8P4T | pdb_00008p4t

The spike complex of the Lujo Virus


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.96 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8P4T

This is version 1.2 of the entry. See complete history

Literature

The structure of the Lujo virus spike complex.

Eilon-Ashkenazy, M.Cohen-Dvashi, H.Borni, S.Shaked, R.Calinsky, R.Levy, Y.Diskin, R.

(2024) Nat Commun 15: 7175-7175

  • DOI: https://doi.org/10.1038/s41467-024-51606-0
  • Primary Citation Related Structures: 
    8P4T

  • PubMed Abstract: 

    Lujo virus (LUJV) is a human pathogen that was the cause of a deadly hemorrhagic fever outbreak in Africa. LUJV is a divergent member of the Arenaviridae with some similarities to both the "Old World" and "New World" serogroups, but it uses a cell-entry receptor, neuropilin-2 (NRP2), that is distinct from the receptors of OW and NW viruses. Though the receptor binding domain of LUJV has been characterized structurally, the overall organization of the trimeric spike complex and how NRP2 is recognized in this context were unknown. Here, we present the structure of the membrane-embedded LUJV spike complex determined by cryo-electron microscopy. Analysis of the structure suggested that a single NRP2 molecule is bound at the apex of the trimeric spike and that multiple subunits of the trimer contact the receptor. The binding of NRP2 involves an intriguing arginine-methionine interaction, which we analyzed using quantum mechanical modeling methods. We compare the LUJV spike structure with the only other available structure of a complete arenaviral spike, which is the Lassa virus. The similarities and differences between them shed light on Arenavirus evolution, inform vaccine design, and provide information that will be useful in combating future Arenavirus outbreaks.


  • Organizational Affiliation
    • Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel.

Macromolecule Content 

  • Total Structure Weight: 173.69 kDa 
  • Atom Count: 9,976 
  • Modeled Residue Count: 1,122 
  • Deposited Residue Count: 1,404 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GlycoproteinA,
D [auth B],
E [auth C]
163Mammarenavirus lujoenseMutation(s): 0 
UniProt
Find proteins for C5ILC1 (Mammarenavirus lujoense)
Explore C5ILC1 
Go to UniProtKB:  C5ILC1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC5ILC1
Glycosylation
Glycosylation Sites: 6
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
GlycoproteinB [auth a],
H [auth b],
I [auth c]
247Mammarenavirus lujoenseMutation(s): 0 
UniProt
Find proteins for C5ILC1 (Mammarenavirus lujoense)
Explore C5ILC1 
Go to UniProtKB:  C5ILC1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC5ILC1
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
GlycoproteinC [auth SA],
F [auth SB],
G [auth SC]
58Mammarenavirus lujoenseMutation(s): 0 
UniProt
Find proteins for C5ILC1 (Mammarenavirus lujoense)
Explore C5ILC1 
Go to UniProtKB:  C5ILC1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC5ILC1
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-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-glucopyranoseJ [auth D],
M [auth G],
O [auth I]
5N-Glycosylation
Glycosylation Resources
GlyTouCan: G42466VF
GlyCosmos: G42466VF
GlyGen: G42466VF
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-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-glucopyranoseK [auth E],
N [auth H],
P [auth J]
7N-Glycosylation
Glycosylation Resources
GlyTouCan: G23799GS
GlyCosmos: G23799GS
GlyGen: G23799GS
Entity ID: 6
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseL [auth F],
Q [auth K],
R [auth L]
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
AA [auth B]
BA [auth B]
CA [auth B]
DA [auth B]
EA [auth C]
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
EA [auth C],
FA [auth C],
GA [auth C],
HA [auth C],
IA [auth b],
JA [auth b],
KA [auth b],
LA [auth c],
MA [auth c],
NA [auth c],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
X [auth a],
Y [auth a],
Z [auth a]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
W [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.96 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1_5286

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Israel Science FoundationIsrael209/20

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-12
    Type: Initial release
  • Version 1.1: 2024-09-04
    Changes: Data collection, Database references
  • Version 1.2: 2024-11-13
    Changes: Data collection, Structure summary