7B09 | pdb_00007b09

Puumala virus glycoprotein (Gc) in complex with fab fragment P-4G2.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 13.4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

wwPDB Validation 3D Report Full Report

Validation slider image for 7B09

This is version 1.2 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 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.

Macromolecule Content 

  • Total Structure Weight: 140.18 kDa 
  • Atom Count: 9,073 
  • Modeled Residue Count: 1,178 
  • Deposited Residue Count: 1,274 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Heavy chain of fab fragment P-4G2A [auth H]231Myodes glareolusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Light chain of fab fragment P-4G2B [auth L]216Myodes glareolusMutation(s): 0 
Find similar proteins by:|  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
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope polyproteinD [auth B]367Orthohantavirus 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: 2
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE [auth C]2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 6
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseF [auth E]4N-Glycosylation
Glycosylation Resources
GlyTouCan: G81315DD
GlyCosmos: G81315DD
GlyGen: G81315DD

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
G [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 13.4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONDynamo

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)United Kingdom649053

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-16
    Type: Initial release
  • Version 1.1: 2021-01-13
    Changes: Database references
  • Version 1.2: 2024-11-13
    Changes: Data collection, Database references, Structure summary