9EQ4 | pdb_00009eq4

Structure of IgE HMM5 bound to FceRIa cryo-EM class 5

PDB DOI: https://doi.org/10.2210/pdb9EQ4/pdb
EM Map EMD-19896: EMDB EMDataResource

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

Deposited: 2024-03-20 Released: 2024-04-03
Deposition Author(s): Andersen, G.R., Jensen, R.K.
Funding Organization(s): Novo Nordisk Foundation, Lundbeckfonden, Danish Council for Independent Research

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 8.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

The dynamics of hinge flexibility in receptor bound immunoglobulin E revealed by electron microscopy

Jensen, R.K., Miehe, M., Gandini, R., Jorgensen, M.H., Spillner, E., Andersen, G.R.

(2023) bioRxiv

DOI: https://doi.org/10.1101/2023.02.17.528943

Macromolecule Content

Total Structure Weight: 195.89 kDa
Atom Count: 13,632
Modeled Residue Count: 1,697
Deposited Residue Count: 1,707
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IgE HMM5 heavy chain	A [auth H], D [auth X]	551	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
IgE HMM5 light chain	B [auth L], E [auth Y]	217	Homo sapiens	Mutation(s): 0

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12319
Glycosylation
Glycosylation Sites: 7	Glycosylation Focus chain C [auth R]	Go to GlyGen: P12319-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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], M [auth I], N [auth J]	5		N-Glycosylation	Interactions Focus chain F [auth A] Focus chain L [auth G] Focus chain M [auth I] Focus chain N [auth J] Interactions & Density Focus chain F [auth A] Focus chain L [auth G] Focus chain M [auth I] Focus chain N [auth J]
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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]	5		N-Glycosylation	Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
Glycosylation Resources
GlyTouCan: G21381MC GlyCosmos: G21381MC GlyGen: G21381MC

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
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 C], K [auth F]	4		N-Glycosylation	Interactions Focus chain H [auth C] Focus chain K [auth F] Interactions & Density Focus chain H [auth C] Focus chain K [auth F]
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Entity ID: 7
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	I [auth D]	3		N-Glycosylation	Interactions Focus chain I [auth D] Interactions & Density Focus chain I [auth D]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J [auth E]	2		N-Glycosylation	Interactions Focus chain J [auth E] Interactions & Density Focus chain J [auth E]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 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 O [auth H] SDF format, chain P [auth H] SDF format, chain Q [auth H] SDF format, chain S [auth X] SDF format, chain U [auth X] SDF format, chain V [auth X] SDF format, chain T [auth X] SDF format, chain R [auth H] MOL2 format, chain O [auth H] MOL2 format, chain P [auth H] MOL2 format, chain Q [auth H] MOL2 format, chain S [auth X] MOL2 format, chain U [auth X] MOL2 format, chain V [auth X] MOL2 format, chain T [auth X] MOL2 format, chain R [auth H] mmCIF format, chain O [auth H] mmCIF format, chain P [auth H] mmCIF format, chain Q [auth H] mmCIF format, chain S [auth X] mmCIF format, chain U [auth X] mmCIF format, chain V [auth X] mmCIF format, chain T [auth X] mmCIF format, chain R [auth H]	O [auth H] P [auth H] Q [auth H] R [auth H] S [auth X] O [auth H], P [auth H], Q [auth H], R [auth H], S [auth X], T [auth X], U [auth X], V [auth X]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain O [auth H] Focus chain P [auth H] Focus chain Q [auth H] Focus chain R [auth H] Focus chain S [auth X] Focus chain T [auth X] Focus chain U [auth X] Focus chain V [auth X] Interactions & Density Focus chain O [auth H] Focus chain P [auth H] Focus chain Q [auth H] Focus chain R [auth H] Focus chain S [auth X] Focus chain T [auth X] Focus chain U [auth X] Focus chain V [auth X]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 8.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-04-03

Deposition Author(s):

Andersen, G.R.

Jensen, R.K.

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 (Full details and data files)

Version 1.0: 2024-04-03
Type: Initial release
Version 1.1: 2024-10-23
Changes: Data collection, Database references, Structure summary
Version 1.2: 2025-07-09
Changes: Data collection