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- PDB-5ys2: Structure of the domain IV(D_IV) of Pseudorabies virus glycoprote... -

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Basic information

Entry
Database: PDB / ID: 5ys2
TitleStructure of the domain IV(D_IV) of Pseudorabies virus glycoprotein B( PRV gB)
ComponentsEnvelope glycoprotein B,Envelope glycoprotein B
KeywordsVIRAL PROTEIN / fusion
Function / homology
Function and homology information


host cell endosome / host cell Golgi apparatus / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / membrane
Similarity search - Function
SH3 type barrels. - #1230 / : / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B, PH-like domain 1 / Herpesvirus Glycoprotein B, PH-like domain 2 / Herpesvirus Glycoprotein B, PH-like domain 2 superfamily / Herpesvirus Glycoprotein B ectodomain / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B PH-like domain / SH3 type barrels. ...SH3 type barrels. - #1230 / : / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B, PH-like domain 1 / Herpesvirus Glycoprotein B, PH-like domain 2 / Herpesvirus Glycoprotein B, PH-like domain 2 superfamily / Herpesvirus Glycoprotein B ectodomain / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B PH-like domain / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Glycoprotein B / Glycoprotein gB / GB
Similarity search - Component
Biological speciesSuid alphaherpesvirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.698 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 12, 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 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envelope glycoprotein B,Envelope glycoprotein B
B: Envelope glycoprotein B,Envelope glycoprotein B
C: Envelope glycoprotein B,Envelope glycoprotein B
D: Envelope glycoprotein B,Envelope glycoprotein B
E: Envelope glycoprotein B,Envelope glycoprotein B
F: Envelope glycoprotein B,Envelope glycoprotein B


Theoretical massNumber of molelcules
Total (without water)165,5856
Polymers165,5856
Non-polymers00
Water00
1
A: Envelope glycoprotein B,Envelope glycoprotein B
B: Envelope glycoprotein B,Envelope glycoprotein B
C: Envelope glycoprotein B,Envelope glycoprotein B


Theoretical massNumber of molelcules
Total (without water)82,7933
Polymers82,7933
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11130 Å2
ΔGint-77 kcal/mol
Surface area26060 Å2
MethodPISA
2
D: Envelope glycoprotein B,Envelope glycoprotein B
E: Envelope glycoprotein B,Envelope glycoprotein B
F: Envelope glycoprotein B,Envelope glycoprotein B


Theoretical massNumber of molelcules
Total (without water)82,7933
Polymers82,7933
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11100 Å2
ΔGint-73 kcal/mol
Surface area26180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.911, 119.850, 123.771
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein
Envelope glycoprotein B,Envelope glycoprotein B / PRV gB D_IV / gB


Mass: 27597.557 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: The fusion protein of PRV gB (residues 62-148), linker GGSG, PRV gB (residues 489-700), and tags HHHHHHHH
Source: (gene. exp.) Suid alphaherpesvirus 1 / Gene: gB / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: A0A0U3FH21, UniProt: A0A1Q0AKY1, UniProt: T2FL65*PLUS
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: 2.06 Å3/Da / Density % sol: 40.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.05 M calcium chloride dihydrate, 0.1 M MES, pH 6.0

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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: Jan 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.698→50 Å / Num. obs: 38191 / % possible obs: 99.6 % / Redundancy: 4.4 % / Net I/σ(I): 15.078
Reflection shellResolution: 2.7→2.8 Å

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXDphasing
RefinementResolution: 2.698→46.518 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.39
RfactorNum. reflection% reflection
Rfree0.2911 1913 5.01 %
Rwork0.2267 --
obs0.23 38147 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.698→46.518 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8134 0 0 0 8134
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018301
X-RAY DIFFRACTIONf_angle_d1.38911220
X-RAY DIFFRACTIONf_dihedral_angle_d18.523122
X-RAY DIFFRACTIONf_chiral_restr0.0951238
X-RAY DIFFRACTIONf_plane_restr0.0061472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6981-2.76560.41081270.32652517X-RAY DIFFRACTION99
2.7656-2.84040.37531630.31222515X-RAY DIFFRACTION100
2.8404-2.92390.37431380.29572569X-RAY DIFFRACTION100
2.9239-3.01830.34251260.27852573X-RAY DIFFRACTION100
3.0183-3.12610.38561070.29552575X-RAY DIFFRACTION100
3.1261-3.25130.35531350.27552582X-RAY DIFFRACTION100
3.2513-3.39920.39211200.26862594X-RAY DIFFRACTION100
3.3992-3.57840.33891650.25632546X-RAY DIFFRACTION100
3.5784-3.80250.31061440.23512578X-RAY DIFFRACTION100
3.8025-4.09590.28111320.21512602X-RAY DIFFRACTION100
4.0959-4.50780.221220.17932607X-RAY DIFFRACTION99
4.5078-5.15930.24291500.17612605X-RAY DIFFRACTION99
5.1593-6.49740.26141340.21422643X-RAY DIFFRACTION99
6.4974-46.52470.25831500.20882728X-RAY DIFFRACTION98
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)
10.04910.0272-0.00720.22690.02370.03240.0779-0.1607-0.03440.0918-0.048-0.2485-0.07850.12190.07670.1577-0.1169-0.01110.19460.03550.14519.5719-2.473636.092
20.11670.09290.0230.1724-0.04130.2063-0.1160.16610.0427-0.1749-0.0277-0.008-0.10650.1086-0.10640.1803-0.07730.00910.17140.00130.2038-2.5042-15.070118.1537
30.19140.1176-0.10290.18010.0310.3094-0.0988-0.0919-0.0608-0.0087-0.23310.0357-0.0720.0527-0.5930.0417-0.09480.0421-0.0050.1358-0.0664-11.3211-15.95941.4073
40.14030.07090.04360.0667-0.04240.11420.04970.111-0.154-0.08-0.0313-0.05720.12750.05750.00860.1342-0.0167-0.10610.126-0.00720.1053-55.2195-36.09113.7497
50.1354-0.0221-0.04050.0654-0.03020.0722-0.0978-0.04090.0365-0.06140.07890.0340.00030.0686-0.02410.1587-0.0048-0.08110.1333-0.01760.1731-45.1295-15.791514.1022
60.1209-0.04420.06830.07570.01690.09760.02650.0645-0.0944-0.00640.01980.09720.00150.06550.04320.05890.0063-0.05450.0304-0.02390.0801-34.4166-37.590417.6519
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F

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