[English] 日本語
Yorodumi
- PDB-5ys2: Structure of the domain IV(D_IV) of Pseudorabies virus glycoprote... -

+
Open data


ID or keywords:

Loading...

-
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 Golgi membrane / host cell endosome membrane / membrane => GO:0016020 / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
SH3 type barrels. - #1230 / Herpesvirus Glycoprotein B ectodomain / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B, PH-like domain 1 / Herpesvirus Glycoprotein B, PH-like domain 2 / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B PH-like domain / Herpesvirus Glycoprotein B, PH-like domain 2 superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein B / Envelope glycoprotein B / Envelope glycoprotein B
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more