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- PDB-3uzv: Crystal structure of the dengue virus serotype 2 envelope protein... -

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Basic information

Entry
Database: PDB / ID: 3uzv
TitleCrystal structure of the dengue virus serotype 2 envelope protein domain III in complex with the variable domains of Mab 4E11
Components
  • anti-dengue Mab 4E11
  • envelope protein
KeywordsIMMUNE SYSTEM / dengue antibody neutralization
Function / homology
Function and homology information


flavivirin / 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 / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport ...flavivirin / 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 / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / 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 / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane
Similarity search - Function
Immunoglobulin-like - #350 / 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 ...Immunoglobulin-like - #350 / 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 / Immunoglobulins / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
ETHANOL / Genome polyprotein
Similarity search - Component
Biological speciesDengue virus 2
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCockburn, J.J.B. / Navarro Sanchez, M.E. / Fretes, N. / Urvoas, A. / Staropoli, I. / Kikuti, C.M. / Coffey, L.L. / Arenzana Seisdedos, F. / Bedouelle, H. / Rey, F.A.
CitationJournal: Structure / Year: 2012
Title: Mechanism of dengue virus broad cross-neutralization by a monoclonal antibody.
Authors: Cockburn, J.J. / Navarro Sanchez, M.E. / Fretes, N. / Urvoas, A. / Staropoli, I. / Kikuti, C.M. / Coffey, L.L. / Arenzana Seisdedos, F. / Bedouelle, H. / Rey, F.A.
History
DepositionDec 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: envelope protein
B: anti-dengue Mab 4E11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1593
Polymers40,1132
Non-polymers461
Water2,018112
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.460, 60.460, 207.460
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein envelope protein


Mass: 12866.834 Da / Num. of mol.: 1 / Fragment: domain III (UNP residues 576-680)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus 2 / Strain: Jamaica/1409/1983 / Plasmid: pET20b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07564
#2: Antibody anti-dengue Mab 4E11


Mass: 27246.186 Da / Num. of mol.: 1 / Fragment: Single chain variable fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pLB1 / Production host: Escherichia coli (E. coli) / Strain (production host): HB2151
#3: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.36 Å3/Da / Density % sol: 47.95 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: JBS Classic 8 solution D1 (30% ethanol, 12% PEG 6K and 0.1M sodium acetate) diluted 70% in H20, pH 6.5, vapor diffusion, sitting drop, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0721 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2008 / Details: Dynamically bendable mirror
RadiationMonochromator: LN2 cooled Fixed-exit Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0721 Å / Relative weight: 1
ReflectionResolution: 2.1→45.5 Å / Num. all: 22893 / Num. obs: 22893 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.1 % / Biso Wilson estimate: 53.06 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 23.5
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 3.3 / % possible all: 97.5

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Processing

Software
NameVersionClassificationNB
BUSTER-TNTBUSTER 2.9.3refinement
PDB_EXTRACT3.1data extraction
XDSdata scaling
XDSdata reduction
SCALAdata scaling
PHASERphasing
BUSTER2.9.3refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UZQ, 1OAN

3uzq

1oan


Resolution: 2.1→45.52 Å / Cor.coef. Fo:Fc: 0.9427 / Cor.coef. Fo:Fc free: 0.9433 / Occupancy max: 1 / Occupancy min: 0 / SU R Cruickshank DPI: 0.202 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2144 1146 5.01 %RANDOM
Rwork0.2056 ---
all0.2061 22880 --
obs0.2061 22880 97.52 %-
Displacement parametersBiso max: 173.58 Å2 / Biso mean: 60.9344 Å2 / Biso min: 36.15 Å2
Baniso -1Baniso -2Baniso -3
1--5.2445 Å20 Å20 Å2
2---5.2445 Å20 Å2
3---10.4891 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: LAST / Resolution: 2.1→45.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2524 0 3 112 2639
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d889SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes59HARMONIC2
X-RAY DIFFRACTIONt_gen_planes377HARMONIC5
X-RAY DIFFRACTIONt_it2601HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion344SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2978SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2601HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg3526HARMONIC20.97
X-RAY DIFFRACTIONt_omega_torsion2.58
X-RAY DIFFRACTIONt_other_torsion17.45
LS refinement shellResolution: 2.1→2.2 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2696 145 4.83 %
Rwork0.2165 2857 -
all0.2189 3002 -
obs--97.52 %
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)
13.02210.20862.0421.3062-0.49625.11810.03820.01970.147-0.0225-0.00020.1436-0.0396-0.3113-0.038-0.06960.0587-0.0439-0.0497-0.073-0.056-25.98429.8857-39.7809
21.6453-0.1638-0.69632.01530.70372.89010.18220.0585-0.2671-0.0062-0.0174-0.15130.54420.5358-0.1648-0.00120.1506-0.1118-0.0137-0.1023-0.0951-9.7853-2.9819-34.2339
33.52031.3317-1.74693.18630.35283.96720.1192-0.5241-0.24150.1537-0.02250.11930.40790.1691-0.0966-0.0432-0.14590.0066-0.0082-0.0449-0.1394-20.66724.6117-10.736
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ B|2 - B|117 }B2 - 117
2X-RAY DIFFRACTION2{ B|132 - B|244 }B132 - 244
3X-RAY DIFFRACTION3{ A|295 - A|342 A|346 - A|394}A295 - 342
4X-RAY DIFFRACTION3{ A|295 - A|342 A|346 - A|394}A346 - 394

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