7CZF

Crystal structure of Kaposi Sarcoma associated herpesvirus (KSHV ) gHgL in complex with the ligand binding domian (LBD) of EphA2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.241 

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This is version 1.3 of the entry. See complete history


Literature

Molecular basis of EphA2 recognition by gHgL from gammaherpesviruses.

Su, C.Wu, L.Chai, Y.Qi, J.Tan, S.Gao, G.F.Song, H.Yan, J.

(2020) Nat Commun 11: 5964-5964

  • DOI: 10.1038/s41467-020-19617-9
  • Primary Citation of Related Structures:  
    7CZE, 7CZF

  • PubMed Abstract: 
  • The human γ-herpesviruses Kaposi sarcoma associated herpesvirus (KSHV) and Epstein-Barr virus (EBV) are associated with many human malignancies. Viral glycoprotein H (gH) and glycoprotein L (gL) are crucial for the cell tropism by binding to specific receptors ...

    The human γ-herpesviruses Kaposi sarcoma associated herpesvirus (KSHV) and Epstein-Barr virus (EBV) are associated with many human malignancies. Viral glycoprotein H (gH) and glycoprotein L (gL) are crucial for the cell tropism by binding to specific receptors. Recently, EphA2 was identified as the specific entry receptor for both KSHV and EBV. Here, we characterized the crystal structures of KSHV gHgL or EBV gHgL in complex with the ligand binding domain (LBD) of EphA2. Both KSHV and EBV gHgL bind to the channel and peripheral regions of LBD primarily using gL. Extensive interactions with more contacts contribute to the higher affinity of KSHV gHgL to LBD than that of EBV gHgL. These binding characteristics were verified using cell-based fusion assays with mutations in key EphA2 residues. Our experiments suggest that multiple animal γ-herpesviruses could use EphA2 as an entry receptor, implying a potential threat to human health.


    Organizational Affiliation

    University of Chinese Academy of Sciences, Beijing, 100049, China. yanjh@im.ac.cn.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ephrin type-A receptor 2A, D185Homo sapiensMutation(s): 0 
Gene Names: EPHA2ECK
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P29317 (Homo sapiens)
Explore P29317 
Go to UniProtKB:  P29317
PHAROS:  P29317
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UniProt GroupP29317
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Envelope glycoprotein HB, E677Human gammaherpesvirus 8Mutation(s): 0 
Gene Names: ORF22gHHHV8GK18_gp26
UniProt
Find proteins for Q98142 (Human herpesvirus 8)
Explore Q98142 
Go to UniProtKB:  Q98142
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UniProt GroupQ98142
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Envelope glycoprotein LC, F157Human gammaherpesvirus 8Mutation(s): 0 
Gene Names: ORF47gLORF46HHV8GK18_gp49
UniProt
Find proteins for Q76RG7 (Human herpesvirus 8)
Explore Q76RG7 
Go to UniProtKB:  Q76RG7
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UniProt GroupQ76RG7
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth L],
I [auth a],
K,
L [auth N]
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseH [auth S]6N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G73409CU
GlyCosmos:  G73409CU
GlyGen:  G73409CU
Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseJ [auth H]3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.241 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.803α = 90
b = 153.196β = 90
c = 275.228γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-21
    Type: Initial release
  • Version 1.1: 2020-10-28
    Changes: Data collection
  • Version 1.2: 2020-12-02
    Changes: Database references
  • Version 1.3: 2020-12-09
    Changes: Database references