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- PDB-4ala: Structure of Dengue virus DIII in complex with Fab 2H12 -

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Basic information

Entry
Database: PDB / ID: 4ala
TitleStructure of Dengue virus DIII in complex with Fab 2H12
Components
  • ENVELOPE PROTEIN
  • FAB 2H12 HEAVY CHAIN
  • FAB 2H12 LIGHT CHAIN
KeywordsIMMUNE SYSTEM / ANTIBODY / NEUTRALISATION
Function / homology
Function and homology information


clathrin-dependent endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / protein dimerization activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / membrane
Similarity search - Function
Immunoglobulin-like - #350 / Flavivirus envelope glycoprotein E, stem/anchor domain / 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 ...Immunoglobulin-like - #350 / Flavivirus envelope glycoprotein E, stem/anchor domain / 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 / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesDENGUE VIRUS 3
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsMidgley, C.M. / Flanagan, A. / Mongkolsapaya, J. / Grimes, J.M. / Screaton, G.R.
CitationJournal: J.Immunol. / Year: 2012
Title: Structural Analysis of a Dengue Cross-Reactive Antibody Complexed with Envelope Domain III Reveals the Molecular Basis of Cross-Reactivity.
Authors: Midgley, C.M. / Flanagan, A. / Tran, H.B. / Dejnirattisai, W. / Chawansuntati, K. / Jumnainsong, A. / Wongwiwat, W. / Duangchinda, T. / Mongkolsapaya, J. / Grimes, J.M. / Screaton, G.R.
History
DepositionMar 2, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: ENVELOPE PROTEIN
H: FAB 2H12 HEAVY CHAIN
L: FAB 2H12 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0997
Polymers57,7303
Non-polymers3684
Water8,089449
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-36.3 kcal/mol
Surface area28340 Å2
MethodPQS
Unit cell
Length a, b, c (Å)40.590, 126.040, 52.990
Angle α, β, γ (deg.)90.00, 95.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ENVELOPE PROTEIN / E GLYCOPROTEIN


Mass: 11134.793 Da / Num. of mol.: 1 / Fragment: DOMAIN III, RESIDUES 293-393
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DENGUE VIRUS 3 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q7TGD1
#2: Antibody FAB 2H12 HEAVY CHAIN


Mass: 23037.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: HYBRIDOMA / Source: (natural) MUS MUSCULUS (house mouse) / Cell: B-CELLS / Organ: SPLEEN
#3: Antibody FAB 2H12 LIGHT CHAIN


Mass: 23558.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: HYBRIDOMA / Source: (natural) MUS MUSCULUS (house mouse) / Cell: B-CELLS / Organ: SPLEEN
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / 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: 2.34 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 7.5 / Details: 20% PEG 3350, 0.2M DI-HYDROGEN PHOSPHATE, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.975
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.84→38 Å / Num. obs: 44605 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 26.33 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 15
Reflection shellResolution: 1.84→1.88 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.98 / Mean I/σ(I) obs: 2 / % possible all: 80

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→19.94 Å / Cor.coef. Fo:Fc: 0.9526 / Cor.coef. Fo:Fc free: 0.933 / SU R Cruickshank DPI: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.135 / SU Rfree Blow DPI: 0.125 / SU Rfree Cruickshank DPI: 0.124
RfactorNum. reflection% reflectionSelection details
Rfree0.2139 2228 5.03 %RANDOM
Rwork0.177 ---
obs0.1788 44332 96.85 %-
Displacement parametersBiso mean: 31.99 Å2
Baniso -1Baniso -2Baniso -3
1-1.0944 Å20 Å2-0.7325 Å2
2--0.4357 Å20 Å2
3----1.53 Å2
Refine analyzeLuzzati coordinate error obs: 0.243 Å
Refinement stepCycle: LAST / Resolution: 1.84→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3822 0 24 449 4295
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013951HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.145379HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1305SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes83HARMONIC2
X-RAY DIFFRACTIONt_gen_planes558HARMONIC5
X-RAY DIFFRACTIONt_it3951HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.75
X-RAY DIFFRACTIONt_other_torsion17.3
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion537SEMIHARMONIC5
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_contact4704SEMIHARMONIC4
LS refinement shellResolution: 1.84→1.89 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2731 138 5.1 %
Rwork0.237 2567 -
all0.2389 2705 -
obs--96.85 %
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)
11.22721.38530.90321.54260.63935.439-0.16720.0825-0.0657-0.28090.0233-0.05610.53620.10680.14390.04140.00770.0526-0.114-0.0313-0.084912.644232.9806-5.087
20.10361.58740.84175.525-0.91814.5497-0.0226-0.001-0.0875-0.05330.0106-0.03830.2209-0.19660.01190.055-0.07990.12930.058-0.0382-0.08097.909325.5336-1.8932
3-0.2531-0.02511.219800.53650.7808-0.00270.0776-0.0013-0.009-0.01390.14920.0157-0.09030.01660.05040.0036-0.0028-0.0445-0.0821-0.03555.858733.892-4.5509
40.7414-1.5288-2.86181.6539-0.0973-0.5820.00620.0005-0.1617-0.0255-0.1119-0.16070.0780.250.1057-0.02420.13640.1891-0.02070.00350.085321.310728.2101-4.6125
50.6606-1.7074-0.11221.55370.04270.7415-0.0142-0.01080.1721-0.1305-0.0103-0.1414-0.22320.07910.02450.0253-0.0383-0.0631-0.0870.0307-0.061710.891662.38678.5541
60.7165-0.36450.17311.23170.30781.835-0.05740.0109-0.0237-0.1847-0.00470.0122-0.2150.04610.0621-0.0688-0.0379-0.0276-0.12770.0261-0.13249.554953.61687.4187
71.5799-1.0876-1.23843.34451.07336.73340.1535-0.10310.25080.06770.2649-0.13710.08990.3415-0.4185-0.11290.0267-0.0258-0.0349-0.0621-0.0395-7.160774.276229.6975
83.3506-0.2437-0.74353.9052-1.33160.6543-0.08020.10340.39760.05280.16820.0711-0.23810.1374-0.088-0.0476-0.04840.0257-0.0117-0.06730.0182-5.141582.390229.023
90.6896-0.0825-0.14651.30360.24473.0481-0.0967-0.0316-0.05180.1279-0.0428-0.03760.089-0.14240.13950.0227-0.0052-0.0179-0.0170.0078-0.01186.130941.917725.2238
100.82480.1313-0.48371.369-0.13634.2422-0.0202-0.1361-0.07710.1864-0.0562-0.1375-0.05510.20980.0764-0.0172-0.0257-0.0277-0.07410.0193-0.061311.87643.165325.5206
112.5315-1.71641.10332.1064-0.7892.44650.1478-0.0067-0.1190.01790.06570.22450.2987-0.112-0.2136-0.04730.0164-0.0651-0.0668-0.0022-0.0662-15.956565.290635.8484
121.7945-0.81640.8420.9861-0.23941.85280.1759-0.1219-0.14750.01280.02850.15780.3622-0.2908-0.2043-0.02020.014-0.05140.02680.0153-0.0088-18.733265.85635.102
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN C AND RESID 300-327)
2X-RAY DIFFRACTION2(CHAIN C AND RESID 328-360)
3X-RAY DIFFRACTION3(CHAIN C AND RESID 361-368)
4X-RAY DIFFRACTION4(CHAIN C AND RESID 369-391)
5X-RAY DIFFRACTION5(CHAIN H AND RESID 1-27)
6X-RAY DIFFRACTION6(CHAIN H AND RESID 28-119)
7X-RAY DIFFRACTION7(CHAIN H AND RESID 120-194)
8X-RAY DIFFRACTION8(CHAIN H AND RESID 195-217)
9X-RAY DIFFRACTION9(CHAIN L AND RESID 1-44)
10X-RAY DIFFRACTION10(CHAIN L AND RESID 45-104)
11X-RAY DIFFRACTION11(CHAIN L AND RESID 105-155)
12X-RAY DIFFRACTION12(CHAIN L AND RESID 156-212)

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