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- PDB-4gq9: Chikungunya virus neutralizing antibody 9.8B Fab fragment -

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Basic information

Entry
Database: PDB / ID: 4gq9
TitleChikungunya virus neutralizing antibody 9.8B Fab fragment
Components
  • Chikungunya virus neutralizing antibody 9.8B Fab fragment heavy chain
  • Chikungunya virus neutralizing antibody 9.8B Fab fragment light chain
KeywordsVIRAL PROTEIN / IgG fold / antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.995 Å
AuthorsSun, S. / Rossmann, M.G.
CitationJournal: Elife / Year: 2013
Title: Structural analyses at pseudo atomic resolution of Chikungunya virus and antibodies show mechanisms of neutralization.
Authors: Siyang Sun / Ye Xiang / Wataru Akahata / Heather Holdaway / Pankaj Pal / Xinzheng Zhang / Michael S Diamond / Gary J Nabel / Michael G Rossmann /
Abstract: A 5.3 Å resolution, cryo-electron microscopy (cryoEM) map of Chikungunya virus-like particles (VLPs) has been interpreted using the previously published crystal structure of the Chikungunya E1-E2 ...A 5.3 Å resolution, cryo-electron microscopy (cryoEM) map of Chikungunya virus-like particles (VLPs) has been interpreted using the previously published crystal structure of the Chikungunya E1-E2 glycoprotein heterodimer. The heterodimer structure was divided into domains to obtain a good fit to the cryoEM density. Differences in the T = 4 quasi-equivalent heterodimer components show their adaptation to different environments. The spikes on the icosahedral 3-fold axes and those in general positions are significantly different, possibly representing different phases during initial generation of fusogenic E1 trimers. CryoEM maps of neutralizing Fab fragments complexed with VLPs have been interpreted using the crystal structures of the Fab fragments and the VLP structure. Based on these analyses the CHK-152 antibody was shown to stabilize the viral surface, hindering the exposure of the fusion-loop, likely neutralizing infection by blocking fusion. The CHK-9, m10 and m242 antibodies surround the receptor-attachment site, probably inhibiting infection by blocking cell attachment. DOI:http://dx.doi.org/10.7554/eLife.00435.001.
History
DepositionAug 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Sep 13, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Chikungunya virus neutralizing antibody 9.8B Fab fragment light chain
H: Chikungunya virus neutralizing antibody 9.8B Fab fragment heavy chain


Theoretical massNumber of molelcules
Total (without water)46,7452
Polymers46,7452
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-24 kcal/mol
Surface area20480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.859, 57.726, 118.108
Angle α, β, γ (deg.)90.00, 97.51, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Chikungunya virus neutralizing antibody 9.8B Fab fragment light chain


Mass: 23303.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody Chikungunya virus neutralizing antibody 9.8B Fab fragment heavy chain


Mass: 23441.291 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
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: 3.18 Å3/Da / Density % sol: 61.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% PEG 3350, 0.1M Tris-Cl pH 8.5 and 0.2M lithium sulfate., VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.96801 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 23, 2010 / Details: mirrors
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96801 Å / Relative weight: 1
ReflectionResolution: 2.995→50 Å / Num. all: 11921 / Num. obs: 11714 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 62.7 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 22.5
Reflection shellResolution: 2.995→3.05 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 4.3 / Num. unique all: 590 / % possible all: 98

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DGG

3dgg


Resolution: 2.995→43.42 Å / Cor.coef. Fo:Fc: 0.803 / Cor.coef. Fo:Fc free: 0.726 / SU B: 92.327 / SU ML: 0.749 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.59 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.3593 568 4.8 %RANDOM
Rwork0.32334 ---
all0.3251 11921 --
obs0.3251 11349 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 82.987 Å2
Baniso -1Baniso -2Baniso -3
1--1.3 Å20 Å2-1.72 Å2
2--2.05 Å20 Å2
3----1.2 Å2
Refinement stepCycle: LAST / Resolution: 2.995→43.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3280 0 0 0 3280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223362
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.911.9494584
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9445428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.39824.206126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.51615541
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.5351513
X-RAY DIFFRACTIONr_chiral_restr0.0620.2523
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022508
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1660.21182
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2880.22215
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0880.2103
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.231
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0280.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.0591.52200
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.10623487
X-RAY DIFFRACTIONr_scbond_it0.10831358
X-RAY DIFFRACTIONr_scangle_it0.1814.51097
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.995→3.073 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 33 -
Rwork0.39 776 -
obs-776 91.72 %
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)
16.7245-0.32080.49947.63140.43865.537-0.05570.6203-0.3623-0.48690.08140.08580.4370.1445-0.02570.1625-0.05180.05750.1487-0.07670.0714-24.1931-5.338246.7465
28.24731.8107-3.29938.0835-2.27516.3136-0.07830.7431-0.3054-1.7219-0.2386-0.83590.25690.73870.31691.59520.0468-0.07981.3388-0.35310.2677-22.7657-1.466410.1907
36.3499-0.05860.25125.79981.14515.8852-0.17210.57040.3375-0.42110.0928-0.203-0.31350.3590.07920.1803-0.059-0.06230.17030.03640.1093-15.836815.307346.4389
414.29850.22921.47973.94870.66122.16880.12751.02580.798-1.2551-0.29411.08990.1233-0.29190.16661.4290.0503-0.30251.42640.22530.4337-30.346612.772813.5418
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 106
2X-RAY DIFFRACTION2L107 - 212
3X-RAY DIFFRACTION3H1 - 118
4X-RAY DIFFRACTION4H119 - 218

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