8VF1 | pdb_00008vf1

Crystal Structure of the Hendra Virus Attachment G glycoprotein (HeV-G)

PDB DOI: https://doi.org/10.2210/pdb8VF1/pdb

Classification: VIRAL PROTEIN
Organism(s): Henipavirus hendraense
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2023-12-21 Released: 2025-03-19
Deposition Author(s): Ve, T., von Itzstein, M.S., Winger, M., Malde, A.K., Holt, S., McAtamney, S., Hartley-Tassell, L., Maggioni, A., von Itzstein, M.
Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia), Australian Research Council (ARC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.266 (Depositor), 0.263 (DCC)
R-Value Work:
0.215 (Depositor), 0.216 (DCC)
R-Value Observed:
0.218 (Depositor)

Starting Model: experimental
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Literature

Nipah and Hendra Viruses Use an Adjustable Latch in Receptor Engagement.

von Itzstein, M.S., Winger, M., Malde, A.K., Holt, S., McAtamney, S., Hartley-Tassell, L., Ve, T., Maggioni, A., von Itzstein, M.

(2025) ACS Infect Dis

PubMed: 41003672 Search on PubMed
DOI: https://doi.org/10.1021/acsinfecdis.4c01040
Primary Citation of Related Structures:
8VF1

PubMed Abstract:
Nipah (NiV) and Hendra viruses (HeV) have emerged as deadly zoonotic pathogens over the last three decades. Like all paramyxoviruses, Henipaviruses utilize a surface glycoprotein to attach to and invade targeted cells. Inhibiting this attachment glycoprotein is a promising strategy for developing effective antihenipaviral drugs. A multidisciplinary approach has been employed to investigate the structures of HeV and NiV attachment glycoproteins, identifying a flexible region near their binding site. This region, loop 240, can adopt an open conformation in unliganded attachment glycoproteins and a closed "latch" conformation in the presence of their cognate receptor Ephrin B2. Site-directed mutagenesis of the HeV attachment glycoproteins has shown that the engagement of R242 with Ephrin B2 plays an important role in the binding mechanism. This discovery provides greater insight into the dynamic nature of henipaviral attachment proteins and has implications for antiviral drug development.

Organizational Affiliation

Institute for Biomedicine and Glycomics, Gold Coast Campus, Griffith University Queensland, Southport 4222, Australia.

Macromolecule Content

Total Structure Weight: 104.41 kDa
Atom Count: 6,770
Modeled Residue Count: 836
Deposited Residue Count: 906
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoprotein G	A, B	453	Henipavirus hendraense	Mutation(s): 0
UniProt
Find proteins for O89343 (Hendra virus (isolate Horse/Autralia/Hendra/1994)) Explore O89343 Go to UniProtKB: O89343
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O89343
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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	C, D	5		N-Glycosylation	Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], G [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.266 (Depositor), 0.263 (DCC)
R-Value Work: 0.215 (Depositor), 0.216 (DCC)
R-Value Observed: 0.218 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.822	α = 90
b = 80.155	β = 106.483
c = 95.136	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-03-19

Deposition Author(s):

Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	APP1047824
Australian Research Council (ARC)	Australia	DP1094549
Australian Research Council (ARC)	Australia	DE17010078