6EYO

Structure of extended IgE-Fc in complex with two anti-IgE Fabs

• PDB DOI: https://doi.org/10.2210/pdb6EYO/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Mus musculus, Homo sapiens
• Mutation(s): No 


• Deposited: 2017-11-13 Released: 2018-08-15 
• Deposition Author(s): Chen, J.B., Ramadani, F., Pang, M.O.Y., Beavil, R.L., Holdom, M.D., Mitropoulou, A.N., Beavil, A.J., Gould, H.J., Chang, T.W., Sutton, B.J., McDonnell, J.M., Davies, A.M.
• Funding Organization(s): Medical Research Council (United Kingdom), Asthma UK, Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.70 Å
• R-Value Free: 0.288 
• R-Value Work: 0.247 
• R-Value Observed: 0.250 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 

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

Macromolecule Content

• Total Structure Weight: 171.73 kDa 
• Atom Count: 10,385 
• Modelled Residue Count: 1,439 
• Deposited Residue Count: 1,544 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobulin heavy constant epsilon	A, B	327	Homo sapiens	Mutation(s): 0  Gene Names: IGHE
UniProt & NIH Common Fund Data Resources
Find proteins for P01854 (Homo sapiens) Explore P01854  Go to UniProtKB:  P01854
PHAROS:  P01854 GTEx:  ENSG00000211891

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
8D6 Fab heavy chain	C [auth I], D [auth H]	227	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
8D6 Fab light chain	E [auth M], F [auth L]	218	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth C]	7		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G07617FP GlyCosmos:  G07617FP GlyGen:  G07617FP

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H [auth D]	6		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G56014GC GlyCosmos:  G56014GC GlyGen:  G56014GC

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.70 Å
• R-Value Free: 0.288 
• R-Value Work: 0.247 
• R-Value Observed: 0.250 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.483	α = 90
b = 119.601	β = 90
c = 132.994	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-08-15 
Deposition Author(s): Chen, J.B., Ramadani, F., Pang, M.O.Y., Beavil, R.L., Holdom, M.D., Mitropoulou, A.N., Beavil, A.J., Gould, H.J., Chang, T.W., Sutton, B.J., McDonnell, J.M., Davies, A.M.

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Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	G1100090
Asthma UK	United Kingdom	AUK-PG-2013-183
Wellcome Trust	United Kingdom	085944

Revision History  

• Version 1.0: 2018-08-15
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary