8C1C | pdb_00008c1c

Structure of IgE bound to the ectodomain of FceRIa

• PDB DOI: https://doi.org/10.2210/pdb8C1C/pdb
• EM Map EMD-16378: EMDB EMDataResource

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


• Deposited: 2022-12-20 Released: 2023-03-29 
• Deposition Author(s): Andersen, G.R., Jensen, R.K.
• Funding Organization(s): Novo Nordisk Foundation, Lundbeckfonden, Danish Council for Independent Research

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of IgE bound to the ectodomain of FceRIa

Andersen, G.R., Jensen, R.K.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B2C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A2B1C1D1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

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

Biological Assembly Evidence: SAXS

Macromolecule Content 

• Total Structure Weight: 142.43 kDa 
• Atom Count: 9,983 
• Modeled Residue Count: 1,237 
• Deposited Residue Count: 1,237 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobulin heavy constant epsilon	A [auth H], D [auth X]	426	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
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P01854-2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobulin kappa constant	B [auth L], E [auth Y]	107	Homo sapiens	Mutation(s): 0  Gene Names: IGKC
UniProt & NIH Common Fund Data Resources
Find proteins for P01834 (Homo sapiens) Explore P01834  Go to UniProtKB:  P01834
PHAROS:  P01834

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
High affinity immunoglobulin epsilon receptor subunit alpha	C [auth R]	171	Homo sapiens	Mutation(s): 0  Gene Names: FCER1A, FCE1A
UniProt & NIH Common Fund Data Resources
Find proteins for P12319 (Homo sapiens) Explore P12319  Go to UniProtKB:  P12319
PHAROS:  P12319 GTEx:  ENSG00000179639
Glycosylation
Glycosylation Sites: 7		Go to GlyGen: P12319-1

Oligosaccharides

Help

Entity ID: 4
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)-2-acetamido-2-deoxy-beta-D-glucopyranose	F [auth A], L [auth G]	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth B], H [auth C]	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21381MC GlyCosmos:  G21381MC GlyGen:  G21381MC

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I [auth D], J [auth E], K [auth F]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	M [auth R], N [auth R]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-03-29 
Deposition Author(s): Andersen, G.R., Jensen, R.K.

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Funding Organization	Location	Grant Number
Novo Nordisk Foundation	Denmark	NNF18OC0052105
Lundbeckfonden	Denmark	R155-2015-2666
Danish Council for Independent Research	Denmark	0135-00061B

Revision History  

• Version 1.0: 2023-03-29
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Structure summary
• Version 1.2: 2025-07-09
  Changes: Data collection