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- PDB-5wtg: Crystal structure of the Fab fragment of anti-HAV antibody R10 -

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Basic information

Entry
Database: PDB / ID: 5wtg
TitleCrystal structure of the Fab fragment of anti-HAV antibody R10
Components
  • FAB Heavy chainFragment antigen-binding
  • FAB Light chainFragment antigen-binding
KeywordsIMMUNE SYSTEM / HAV / Neutralizing mechanism / Receptor recognition / Viral entry
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.907 Å
AuthorsWang, X. / Zhu, L. / Dang, M. / Hu, Z. / Gao, Q. / Yuan, S. / Sun, Y. / Zhang, B. / Ren, J. / Walter, T.S. ...Wang, X. / Zhu, L. / Dang, M. / Hu, Z. / Gao, Q. / Yuan, S. / Sun, Y. / Zhang, B. / Ren, J. / Walter, T.S. / Wang, J. / Fry, E.E. / Stuart, D.I. / Rao, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation31570717 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2017
Title: Potent neutralization of hepatitis A virus reveals a receptor mimic mechanism and the receptor recognition site.
Authors: Xiangxi Wang / Ling Zhu / Minghao Dang / Zhongyu Hu / Qiang Gao / Shuai Yuan / Yao Sun / Bo Zhang / Jingshan Ren / Abhay Kotecha / Thomas S Walter / Junzhi Wang / Elizabeth E Fry / David I Stuart / Zihe Rao /
Abstract: Hepatitis A virus (HAV) infects ∼1.4 million people annually and, although there is a vaccine, there are no licensed therapeutic drugs. HAV is unusually stable (making disinfection problematic) and ...Hepatitis A virus (HAV) infects ∼1.4 million people annually and, although there is a vaccine, there are no licensed therapeutic drugs. HAV is unusually stable (making disinfection problematic) and little is known of how it enters cells and releases its RNA. Here we report a potent HAV-specific monoclonal antibody, R10, which neutralizes HAV infection by blocking attachment to the host cell. High-resolution cryo-EM structures of HAV full and empty particles and of the complex of HAV with R10 Fab reveal the atomic details of antibody binding and point to a receptor recognition site at the pentamer interface. These results, together with our observation that the R10 Fab destabilizes the capsid, suggest the use of a receptor mimic mechanism to neutralize virus infection, providing new opportunities for therapeutic intervention.
History
DepositionDec 11, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Database references
Revision 1.2Aug 30, 2017Group: Data collection / Category: diffrn_detector / diffrn_source
Item: _diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Nov 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FAB Light chain
B: FAB Heavy chain
C: FAB Light chain
D: FAB Heavy chain


Theoretical massNumber of molelcules
Total (without water)93,9164
Polymers93,9164
Non-polymers00
Water0
1
A: FAB Light chain
B: FAB Heavy chain


Theoretical massNumber of molelcules
Total (without water)46,9582
Polymers46,9582
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-26 kcal/mol
Surface area19580 Å2
MethodPISA
2
C: FAB Light chain
D: FAB Heavy chain


Theoretical massNumber of molelcules
Total (without water)46,9582
Polymers46,9582
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-26 kcal/mol
Surface area19580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.512, 140.522, 68.924
Angle α, β, γ (deg.)90.00, 110.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody FAB Light chain / Fragment antigen-binding


Mass: 23283.535 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody FAB Heavy chain / Fragment antigen-binding


Mass: 23674.654 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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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: 2.56 Å3/Da / Density % sol: 51.9 % / Description: cubic
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% PEG3350, 0.2M Sodium Thiocyanate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.997 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.997 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 20094 / % possible obs: 97.9 % / Redundancy: 3.1 % / Biso Wilson estimate: 65 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 3.68
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.5 % / % possible all: 95.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data processing
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EJO

1ejo


Resolution: 2.907→49.232 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.65
RfactorNum. reflection% reflection
Rfree0.2664 984 4.9 %
Rwork0.2009 --
obs0.2042 20063 97.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.907→49.232 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6531 0 0 0 6531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016705
X-RAY DIFFRACTIONf_angle_d1.1759138
X-RAY DIFFRACTIONf_dihedral_angle_d17.0523974
X-RAY DIFFRACTIONf_chiral_restr0.0581020
X-RAY DIFFRACTIONf_plane_restr0.0071151
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9071-3.06030.34941300.2822562X-RAY DIFFRACTION91
3.0603-3.2520.32891420.25432705X-RAY DIFFRACTION97
3.252-3.5030.2941210.2272752X-RAY DIFFRACTION98
3.503-3.85550.28411310.19562733X-RAY DIFFRACTION98
3.8555-4.4130.2411400.16922768X-RAY DIFFRACTION99
4.413-5.55870.20591670.15242755X-RAY DIFFRACTION99
5.5587-49.23930.23351530.17612804X-RAY DIFFRACTION99

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