7SGF | pdb_00007sgf

Lassa virus glycoprotein construct (Josiah GPC-I53-50A) in complex with LAVA01 antibody


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.41 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7SGF

This is version 1.3 of the entry. See complete history

Literature

Lassa virus glycoprotein nanoparticles elicit neutralizing antibody responses and protection.

Brouwer, P.J.M.Antanasijevic, A.Ronk, A.J.Muller-Krauter, H.Watanabe, Y.Claireaux, M.Perrett, H.R.Bijl, T.P.L.Grobben, M.Umotoy, J.C.Schriek, A.I.Burger, J.A.Tejjani, K.Lloyd, N.M.Steijaert, T.H.van Haaren, M.M.Sliepen, K.de Taeye, S.W.van Gils, M.J.Crispin, M.Strecker, T.Bukreyev, A.Ward, A.B.Sanders, R.W.

(2022) Cell Host Microbe 30: 1759

  • DOI: https://doi.org/10.1016/j.chom.2022.10.018
  • Primary Citation Related Structures: 
    7SGD, 7SGE, 7SGF

  • PubMed Abstract: 

    The Lassa virus is endemic in parts of West Africa, and it causes hemorrhagic fever with high mortality. The development of a recombinant protein vaccine has been hampered by the instability of soluble Lassa virus glycoprotein complex (GPC) trimers, which disassemble into monomeric subunits after expression. Here, we use two-component protein nanoparticles consisting of trimeric and pentameric subunits to stabilize GPC in a trimeric conformation. These GPC nanoparticles present twenty prefusion GPC trimers on the surface of an icosahedral particle. Cryo-EM studies of GPC nanoparticles demonstrated a well-ordered structure and yielded a high-resolution structure of an unliganded GPC. These nanoparticles induced potent humoral immune responses in rabbits and protective immunity against the lethal Lassa virus challenge in guinea pigs. Additionally, we isolated a neutralizing antibody that mapped to the putative receptor-binding site, revealing a previously undefined site of vulnerability. Collectively, these findings offer potential approaches to vaccine and therapeutic design for the Lassa virus.


  • Organizational Affiliation
    • Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands; Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

Macromolecule Content 

  • Total Structure Weight: 543.99 kDa 
  • Atom Count: 12,078 
  • Modeled Residue Count: 1,641 
  • Deposited Residue Count: 4,776 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GPC-I53-50A665Mammarenavirus lassaenseMutation(s): 0 
UniProt
Find proteins for P08669 (Lassa virus (strain Mouse/Sierra Leone/Josiah/1976))
Explore P08669 
Go to UniProtKB:  P08669
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08669
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
LAVA01 mAb - Heavy ChainC [auth H],
G [auth J],
K [auth M]
142Oryctolagus cuniculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
LAVA01 mAb - Light ChainD [auth L],
H [auth K],
L [auth N]
120Oryctolagus cuniculusMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
DA [auth d],
EA [auth e],
IA [auth i],
M [auth D],
MA [auth m],
DA [auth d],
EA [auth e],
IA [auth i],
M [auth D],
MA [auth m],
Q [auth I],
U [auth R],
V [auth S],
Z [auth W]
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth X],
FA [auth f],
HA [auth h],
JA [auth j],
N [auth E],
AA [auth X],
FA [auth f],
HA [auth h],
JA [auth j],
N [auth E],
P [auth G],
R [auth O],
W [auth T],
Y [auth V]
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 6
MoleculeChains Length2D Diagram GlycosylationD Interactions
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-glucopyranoseGA [auth g],
O [auth F],
X [auth U]
5N-Glycosylation
Glycosylation Resources
GlyTouCan: G22768VO
GlyCosmos: G22768VO
GlyGen: G22768VO
Entity ID: 7
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseBA [auth Y],
KA [auth k],
S [auth P]
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G32152BH
GlyCosmos: G32152BH
GlyGen: G32152BH
Entity ID: 8
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseCA [auth Z],
LA [auth l],
T [auth Q]
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G21290RB
GlyCosmos: G21290RB
GlyGen: G21290RB

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.41 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTRosettaEM
MODEL REFINEMENTCoot
RECONSTRUCTIONRELION3.0

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited StatesOPP1170236

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-12
    Type: Initial release
  • Version 1.1: 2022-11-30
    Changes: Database references, Refinement description
  • Version 1.2: 2022-12-28
    Changes: Database references
  • Version 1.3: 2024-10-23
    Changes: Data collection, Refinement description, Structure summary