17.514 / SU ML: 0.331 / Cross valid method: THROUGHOUT / ESU R: 8.166 / ESU R Free: 0.385 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27277 938 4.9 %RANDOM
Rwork0.23392 ---
obs0.23584 18330 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 53.644 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20.1 Å2-0 Å2
2--0.1 Å2-0 Å2
3----0.32 Å2
Refinement stepCycle: 1 / Resolution: 2.78→40.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4544 0 20 11 4575
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194644
X-RAY DIFFRACTIONr_bond_other_d0.0070.024534
X-RAY DIFFRACTIONr_angle_refined_deg1.5121.9756273
X-RAY DIFFRACTIONr_angle_other_deg1.5383.00210506
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2395588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.21525.172174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.31215853
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8861518
X-RAY DIFFRACTIONr_chiral_restr0.0720.2719
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215106
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02924
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A53140.12
12B53140.12
21A54730.11
22D54730.11
31A52670.12
32C52670.12
41A53200.11
42E53200.11
51A53470.14
52F53470.14
61B54260.1
62D54260.1
71B53420.1
72C53420.1
81B53200.1
82E53200.1
91B54170.12
92F54170.12
101D52390.12
102C52390.12
111D53060.1
112E53060.1
121D53690.13
122F53690.13
131C51460.12
132E51460.12
141C51460.14
142F51460.14
151E53460.1
152F53460.1
LS refinement shellResolution: 2.778→2.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.44 70 -
Rwork0.34 1318 -
obs--97.75 %

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