4UTA

Crystal structure of dengue 2 virus envelope glycoprotein in complex with the Fab fragment of the broadly neutralizing human antibody EDE1 C8

• PDB DOI: https://doi.org/10.2210/pdb4UTA/pdb

• Classification: IMMUNE SYSTEM-VIRAL PROTEIN COMPLEX
• Organism(s): dengue virus type 2, Homo sapiens
• Expression System: Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2014-07-18 Released: 2015-01-28 
• Deposition Author(s): Rouvinski, A., Guardado-Calvo, P., Barba-Spaeth, G., Duquerroy, S., Vaney, M.C., Rey, F.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.248 
• R-Value Work: 0.213 
• R-Value Observed: 0.214 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 202.01 kDa 
• Atom Count: 12,683 
• Modelled Residue Count: 1,619 
• Deposited Residue Count: 1,828 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENVELOPE GLYCOPROTEIN E	A, B	425	dengue virus type 2	Mutation(s): 0
UniProt
Find proteins for A0A0B4SHY9 (dengue virus type 2) Explore A0A0B4SHY9  Go to UniProtKB:  A0A0B4SHY9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BROADLY NEUTRALIZING HUMAN ANTIBODY EDE1 C8 HEAVY CHAIN	C [auth H], D [auth I]	272	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
BROADLY NEUTRALIZING HUMAN ANTIBODY EDE1 C8 LIGHT CHAIN	E [auth L], F [auth M]	217	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth C]	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G32152BH GlyCosmos:  G32152BH GlyGen:  G32152BH

Entity ID: 5
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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	H [auth D]	6		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G82348BZ GlyCosmos:  G82348BZ GlyGen:  G82348BZ

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.248 
• R-Value Work: 0.213 
• R-Value Observed: 0.214 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.657	α = 90
b = 191.342	β = 90
c = 203.663	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-28 
Deposition Author(s): Rouvinski, A., Guardado-Calvo, P., Barba-Spaeth, G., Duquerroy, S., Vaney, M.C., Rey, F.A.

Revision History  

• Version 1.0: 2015-01-28
  Type: Initial release
  
• Version 1.1: 2015-04-08
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description, Structure summary