7KV8

Chimeric flavivirus between Binjari virus and Dengue virus serotype-2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

A unified route for flavivirus structures uncovers essential pocket factors conserved across pathogenic viruses.

Hardy, J.M.Newton, N.D.Modhiran, N.Scott, C.A.P.Venugopal, H.Vet, L.J.Young, P.R.Hall, R.A.Hobson-Peters, J.Coulibaly, F.Watterson, D.

(2021) Nat Commun 12: 3266-3266

  • DOI: https://doi.org/10.1038/s41467-021-22773-1
  • Primary Citation of Related Structures:  
    7KV8, 7KV9, 7KVA, 7KVB

  • PubMed Abstract: 

    The epidemic emergence of relatively rare and geographically isolated flaviviruses adds to the ongoing disease burden of viruses such as dengue. Structural analysis is key to understand and combat these pathogens. Here, we present a chimeric platform based on an insect-specific flavivirus for the safe and rapid structural analysis of pathogenic viruses. We use this approach to resolve the architecture of two neurotropic viruses and a structure of dengue virus at 2.5  Å, the highest resolution for an enveloped virion. These reconstructions allow improved modelling of the stem region of the envelope protein, revealing two lipid-like ligands within highly conserved pockets. We show that these sites are essential for viral growth and important for viral maturation. These findings define a hallmark of flavivirus virions and a potential target for broad-spectrum antivirals and vaccine design. We anticipate the chimeric platform to be widely applicable for investigating flavivirus biology.


  • Organizational Affiliation

    Infection and Immunity Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope protein E
A, B, C
495dengue virus type 2Mutation(s): 0 
UniProt
Find proteins for P18356 (Dengue virus type 2 (strain Thailand/PUO-218/1980))
Explore P18356 
Go to UniProtKB:  P18356
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18356
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Matrix protein MD [auth a],
E [auth b],
F [auth c]
75dengue virus type 2Mutation(s): 0 
UniProt
Find proteins for A0A346TIJ9 (dengue virus type 2)
Explore A0A346TIJ9 
Go to UniProtKB:  A0A346TIJ9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A346TIJ9
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6OU (Subject of Investigation/LOI)
Query on 6OU

Download Ideal Coordinates CCD File 
I [auth A],
M [auth B],
Q [auth C]
[(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate
C39 H76 N O8 P
FHQVHHIBKUMWTI-OTMQOFQLSA-N
1Q0 (Subject of Investigation/LOI)
Query on 1Q0

Download Ideal Coordinates CCD File 
J [auth A],
N [auth B],
R [auth C]
(2S,3R,4Z)-3-hydroxy-2-[(9E)-octadec-9-enoylamino]octadec-4-en-1-yl dihydrogen phosphate
C36 H70 N O6 P
HOOJDMQIUTXSPU-GINUSHNTSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
K [auth B]
L [auth B]
O [auth C]
G [auth A],
H [auth A],
K [auth B],
L [auth B],
O [auth C],
P [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18
RECONSTRUCTIONRELION3.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1164216

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-23
    Type: Initial release
  • Version 1.1: 2021-07-14
    Changes: Database references
  • Version 2.0: 2021-11-24
    Changes: Advisory, Atomic model, Database references, Derived calculations, Structure summary