9MHE | pdb_00009mhe

Native tagless Lassa virus spike complex bound to ARN-75039 at pH 8.0


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.01 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9MHE

This is version 1.2 of the entry. See complete history

Literature

pH-induced conformational changes and inhibition of the Lassa virus spike complex.

Katz, M.Cohen-Dvashi, H.Borni, S.Ruedas, J.Henkel, G.McCormack, K.Diskin, R.

(2025) Cell Host Microbe 33: 1577-1588.e7

  • DOI: https://doi.org/10.1016/j.chom.2025.07.020
  • Primary Citation Related Structures: 
    9MHE, 9MIV, 9MIY, 9MJ1, 9MJ2, 9R8U

  • PubMed Abstract: 

    Lassa virus (LASV) is a devastating human pathogen with no vaccines and limited therapeutics. The LASV class-I spike complex engages target cells via binding its primary host receptor, matriglycan, followed by macropinocytosis and binding of its secondary receptor, lysosomal-associated membrane protein 1 (LAMP1), to trigger virus fusion. This process occurs across multiple pH-dependent steps, but the molecular events remain largely unknown. Through high-resolution structures, we study the pH-induced conformational changes of the spike preceding membrane fusion. We reveal pH-sensitive metal coordination sites that control the integrity of the spike's native state, elucidate a reorganization of the spike's transmembrane region, and provide a mechanism for dissociation from its primary receptor. Using the entry inhibitor ARN-75039, we validate our findings and establish the molecular basis for the binding and function of this investigational drug. These data define the molecular basis for the cell entry of LASV and will promote efforts in combating this virus and potentially related viral pathogens.


  • Organizational Affiliation
    • Department of Chemical and Structural Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel.

Macromolecule Content 

  • Total Structure Weight: 337.81 kDa 
  • Atom Count: 17,624 
  • Modeled Residue Count: 1,930 
  • Deposited Residue Count: 2,862 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glycoprotein G2A [auth a],
E [auth b],
F [auth c]
232Lassa virus JosiahMutation(s): 0 
Gene Names: GPCGP-C
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: 3
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Glycoprotein G1B [auth A],
C [auth B],
D [auth C]
259Lassa virus JosiahMutation(s): 0 
Gene Names: GPCGP-C
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: 7
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
12.1F Heavy chainG [auth H],
K [auth D],
L [auth F]
249Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
12.1F Light chainH [auth L],
I [auth E],
J [auth G]
214Homo sapiensMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(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-glucopyranoseFA [auth f],
M [auth I]
6N-Glycosylation
Glycosylation Resources
GlyTouCan: G61751GZ
GlyCosmos: G61751GZ
GlyGen: G61751GZ
Entity ID: 6
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseN [auth J],
T [auth Q]
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 7
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-glucopyranoseBA [auth Y],
O [auth K],
Q [auth N],
W [auth T]
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE
Entity ID: 8
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-glucopyranoseAA [auth X],
P [auth M],
V [auth S]
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G32152BH
GlyCosmos: G32152BH
GlyGen: G32152BH
Entity ID: 9
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(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-glucopyranoseCA [auth Z],
R [auth O],
X [auth U]
7N-Glycosylation
Glycosylation Resources
GlyTouCan: G69411IG
GlyCosmos: G69411IG
GlyGen: G69411IG
Entity ID: 10
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-glucopyranoseDA [auth d],
S [auth P],
Y [auth V]
5N-Glycosylation
Glycosylation Resources
GlyTouCan: G42466VF
GlyCosmos: G42466VF
GlyGen: G42466VF
Entity ID: 11
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-glucopyranoseU [auth R],
Z [auth W]
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G81315DD
GlyCosmos: G81315DD
GlyGen: G81315DD
Entity ID: 12
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-glucopyranoseEA [auth e]5N-Glycosylation
Glycosylation Resources
GlyTouCan: G22768VO
GlyCosmos: G22768VO
GlyGen: G22768VO

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1BK9
(Subject of Investigation/LOI)

Query on A1BK9



Download:Ideal Coordinates CCD File
QA [auth c](4S)-3-(4-tert-butoxyphenyl)-7-methyl-6-{4-[(propan-2-yl)oxy]phenyl}imidazo[1,2-a]pyridine
C27 H30 N2 O2
TWUXCBSMDFLDBC-UHFFFAOYSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
GA [auth a]
HA [auth a]
KA [auth A]
LA [auth B]
MA [auth C]
GA [auth a],
HA [auth a],
KA [auth A],
LA [auth B],
MA [auth C],
NA [auth C],
OA [auth b],
PA [auth b],
RA [auth c],
SA [auth c]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
UNX

Query on UNX



Download:Ideal Coordinates CCD File
IA [auth a],
JA [auth a]
UNKNOWN ATOM OR ION
X

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.01 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIXdev_5278

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-27
    Type: Initial release
  • Version 1.1: 2025-09-17
    Changes: Data collection, Database references
  • Version 1.2: 2025-09-24
    Changes: Data collection, Database references