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- PDB-5ysl: Crystal structure of antibody 1H1 Fab -

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Basic information

Entry
Database: PDB / ID: 5ysl
TitleCrystal structure of antibody 1H1 Fab
Components
  • 1H1 heavy chain
  • 1H1 light chain
KeywordsIMMUNE SYSTEM / Fragment / FAB FRAGMENT / FICIN DIGESTION / INTACT ANTIBODY IgG1
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHu, X.L. / Yang, F.L.
CitationJournal: PLoS Pathog / Year: 2017
Title: Two classes of protective antibodies against Pseudorabies virus variant glycoprotein B: Implications for vaccine design.
Authors: Xiangdong Li / Fanli Yang / Xule Hu / Feifei Tan / Jianxun Qi / Ruchao Peng / Min Wang / Yan Chai / Liying Hao / Junhua Deng / Chenyu Bai / Juan Wang / Hao Song / Shuguang Tan / Guangwen Lu ...Authors: Xiangdong Li / Fanli Yang / Xule Hu / Feifei Tan / Jianxun Qi / Ruchao Peng / Min Wang / Yan Chai / Liying Hao / Junhua Deng / Chenyu Bai / Juan Wang / Hao Song / Shuguang Tan / Guangwen Lu / George F Gao / Yi Shi / Kegong Tian /
Abstract: Pseudorabies virus (PRV) belongs to the Herpesviridae family, and is an important veterinary pathogen. Highly pathogenic PRV variants have caused severe epidemics in China since 2011, causing huge ...Pseudorabies virus (PRV) belongs to the Herpesviridae family, and is an important veterinary pathogen. Highly pathogenic PRV variants have caused severe epidemics in China since 2011, causing huge economic losses. To tackle the epidemics, we identified a panel of mouse monoclonal antibodies (mAbs) against PRV glycoprotein B (gB) that effectively block PRV infection. Among these 15 mAbs, fourteen of them block PRV entry in a complement-dependent manner. The remaining one, 1H1 mAb, however can directly neutralize the virus independent of complement and displays broad-spectrum neutralizing activities. We further determined the crystal structure of PRV gB and mapped the epitopes of these antibodies on the structure. Interestingly, all the complement-dependent neutralizing antibodies bind gB at the crown region (domain IV). In contrast, the epitope of 1H1 mAb is located at the bottom of domain I, which includes the fusion loops, indicating 1H1 mAb might neutralize the virus by interfering with the membrane fusion process. Our studies demonstrate that gB contains multiple B-cell epitopes in its crown and base regions and that antibodies targeting different epitopes block virus infection through different mechanisms. These findings would provide important clues for antiviral drug design and vaccine development.
History
DepositionNov 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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 13, 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: 1H1 heavy chain
B: 1H1 light chain
C: 1H1 heavy chain
D: 1H1 light chain
E: 1H1 heavy chain
F: 1H1 light chain
G: 1H1 heavy chain
H: 1H1 light chain


Theoretical massNumber of molelcules
Total (without water)189,2658
Polymers189,2658
Non-polymers00
Water00
1
A: 1H1 heavy chain
B: 1H1 light chain


Theoretical massNumber of molelcules
Total (without water)47,3162
Polymers47,3162
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-21 kcal/mol
Surface area19250 Å2
MethodPISA
2
C: 1H1 heavy chain
D: 1H1 light chain


Theoretical massNumber of molelcules
Total (without water)47,3162
Polymers47,3162
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-22 kcal/mol
Surface area19180 Å2
MethodPISA
3
E: 1H1 heavy chain
F: 1H1 light chain


Theoretical massNumber of molelcules
Total (without water)47,3162
Polymers47,3162
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-22 kcal/mol
Surface area19260 Å2
MethodPISA
4
G: 1H1 heavy chain
H: 1H1 light chain


Theoretical massNumber of molelcules
Total (without water)47,3162
Polymers47,3162
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-22 kcal/mol
Surface area19360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.183, 81.091, 98.472
Angle α, β, γ (deg.)85.68, 82.85, 71.45
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody
1H1 heavy chain


Mass: 23650.258 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody
1H1 light chain


Mass: 23666.078 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
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: 2.41 Å3/Da / Density % sol: 48.97 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.8 / Details: 0.2 M potassium sulfate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 64042 / % possible obs: 98.3 % / Redundancy: 2.9 % / Net I/σ(I): 13.326
Reflection shellResolution: 2.5→2.59 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXDphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SY6

1sy6


Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.921 / SU B: 11.272 / SU ML: 0.248 / Cross valid method: THROUGHOUT / ESU R: 0.646 / ESU R Free: 0.322 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27337 3251 5.1 %RANDOM
Rwork0.21239 ---
obs0.21552 60791 97.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 47.266 Å2
Baniso -1Baniso -2Baniso -3
1-2.93 Å20.15 Å20.66 Å2
2---1.32 Å2-0.7 Å2
3----1.03 Å2
Refinement stepCycle: 1 / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12923 0 0 0 12923
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0213271
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211937
X-RAY DIFFRACTIONr_angle_refined_deg1.7871.93618086
X-RAY DIFFRACTIONr_angle_other_deg1.049327692
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.27151681
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.82924.206504
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.735152069
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5791544
X-RAY DIFFRACTIONr_chiral_restr0.1070.22034
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02114879
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022957
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.5954.6086760
X-RAY DIFFRACTIONr_mcbond_other3.5934.6086759
X-RAY DIFFRACTIONr_mcangle_it5.3586.9078429
X-RAY DIFFRACTIONr_mcangle_other5.3586.9078430
X-RAY DIFFRACTIONr_scbond_it3.9114.9086511
X-RAY DIFFRACTIONr_scbond_other3.914.9096512
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9847.2039658
X-RAY DIFFRACTIONr_long_range_B_refined8.40136.71113624
X-RAY DIFFRACTIONr_long_range_B_other8.40236.71413625
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.484→2.548 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 222 -
Rwork0.304 3874 -
obs--83.81 %

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