8EJF

Structure of lineage V Lassa virus glycoprotein complex (strain Soromba-R)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.72 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural conservation of Lassa virus glycoproteins and recognition by neutralizing antibodies.

Perrett, H.R.Brouwer, P.J.M.Hurtado, J.Newby, M.L.Liu, L.Muller-Krauter, H.Muller Aguirre, S.Burger, J.A.Bouhuijs, J.H.Gibson, G.Messmer, T.Schieffelin, J.S.Antanasijevic, A.Boons, G.J.Strecker, T.Crispin, M.Sanders, R.W.Briney, B.Ward, A.B.

(2023) Cell Rep 42: 112524-112524

  • DOI: https://doi.org/10.1016/j.celrep.2023.112524
  • Primary Citation of Related Structures:  
    8EJD, 8EJE, 8EJF, 8EJG, 8EJH, 8EJI, 8EJJ

  • PubMed Abstract: 

    Lassa fever is an acute hemorrhagic fever caused by the zoonotic Lassa virus (LASV). The LASV glycoprotein complex (GPC) mediates viral entry and is the sole target for neutralizing antibodies. Immunogen design is complicated by the metastable nature of recombinant GPCs and the antigenic differences among phylogenetically distinct LASV lineages. Despite the sequence diversity of the GPC, structures of most lineages are lacking. We present the development and characterization of prefusion-stabilized, trimeric GPCs of LASV lineages II, V, and VII, revealing structural conservation despite sequence diversity. High-resolution structures and biophysical characterization of the GPC in complex with GP1-A-specific antibodies suggest their neutralization mechanisms. Finally, we present the isolation and characterization of a trimer-preferring neutralizing antibody belonging to the GPC-B competition group with an epitope that spans adjacent protomers and includes the fusion peptide. Our work provides molecular detail information on LASV antigenic diversity and will guide efforts to design pan-LASV vaccines.


  • Organizational Affiliation

    Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycoprotein GP1A,
C [auth B],
E [auth C]
259Mammarenavirus lassaenseMutation(s): 3 
Gene Names: GPC
UniProt
Find proteins for V9VG48 (Mammarenavirus lassaense)
Explore V9VG48 
Go to UniProtKB:  V9VG48
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV9VG48
Glycosylation
Glycosylation Sites: 7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Glycoprotein GP2B [auth a],
D [auth b],
F [auth c]
406Mammarenavirus lassaenseMutation(s): 2 
Gene Names: GPC
UniProt
Find proteins for Q9WXS1 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9WXS1 
Go to UniProtKB:  Q9WXS1
Find proteins for V9VG48 (Mammarenavirus lassaense)
Explore V9VG48 
Go to UniProtKB:  V9VG48
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsV9VG48Q9WXS1
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D 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-glucopyranose
CA [auth Z],
G [auth D],
J [auth G],
M [auth J],
O [auth L],
CA [auth Z],
G [auth D],
J [auth G],
M [auth J],
O [auth L],
R [auth O],
U [auth R],
W [auth T],
Z [auth W]
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
BA [auth Y],
H [auth E],
I [auth F],
L [auth I],
P [auth M],
BA [auth Y],
H [auth E],
I [auth F],
L [auth I],
P [auth M],
Q [auth N],
T [auth Q],
X [auth U],
Y [auth V]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseAA [auth X],
K [auth H],
S [auth P]
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseDA [auth d],
N [auth K],
V [auth S]
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
EA [auth A]
FA [auth a]
GA [auth a]
HA [auth B]
IA [auth b]
EA [auth A],
FA [auth a],
GA [auth a],
HA [auth B],
IA [auth b],
JA [auth b],
KA [auth C],
LA [auth c],
MA [auth c]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.72 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTRosetta
RECONSTRUCTIONcryoSPARC3.2
RECONSTRUCTIONRELION3.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited StatesINV-004923
Bill & Melinda Gates FoundationUnited StatesOPP1170236

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-07
    Type: Initial release
  • Version 1.1: 2024-05-01
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-10-30
    Changes: Data collection, Structure summary