6THG

Cedar Virus attachment glycoprotein (G) in complex with human ephrin-B1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.07 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.276 
  • R-Value Observed: 0.278 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.3 of the entry. See complete history


Literature

A key region of molecular specificity orchestrates unique ephrin-B1 utilization by Cedar virus.

Pryce, R.Azarm, K.Rissanen, I.Harlos, K.Bowden, T.A.Lee, B.

(2020) Life Sci Alliance 3

  • DOI: https://doi.org/10.26508/lsa.201900578
  • Primary Citation of Related Structures:  
    6THB, 6THG

  • PubMed Abstract: 

    The emergent zoonotic henipaviruses, Hendra, and Nipah are responsible for frequent and fatal disease outbreaks in domestic animals and humans. Specificity of henipavirus attachment glycoproteins (G) for highly species-conserved ephrin ligands underpins their broad host range and is associated with systemic and neurological disease pathologies. Here, we demonstrate that Cedar virus (CedV)-a related henipavirus that is ostensibly nonpathogenic-possesses an idiosyncratic entry receptor repertoire that includes the common henipaviral receptor, ephrin-B2, but, distinct from pathogenic henipaviruses, does not include ephrin-B3. Uniquely among known henipaviruses, CedV can use ephrin-B1 for cellular entry. Structural analyses of CedV-G reveal a key region of molecular specificity that directs ephrin-B1 utilization, while preserving a universal mode of ephrin-B2 recognition. The structural and functional insights presented uncover diversity within the known henipavirus receptor repertoire and suggest that only modest structural changes may be required to modulate receptor specificities within this group of lethal human pathogens.


  • Organizational Affiliation

    Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Attachment glycoproteinA [auth B],
C [auth A],
D [auth E],
E [auth G],
F [auth I]
426Cedar virusMutation(s): 0 
UniProt
Find proteins for J7H333 (Cedar virus)
Explore J7H333 
Go to UniProtKB:  J7H333
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupJ7H333
Glycosylation
Glycosylation Sites: 6
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ephrin-B1B [auth D],
G [auth C],
H [auth F],
I [auth H],
J
151Homo sapiensMutation(s): 0 
Gene Names: EFNB1EFL3EPLG2LERK2
UniProt & NIH Common Fund Data Resources
Find proteins for P98172 (Homo sapiens)
Explore P98172 
Go to UniProtKB:  P98172
PHAROS:  P98172
GTEx:  ENSG00000090776 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP98172
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P98172-1
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
K, M, N, O, Q
K, M, N, O, Q, U
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
L, P, R, S, T
L, P, R, S, T, V, W
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth A]
CA [auth A]
DA [auth A]
EA [auth A]
AA [auth D],
BA [auth A],
CA [auth A],
DA [auth A],
EA [auth A],
FA [auth E],
GA [auth G],
HA [auth G],
IA [auth G],
JA [auth I],
KA [auth I],
LA [auth F],
MA [auth H],
NA [auth J],
X [auth B],
Y [auth B],
Z [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.07 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.276 
  • R-Value Observed: 0.278 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.796α = 90
b = 138.435β = 90
c = 235.394γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMR/L009528/1
Medical Research Council (United Kingdom)United KingdomMR/S007555/1
Wellcome TrustUnited Kingdom203141/Z/16Z
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI123449
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI069317
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI115226

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-18
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2022-03-30
    Changes: Author supporting evidence, Database references, Structure summary
  • Version 2.2: 2024-01-24
    Changes: Data collection, Refinement description
  • Version 2.3: 2024-10-16
    Changes: Structure summary