2Y6S | pdb_00002y6s

Structure of an Ebolavirus-protective antibody in complex with its mucin-domain linear epitope

• PDB DOI: https://doi.org/10.2210/pdb2Y6S/pdb

• Classification: IMMUNE SYSTEM/VIRAL PROTEIN
• Organism(s): Mus musculus, Ebola virus - Zaire (1995)
• Mutation(s): No 


• Deposited: 2011-01-25 Released: 2012-01-11 
• Deposition Author(s): Olal, D.O., Kuehne, A., Lee, J.E., Bale, S., Dye, J.M., Saphire, E.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.287 (Depositor), 0.286 (DCC) 
• R-Value Work: 
  0.236 (Depositor), 0.235 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

Starting Model: experimental

Literature

Structure of an Ebola Virus-Protective Antibody in Complex with its Mucin-Domain Linear Epitope.

Olal, D.O., Kuehne, A., Bale, S., Halfmann, P., Hashiguchi, T., Fusco, M.L., Lee, J.E., King, L.B., Kawaoka, Y., Dye, J.M., Saphire, E.O.

(2012) J Virol 86: 2809

• PubMed: 22171276 
• DOI: https://doi.org/10.1128/JVI.05549-11
• Primary Citation Related Structures: 
  2Y6S


• PubMed Abstract: 
  

  Antibody 14G7 is protective against lethal Ebola virus challenge and recognizes a distinct linear epitope in the prominent mucin-like domain of the Ebola virus glycoprotein GP. The structure of 14G7 in complex with its linear peptide epitope has now been determined to 2.8 Å. The structure shows that this GP sequence forms a tandem β-hairpin structure that binds deeply into a cleft in the antibody-combining site. A key threonine at the apex of one turn is critical for antibody interaction and is conserved among all Ebola viruses. This work provides further insight into the mechanism of protection by antibodies that target the protruding, highly accessible mucin-like domain of Ebola virus and the structural framework for understanding and characterizing candidate immunotherapeutics.

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Organizational Affiliation: 
• Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, USA.

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 PISA (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 PISA (software)

Macromolecule Content 

• Total Structure Weight: 96.34 kDa 
• Atom Count: 6,704 
• Modeled Residue Count: 876 
• Deposited Residue Count: 894 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LIGHT CHAIN	A [auth C], D [auth L]	217	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HEAVY CHAIN	B [auth D], C [auth H]	213	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ENVELOPE GLYCOPROTEIN	E [auth P], F [auth Q]	17	Ebola virus - Zaire (1995)	Mutation(s): 0
UniProt
Find proteins for P87666 (Zaire ebolavirus (strain Kikwit-95)) Explore P87666  Go to UniProtKB:  P87666

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.287 (Depositor), 0.286 (DCC) 
• R-Value Work:  0.236 (Depositor), 0.235 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.554	α = 90
b = 68.376	β = 112.5
c = 92.827	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-11 
Deposition Author(s): Olal, D.O., Kuehne, A., Lee, J.E., Bale, S., Dye, J.M., Saphire, E.O.

Revision History  

• Version 1.0: 2012-01-11
  Type: Initial release
  
• Version 1.1: 2012-02-22
  Changes: Other
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Other, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary