8ZGS

Structure of the ige-fc bound to its high affinity receptor fc(epsilon)ri state2

• PDB DOI: https://doi.org/10.2210/pdb8ZGS/pdb
• EM Map EMD-60089: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  PDBTM


• Deposited: 2024-05-09 Released: 2024-07-10 
• Deposition Author(s): Du, S., Deng, M.J., Xiao, J.Y.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.04 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of the ige-fc bound to its high affinity receptor fc(epsilon)ri state2

Du, S., Deng, M.J., Xiao, J.Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A2B2C1D1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 163.63 kDa 
• Atom Count: 8,915 
• Modelled Residue Count: 1,077 
• Deposited Residue Count: 1,408 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
High affinity immunoglobulin epsilon receptor subunit alpha	A	245	Rattus norvegicus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P12371 (Rattus norvegicus) Explore P12371  Go to UniProtKB:  P12371
Glycosylation
Glycosylation Sites: 3		Go to GlyGen: P12371-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
High affinity immunoglobulin epsilon receptor subunit beta	B	243	Rattus norvegicus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P13386 (Rattus norvegicus) Explore P13386  Go to UniProtKB:  P13386

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
High affinity immunoglobulin epsilon receptor subunit gamma	C, F [auth G]	86	Rattus norvegicus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P20411 (Rattus norvegicus) Explore P20411  Go to UniProtKB:  P20411

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobulin heavy constant epsilon	D [auth E], E [auth F]	374	Rattus norvegicus	Mutation(s): 0  Gene Names: IGHE Membrane Entity: Yes
UniProt
Find proteins for P01855 (Rattus norvegicus) Explore P01855  Go to UniProtKB:  P01855
Glycosylation
Glycosylation Sites: 3		Go to GlyGen: P01855-1

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth T]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 6
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	H [auth D], I [auth H]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Y01 (Subject of Investigation/LOI)	L [auth B]	CHOLESTEROL HEMISUCCINATE C31 H50 O4 WLNARFZDISHUGS-MIXBDBMTSA-N
NAG (Subject of Investigation/LOI)	J [auth A], K [auth A], M [auth E], N [auth E], O [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.04 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-10 
Deposition Author(s): Du, S., Deng, M.J., Xiao, J.Y.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-07-10
  Type: Initial release