6Z06 | pdb_00006z06

Crystal structure of Puumala virus Gc in complex with Fab 4G2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 
    0.264 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.217 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.220 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

This is version 1.3 of the entry. See complete history


Literature

Molecular rationale for antibody-mediated targeting of the hantavirus fusion glycoprotein.

Rissanen, I.Stass, R.Krumm, S.A.Seow, J.Hulswit, R.J.Paesen, G.C.Hepojoki, J.Vapalahti, O.Lundkvist, A.Reynard, O.Volchkov, V.Doores, K.J.Huiskonen, J.T.Bowden, T.A.

(2020) Elife 9

  • DOI: https://doi.org/10.7554/eLife.58242
  • Primary Citation of Related Structures:  
    6Z06, 7B09, 7B0A

  • PubMed Abstract: 

    The intricate lattice of Gn and Gc glycoprotein spike complexes on the hantavirus envelope facilitates host-cell entry and is the primary target of the neutralizing antibody-mediated immune response. Through study of a neutralizing monoclonal antibody termed mAb P-4G2, which neutralizes the zoonotic pathogen Puumala virus (PUUV), we provide a molecular-level basis for antibody-mediated targeting of the hantaviral glycoprotein lattice. Crystallographic analysis demonstrates that P-4G2 binds to a multi-domain site on PUUV Gc and may preclude fusogenic rearrangements of the glycoprotein that are required for host-cell entry. Furthermore, cryo-electron microscopy of PUUV-like particles in the presence of P-4G2 reveals a lattice-independent configuration of the Gc, demonstrating that P-4G2 perturbs the (Gn-Gc) 4 lattice. This work provides a structure-based blueprint for rationalizing antibody-mediated targeting of hantaviruses.


  • Organizational Affiliation

    Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fab 4G2 Heavy chainA [auth H]231Myodes glareolusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab 4G2 Light chainB [auth L]216Myodes glareolusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope polyproteinC [auth A]460Orthohantavirus puumalaenseMutation(s): 0 
Gene Names: gpc
UniProt
Find proteins for Q9WJ31 (Orthohantavirus puumalaense)
Explore Q9WJ31 
Go to UniProtKB:  Q9WJ31
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9WJ31
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free:  0.264 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.217 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.220 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.213α = 90
b = 50.449β = 107.66
c = 124.446γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMR/L009528/1
Medical Research Council (MRC, United Kingdom)United KingdomMR/S007555/1
Medical Research Council (MRC, United Kingdom)United KingdomMR/N002091/1
Medical Research Council (MRC, United Kingdom)United KingdomMR/K024426/1
Academy of FinlandFinland309605
European Research Council (ERC)European Union649053
Wellcome TrustUnited Kingdom203141/Z/16Z
Wellcome TrustUnited Kingdom060208/Z/00/Z
Wellcome TrustUnited Kingdom093305/Z/10/Z

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-30
    Type: Initial release
  • Version 1.1: 2021-01-13
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-11-13
    Changes: Structure summary