9AVF | pdb_00009avf

CCHFV GP38-GnH-DS heterodimer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.237 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.197 (Depositor) 
  • R-Value Observed: 
    0.199 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Engineering and structures of Crimean-Congo hemorrhagic fever virus glycoprotein complexes.

McFadden, E.Monticelli, S.R.Wang, A.Ramamohan, A.R.Batchelor, T.G.Kuehne, A.I.Bakken, R.R.Tse, A.L.Chandran, K.Herbert, A.S.McLellan, J.S.

(2025) Cell 188: 303

  • DOI: https://doi.org/10.1016/j.cell.2024.11.008
  • Primary Citation Related Structures: 
    9AVF, 9B8J

  • PubMed Abstract: 

    Crimean-Congo hemorrhagic fever virus (CCHFV) is a tickborne virus that can cause severe disease in humans with case fatality rates of 10%-40%. Although structures of CCHFV glycoproteins GP38 and Gc have provided insights into viral entry and defined epitopes of neutralizing and protective antibodies, the structure of glycoprotein Gn and its interactions with GP38 and Gc have remained elusive. Here, we use structure-guided protein engineering to produce a stabilized GP38-Gn-Gc heterotrimeric glycoprotein complex (GP38-Gn H-DS -Gc). A cryo-electron microscopy (cryo-EM) structure of this complex provides the molecular basis for GP38's association on the viral surface, reveals the structure of Gn, and demonstrates that GP38-Gn restrains the Gc fusion loops in the prefusion conformation, facilitated by an N-linked glycan attached to Gn. Immunization with GP38-Gn H-DS -Gc conferred 40% protection against lethal IbAr10200 challenge in mice. These data define the architecture of a GP38-Gn-Gc protomer and provide a template for structure-guided vaccine antigen development.


  • Organizational Affiliation
    • Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.

Macromolecule Content 

  • Total Structure Weight: 74.89 kDa 
  • Atom Count: 4,690 
  • Modeled Residue Count: 565 
  • Deposited Residue Count: 658 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GP38
A, C
269Crimean-Congo hemorrhagic fever virus strain IbAr10200Mutation(s): 1 
Gene Names: GP
UniProt
Find proteins for Q8JSZ3 (Crimean-Congo hemorrhagic fever virus (strain Nigeria/IbAr10200/1970))
Explore Q8JSZ3 
Go to UniProtKB:  Q8JSZ3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8JSZ3
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Glycoprotein N
B, D
60Crimean-Congo hemorrhagic fever virus strain IbAr10200Mutation(s): 1 
Gene Names: GP
UniProt
Find proteins for Q8JSZ3 (Crimean-Congo hemorrhagic fever virus (strain Nigeria/IbAr10200/1970))
Explore Q8JSZ3 
Go to UniProtKB:  Q8JSZ3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8JSZ3
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A2G

Query on A2G



Download:Ideal Coordinates CCD File
G [auth A]2-acetamido-2-deoxy-alpha-D-galactopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-CBQIKETKSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
H [auth B]
I [auth C]
J [auth C]
E [auth A],
F [auth A],
H [auth B],
I [auth C],
J [auth C],
K [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.237 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.197 (Depositor) 
  • R-Value Observed: 0.199 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.809α = 90
b = 87.01β = 90
c = 128.759γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI152246
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesU19AI142777
National Institutes of Health/Office of the DirectorUnited StatesS10OD030394

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-11
    Type: Initial release
  • Version 1.1: 2025-01-15
    Changes: Database references, Structure summary
  • Version 1.2: 2025-02-12
    Changes: Database references