4L5F | pdb_00004l5f

Crystal Structure of DENV1-E106 Fab bound to DENV-1 Envelope protein DIII

• PDB DOI: https://doi.org/10.2210/pdb4L5F/pdb

• Classification: VIRAL PROTEIN, IMMUNE SYSTEM
• Organism(s): Mus musculus, dengue virus type 1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-06-11 Released: 2013-12-11 
• Deposition Author(s): Edeling, M.A., Nelson, C.A., Fremont, D.H., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.239 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Literature

Crystal Structure of DENV1-E106 Fab bound to DENV-1 Envelope protein DIII

Edeling, M.A., Austin, S.K., Shrestha, B., Dowd, K.A., Mukherjee, S., Nelson, C.A., Johnson, S., Mabila, M.N., Christian, E.A., Rucker, J., Pierson, T.C., Diamond, M.S., Fremont, D.H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 59.09 kDa 
• Atom Count: 4,157 
• Modeled Residue Count: 529 
• Deposited Residue Count: 542 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of E106 antibody (VH and CH1 of IgG2c)	A [auth H]	218	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope protein	B [auth E]	111	dengue virus type 1	Mutation(s): 0  Gene Names: E
UniProt
Find proteins for Q8BE40 (Dengue virus type 1) Explore Q8BE40  Go to UniProtKB:  Q8BE40

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of E106 antibody (kappa)	C [auth L]	213	Mus musculus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.239 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.661	α = 90
b = 91.823	β = 90
c = 92.599	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-11 
Deposition Author(s): Edeling, M.A., Nelson, C.A., Fremont, D.H., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2013-12-11
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2024-11-27
  Changes: Data collection, Database references, Structure summary