21NZ | pdb_000021nz

Cryo-EM structure of the rat IgE-Fc in complex with FcgammaRIV

PDB DOI: https://doi.org/10.2210/pdb21NZ/pdb
EM Map EMD-67857: EMDB EMDataResource

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

Deposited: 2025-12-21 Released: 2026-08-26
Deposition Author(s): Xu, S.R., Du, S., Xiao, J.Y.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.98 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Cryo-EM structure of the rat IgE-Fc in complex with FcgammaRIV

Xu, S.R., Du, S., Xiao, J.Y.

To be published.

Macromolecule Content

Total Structure Weight: 114.12 kDa
Atom Count: 6,688
Modeled Residue Count: 800
Deposited Residue Count: 972
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Low affinity immunoglobulin gamma Fc region receptor III-A	A	246	Rattus norvegicus	Mutation(s): 0 Gene Names: Fcgr3a, Fcgr4
UniProt
Find proteins for Q6XPU4 (Rattus norvegicus) Explore Q6XPU4 Go to UniProtKB: Q6XPU4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6XPU4
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A	Go to GlyGen: Q6XPU4-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobulin heavy constant epsilon	B, C	363	Rattus norvegicus	Mutation(s): 0 Gene Names: IGHE
UniProt
Find proteins for P01855 (Rattus norvegicus) Explore P01855 Go to UniProtKB: P01855
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01855
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain B Focus chain C	Go to GlyGen: P01855-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, F	3		N-Glycosylation	Interactions Focus chain D Focus chain F Interactions & Density Focus chain D Focus chain F

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	2		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth C] SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain L [auth C] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth C] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth C] mmCIF format, chain J [auth C] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C]	G [auth B] H [auth B] I [auth C] J [auth C] K [auth C] G [auth B], H [auth B], I [auth C], J [auth C], K [auth C], L [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C] Interactions & Density Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C]
BMA (Subject of Investigation/LOI) Query on BMA Download:Ideal Coordinates CCD File SDF format, chain M [auth C] MOL2 format, chain M [auth C] mmCIF format, chain M [auth C]	M [auth C]	beta-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-RWOPYEJCSA-N		Interactions Focus chain M [auth C] Interactions & Density Focus chain M [auth C]