7QQB | pdb_00007qqb

Crystal structure of the envelope glycoprotein complex of Puumala virus in complex with the scFv fragment of the broadly neutralizing human antibody ADI-42898


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.249 (Depositor), 0.254 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.217 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structural and mechanistic basis of neutralization by a pan-hantavirus protective antibody.

Mittler, E.Serris, A.Esterman, E.S.Florez, C.Polanco, L.C.O'Brien, C.M.Slough, M.M.Tynell, J.Groning, R.Sun, Y.Abelson, D.M.Wec, A.Z.Haslwanter, D.Keller, M.Ye, C.Bakken, R.R.Jangra, R.K.Dye, J.M.Ahlm, C.Rappazzo, C.G.Ulrich, R.G.Zeitlin, L.Geoghegan, J.C.Bradfute, S.B.Sidoli, S.Forsell, M.N.E.Strandin, T.Rey, F.A.Herbert, A.S.Walker, L.M.Chandran, K.Guardado-Calvo, P.

(2023) Sci Transl Med 15: eadg1855-eadg1855

  • DOI: https://doi.org/10.1126/scitranslmed.adg1855
  • Primary Citation Related Structures: 
    7QQB

  • PubMed Abstract: 

    Emerging rodent-borne hantaviruses cause severe diseases in humans with no approved vaccines or therapeutics. We recently isolated a monoclonal broadly neutralizing antibody (nAb) from a Puumala virus-experienced human donor. Here, we report its structure bound to its target, the Gn/Gc glycoprotein heterodimer comprising the viral fusion complex. The structure explains the broad activity of the nAb: It recognizes conserved Gc fusion loop sequences and the main chain of variable Gn sequences, thereby straddling the Gn/Gc heterodimer and locking it in its prefusion conformation. We show that the nAb's accelerated dissociation from the divergent Andes virus Gn/Gc at endosomal acidic pH limits its potency against this highly lethal virus and correct this liability by engineering an optimized variant that sets a benchmark as a candidate pan-hantavirus therapeutic.


  • Organizational Affiliation
    • Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.

Macromolecule Content 

  • Total Structure Weight: 256.48 kDa 
  • Atom Count: 7,834 
  • Modeled Residue Count: 1,006 
  • Deposited Residue Count: 2,374 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope polyprotein
A, B
889Orthohantavirus puumalaenseMutation(s): 0 
UniProt
Find proteins for A0A0B4U5I0 (Orthohantavirus puumalaense)
Explore A0A0B4U5I0 
Go to UniProtKB:  A0A0B4U5I0
Find proteins for A0A6M3W7M6 (Orthohantavirus puumalaense)
Explore A0A6M3W7M6 
Go to UniProtKB:  A0A6M3W7M6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsA0A6M3W7M6A0A0B4U5I0
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Single Chain Variable Fragment (scFv) of ADI-42898C [auth H],
D [auth L]
298Homo sapiensMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE [auth C]6N-Glycosylation
Glycosylation Resources
GlyTouCan: G56014GC
GlyCosmos: G56014GC
GlyGen: G56014GC
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseF [auth D],
G [auth E]
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

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

Query on GOL



Download:Ideal Coordinates CCD File
H [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.249 (Depositor), 0.254 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.217 (DCC) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.876α = 90
b = 109.304β = 90
c = 149.54γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-18-CE11-0011

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-21
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-10-23
    Changes: Structure summary