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

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Basic information

Entry
Database: PDB / ID: 3uze
TitleCrystal structure of the dengue virus serotype 3 envelope protein domain III in complex with the variable domains of Mab 4E11
Components
  • Envelope proteinViral envelope
  • Variable domains of murine anti-dengue Mab 4E11
KeywordsIMMUNE SYSTEM / dengue antibody neutralization
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
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 / Immunoglobulins / 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
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Dengue virus 3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Variable domains of murine anti-dengue Mab 4E11
B: Variable domains of murine anti-dengue Mab 4E11
C: Envelope protein
D: Envelope protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,67115
Polymers84,6624
Non-polymers1,00911
Water4,990277
1
A: Variable domains of murine anti-dengue Mab 4E11
C: Envelope protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7948
Polymers42,3312
Non-polymers4626
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Variable domains of murine anti-dengue Mab 4E11
D: Envelope protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8787
Polymers42,3312
Non-polymers5475
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.055, 74.670, 86.888
Angle α, β, γ (deg.)90.000, 104.490, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Antibody / Protein , 2 types, 4 molecules ABCD

#1: Antibody Variable domains of murine anti-dengue Mab 4E11


Mass: 27246.186 Da / Num. of mol.: 2 / 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
#2: Protein Envelope protein / Viral envelope


Mass: 15084.850 Da / Num. of mol.: 2 / Fragment: domain III (UNP residues 293-393)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus 3 / Strain: Thailand/PaH881/1988 / Gene: E / Plasmid: pT351 / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): Schneider 2 / References: UniProt: Q7TGD1, UniProt: P27915*PLUS

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Non-polymers , 4 types, 288 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.66 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 8000, 0.1M HEPES, pH 7.5, 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: 2.037→42.857 Å / Num. all: 40602 / Num. obs: 40602 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rsym value: 0.084 / Net I/σ(I): 10.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.04-2.152.50.4441.71168747500.44476
2.15-2.283.50.36221978356770.36296.9
2.28-2.433.70.24932046655070.24998.8
2.43-2.633.60.1774.21822050740.17798.7
2.63-2.883.80.1216.11776847160.12198.9
2.88-3.223.60.0848.11526542200.08498.2
3.22-3.723.80.063101419137280.06398.5
3.72-4.553.70.05211.51169131660.05298
4.55-6.443.70.04812.2903724220.04897.2
6.44-42.8573.80.04312.7510813420.04395.9

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
BUSTER-TNTBUSTER 2.9.3refinement
PDB_EXTRACT3.1data extraction
XDSdata scaling
XDSdata reduction
PHASERphasing
BUSTER2.9.3refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UZG, 3UZQ

1uzg

3uzq


Resolution: 2.04→40.8 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.9185 / Occupancy max: 1 / Occupancy min: 0.5 / SU R Cruickshank DPI: 0.232 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2338 1981 4.9 %RANDOM
Rwork0.2177 ---
all0.2185 40459 --
obs0.2185 40459 94.62 %-
Displacement parametersBiso max: 127.94 Å2 / Biso mean: 37.2848 Å2 / Biso min: 13.69 Å2
Baniso -1Baniso -2Baniso -3
1--2.8499 Å20 Å22.2582 Å2
2--2.1541 Å20 Å2
3---0.6959 Å2
Refine analyzeLuzzati coordinate error obs: 0.304 Å
Refinement stepCycle: LAST / Resolution: 2.04→40.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4816 0 65 277 5158
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1734SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes115HARMONIC2
X-RAY DIFFRACTIONt_gen_planes724HARMONIC5
X-RAY DIFFRACTIONt_it5032HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion665SEMIHARMONIC5
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_contact5605SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5032HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg6813HARMONIC20.96
X-RAY DIFFRACTIONt_omega_torsion2.31
X-RAY DIFFRACTIONt_other_torsion15.57
LS refinement shellResolution: 2.04→2.09 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2504 98 4.41 %
Rwork0.2281 2126 -
all0.2291 2224 -
obs--94.62 %
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)
11.36730.03640.42361.22860.24721.6562-0.02250.0648-0.04250.11550.01660.0254-0.00720.05120.0059-0.0328-0.0269-0.0162-0.0641-0.0129-0.023926.877-15.405115.5203
22.04330.34160.41392.54160.05181.313-0.01240.261-0.1263-0.09480.02340.14770.00250.0648-0.011-0.0871-0.0111-0.0161-0.0524-0.0373-0.027111.0177-23.74573.0979
31.20970.39060.40621.9761-0.18532.24260.0123-0.11830.14040.06530.01940.0425-0.05310.0893-0.03180.0279-0.0214-0.0175-0.0924-0.0434-0.078232.72771.833730.4485
41.1168-0.10510.28733.8790.88252.21020.0049-0.21980.11880.2263-0.02430.2341-0.0037-0.08830.0193-0.0153-0.02470.0377-0.0561-0.0821-0.108129.202310.041850.1665
52.5477-0.91640.21092.7087-0.73872.0667-0.06810.18850.2177-0.1059-0.0474-0.10680.0862-0.05070.1155-0.0692-0.0177-0.0207-0.09120.0137-0.023413.57521.4405-6.6341
62.2227-2.06420.26745.1542-3.52633.7792-0.1048-0.1979-0.02070.13530.0285-0.08390.2372-0.08530.07630.28230.0560.007-0.26720.0002-0.265837.6507-14.429254.8571
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|2 - A|117 }A2 - 117
2X-RAY DIFFRACTION2{ A|133 - A|245 }A133 - 245
3X-RAY DIFFRACTION3{ B|2 - B|117 }B2 - 117
4X-RAY DIFFRACTION4{ B|134 - B|243 }B134 - 243
5X-RAY DIFFRACTION5{ C|299 - C|314 C|317 - C|361 C|365 - C|397 }C299 - 314
6X-RAY DIFFRACTION5{ C|299 - C|314 C|317 - C|361 C|365 - C|397 }C317 - 361
7X-RAY DIFFRACTION5{ C|299 - C|314 C|317 - C|361 C|365 - C|397 }C365 - 397
8X-RAY DIFFRACTION6{ D|300 - D|314 D|319 - D|341 D|350 - D|359 D|365 - D|382 D|386 - D|393}D300 - 314
9X-RAY DIFFRACTION6{ D|300 - D|314 D|319 - D|341 D|350 - D|359 D|365 - D|382 D|386 - D|393}D319 - 341
10X-RAY DIFFRACTION6{ D|300 - D|314 D|319 - D|341 D|350 - D|359 D|365 - D|382 D|386 - D|393}D350 - 359
11X-RAY DIFFRACTION6{ D|300 - D|314 D|319 - D|341 D|350 - D|359 D|365 - D|382 D|386 - D|393}D365 - 382
12X-RAY DIFFRACTION6{ D|300 - D|314 D|319 - D|341 D|350 - D|359 D|365 - D|382 D|386 - D|393}D386 - 393

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