8Y3L

Cryo-EM structure of dengue virus serotype 2 strain D2Y98P-PP1 in complex with human antibody C10 Fab at 37 deg C


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Role of N-glycosylation at asparagine 153 of dengue envelope protein in immune response

Fibriansah, G.Ng, T.S.Lim, X.N.Tan, A.W.K.Shi, J.Crowe, J.E.Lok, S.M.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope protein
A, C, E
495dengue virus type 2Mutation(s): 0 
Gene Names: E
UniProt
Find proteins for A0A678XB23 (dengue virus type 2)
Explore A0A678XB23 
Go to UniProtKB:  A0A678XB23
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A678XB23
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Membrane polyprotein
B, D, F
75dengue virus type 2Mutation(s): 0 
UniProt
Find proteins for A4GVG9 (dengue virus type 2)
Explore A4GVG9 
Go to UniProtKB:  A4GVG9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4GVG9
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Human antibody C10 Fab (heavy chain)G,
I [auth K]
127Homo sapiensMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Human antibody C10 Fab (light chain)H,
J [auth L]
111Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentSingaporeMOH-OFIRG18may-0007

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-29
    Type: Initial release