9EHU | pdb_00009ehu

Crystal structure of the Gamak virus attachment protein head domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 
    0.227 (Depositor), 0.226 (DCC) 
  • R-Value Work: 
    0.209 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

Starting Model: in silico
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This is version 1.1 of the entry. See complete history


Literature

Structural and Antigenic Characterization of Novel and Diverse Henipavirus Glycoproteins.

May, A.J.Lella, M.Lindenberger, J.Berkman, A.Kumar, U.Dutta, M.Barr, M.Parks, R.Newman, A.Huang, X.Song, K.Ilevbare, V.Sammour, S.Park, C.S.Adhikari, R.D.Devkota, P.Janowska, K.Liu, Y.Scapellato, G.Spence, T.N.Mansouri, K.Edwards, R.J.Saunders, K.O.Haynes, B.F.Acharya, P.

(2025) bioRxiv 

  • DOI: https://doi.org/10.1101/2024.12.11.627382
  • Primary Citation of Related Structures:  
    9EHU, 9MNH, 9MQN

  • PubMed Abstract: 

    Henipaviruses, a genus within the Paramyxoviridae family, include the highly virulent Nipah and Hendra viruses that cause reoccurring outbreaks of deadly disease 1 . Recent discoveries of several new Paramyxoviridae species, including the zoonotic Langya virus 2 , have revealed much higher antigenic diversity than currently characterized and prompted the reorganization of these viruses into the Henipavirus and Parahenipavirus genera 3 . Here, to explore the limits of structural and antigenic variation in both genera, collectively referred to here as HNVs, we constructed an expanded, antigenically diverse panel of HNV fusion and attachment glycoproteins from 56 unique HNV strains that better reflects global HNV diversity. We expressed and purified the fusion protein ectodomains and the attachment protein head domains and characterized their biochemical, biophysical and structural properties. We performed immunization experiments in mice leading to the elicitation of antibodies reactive to multiple HNV fusion proteins. Cryo-electron microscopy structures of diverse fusion proteins elucidated molecular determinants of differential pre-fusion state metastability and higher order contacts. A crystal structure of the Gamak virus attachment head domain revealed an additional domain added to the conserved 6-bladed, β-propeller fold. Taken together, these studies expand the known structural and antigenic limits of the HNVs, reveal new cross-reactive epitopes within both genera and provide foundational data for the development of broadly reactive countermeasures.


  • Organizational Affiliation
    • Duke University, Duke Human Vaccine Institute, Durham NC 27710, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gamak virus attachment protein head domain473ParahenipavirusMutation(s): 0 
UniProt
Find proteins for A0A9Y2E427 (Crocidura tanakae henipavirus)
Explore A0A9Y2E427 
Go to UniProtKB:  A0A9Y2E427
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A9Y2E427
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4 (Subject of Investigation/LOI)
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL (Subject of Investigation/LOI)
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A],
H [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
I [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free:  0.227 (Depositor), 0.226 (DCC) 
  • R-Value Work:  0.209 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.479α = 90
b = 85.479β = 90
c = 162.621γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
MOSFLMdata reduction
Aimlessdata scaling

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 StatesAI165147

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-12
    Type: Initial release
  • Version 1.1: 2025-10-01
    Changes: Source and taxonomy