7MXI

IgE-Fc in complex with DARPins E2_79 and E3_53

• PDB DOI: https://doi.org/10.2210/pdb7MXI/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Homo sapiens, Escherichia coli
• Mutation(s): No 


• Deposited: 2021-05-19 Released: 2021-07-28 
• Deposition Author(s): Pennington, L.F., Jardetzky, T.J.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.256 
• R-Value Work: 0.213 
• R-Value Observed: 0.215 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 6-mer - A4B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 125.46 kDa 
• Atom Count: 7,485 
• Modelled Residue Count: 970 
• Deposited Residue Count: 1,126 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IgE Fc	A, B	247	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
DARPin E3_53	C, E [auth D]	173	synthetic construct	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-IgE Inhibitor E2_79	D [auth E], F	143	synthetic construct	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)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, I	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	H	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.256 
• R-Value Work: 0.213 
• R-Value Observed: 0.215 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.908	α = 90
b = 137.793	β = 105.68
c = 88.25	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-07-28 
Deposition Author(s): Pennington, L.F., Jardetzky, T.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI115469

Revision History  

• Version 1.0: 2021-07-28
  Type: Initial release
  
• Version 1.1: 2021-10-20
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Refinement description