8YWA: IgE receptor binding to IgE

The structure of IgE receptor binding to IgE. Determined by electron microscopy at 3.14 Å resolution. Released 6 Nov 2024.

Method: Electron microscopy
Resolution: 3.14 Å
Organism: Homo sapiens
Chains: 8
Atoms: 9,868
Mol. weight: 264.46 kDa
Ligands: NAG
Released: 6 Nov 2024

Explore 8YWA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8YWA contains 40 α-helices and 110 β-strands across 8 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 4 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	31-34	4	25
β-strand	38	1	26
β-strand	40-42	3	27
β-strand	47-52	6	25
β-strand	63-66	4	28
β-strand	78-80	3	25
β-strand	91-94	4	28
α-helix	102-103	2
β-strand	104	1	28
β-strand	107-109	3	27
β-strand	113-117	5	29
β-strand	118	1	26
β-strand	123	1	30
β-strand	130-134	5	29
α-helix	135-137	3
α-helix	138-140	3
β-strand	141-147	7	31
β-strand	150-154	5	31
β-strand	157	1	31
β-strand	174-180	7	31
β-strand	183-186	4	31
β-strand	195	1	30
α-helix	202-233	32

Chain B: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	19-40	22
α-helix	45-47	3
α-helix	61-80	20
α-helix	84-122	39
α-helix	130-166	37

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	23-52	30

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	23-51	29

Chain h: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	119-123	5	20
α-helix	124-126	3
α-helix	127-131	5
β-strand	135-142	8	20
β-strand	150-155	6	21
β-strand	158-159	2	21
β-strand	164-166	3	20
α-helix	167-169	3
β-strand	170	1	22
β-strand	178	1	22
β-strand	179-185	7	20
α-helix	187-192	6
β-strand	196-201	6	21
α-helix	208	1
β-strand	209-211	3	21

Chain H: 11 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	123-128	6	1
β-strand	141-148	8	1
β-strand	156-160	5	2
β-strand	166-170	5	1
β-strand	174-175	2	3
β-strand	182-183	2	3
β-strand	184-190	7	1
β-strand	199-204	6	2
β-strand	213-218	6	2
β-strand	230-235	6	4
α-helix	236-238	3
β-strand	246-256	11	4
β-strand	262-263	2	5
β-strand	266-267	2	6
β-strand	271	1	6
α-helix	274-276	3
β-strand	277-284	8	4
β-strand	287-297	11	4
α-helix	298-302	5
β-strand	307-308	2	6
β-strand	311-312	2	5
β-strand	317-318	2	5
β-strand	321-322	2	6
β-strand	334-337	4	7
α-helix	342-343	2
α-helix	344-348	5
β-strand	353-360	8	7
β-strand	368-373	6	8
β-strand	383-388	6	7
β-strand	394-400	7	7
α-helix	404-408	5
β-strand	413-418	6	8
β-strand	426-430	5	8
β-strand	441-446	6	9
α-helix	447-449	3
β-strand	456-464	9	9
β-strand	472-477	6	10
β-strand	480-481	2	10
α-helix	482-483	2
α-helix	484-486	3
β-strand	487-489	3	9
α-helix	490-492	3
β-strand	493-494	2	9
β-strand	500-509	10	9
α-helix	510-515	6
β-strand	519-524	6	10
β-strand	533-538	6	10

Chain x: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	119-123	5	23
α-helix	127-131	5
β-strand	135-142	8	23
β-strand	150-155	6	24
β-strand	158-159	2	24
β-strand	164-166	3	23
β-strand	170	1	23
β-strand	178-185	8	23
α-helix	187-192	6
β-strand	196-202	7	24
β-strand	205-211	7	24

Chain X: 11 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	123-128	6	11
β-strand	140-150	11	11
β-strand	156-160	5	12
β-strand	161	1	13
β-strand	163	1	13
β-strand	167-170	4	11
β-strand	174-175	2	11
β-strand	182-191	10	11
β-strand	199-204	6	12
β-strand	213-218	6	12
β-strand	229-235	7	4
α-helix	236-237	2
β-strand	238	1	6
β-strand	246-254	9	4
β-strand	262-267	6	14
β-strand	270-271	2	14
α-helix	274-276	3
β-strand	279-284	6	4
β-strand	287-297	11	4
α-helix	298-302	5
β-strand	307-312	6	14
β-strand	320-322	3	14
α-helix	324-326	3
β-strand	334-337	4	15
α-helix	342	1
α-helix	343-348	6
β-strand	352-360	9	15
β-strand	370	1	16
β-strand	373	1	17
β-strand	385-388	4	15
β-strand	394-401	8	15
α-helix	404-408	5
β-strand	413	1	17
β-strand	414-417	4	16
β-strand	426-429	4	16
β-strand	441-446	6	18
α-helix	447-449	3
β-strand	456-464	9	18
β-strand	472-477	6	19
β-strand	480-481	2	19
α-helix	482-483	2
α-helix	484-486	3
β-strand	487-489	3	18
β-strand	501-509	9	18
α-helix	510-515	6
β-strand	519-524	6	19
β-strand	533-538	6	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Immunoglobulin heavy constant epsilon	H, X	protein	577	Homo sapiens
Immunoglobulin kappa constant	h, x	protein	261	Homo sapiens
High affinity immunoglobulin epsilon receptor subunit alpha	A	protein	267	Homo sapiens	P12319 (AlphaFold model)
High affinity immunoglobulin epsilon receptor subunit beta	B	protein	283	Homo sapiens	Q01362 (AlphaFold model)
High affinity immunoglobulin epsilon receptor subunit gamma	C, D	protein	86	Homo sapiens	P30273 (AlphaFold model)

Sequence of entity 1 (H, X), FASTA

>8YWA_1 Immunoglobulin heavy constant epsilon (chains H, X)
MEFGLSWLFLVAILKGVQCQVQLVQSGAEVRNPGASVKVSCKASGYTFTSYAIHWVRQAP
GHRLEWVGRINTDNGNTKYSQKFHGRVALSRDTSASTTYMDLSSLNSEDTAVYYCARAFY
YSSGVMFDSWGQGALVTVSSASTQSPSVFPLTRCCKNIPSNATSVTLGCLATGYFPEPVM
VTWDTGSLNGTTMTLPATTLTLSGHYATISLLTVSGAWAKQMFTCRVAHTPSSTDWVDNK
TFSVCSRDFTPPTVKILQSSCDGGGHFPPTIQLLCLVSGYTPGTINITWLEDGQVMDVDL
STASTTQEGELASTQSELTLSQKHWLSDRTYTCQVTYQGHTFEDSTKKCADSNPRGVSAY
LSRPSPFDLFIRKSPTITCLVVDLAPSKGTVNLTWSRASGKPVNHSTRKEEKQRNGTLTV
TSTLPVGTRDWIEGETYQCRVTHPHLPRALMRSTTKTSGPRAAPEVYAFATPEWPGSRDK
RTLACLIQNFMPEDISVQWLHNEVQLPDARHSTTQPRKTKGSGFFVFSRLEVTRAEWEQK
DEFICRAVHEAASPSQTVQRAVSVNPGKGGSHHHHHH

Sequence of entity 2 (h, x), FASTA

>8YWA_2 Immunoglobulin kappa constant (chains h, x)
MDMRVPAQLLGLLLLWLSGARCGGSMDYKDDDDKGSPGDEVDAGQSALTQPPSVSGAPGQ
RVSISCTGGSSNFGAGYDVHWYQQLPATAPKLLIYGNNNRPSGVPDRFSGSKSGTSASLA
ITGLQAEDEGDYFCQSFDTSLSGWIFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKAT
LVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSY
SCQVTHEGSTVEKTVAPTECS

Sequence of entity 3 (A), FASTA

>8YWA_3 High affinity immunoglobulin epsilon receptor subunit alpha (chains A)
MDMRVPAQLLGLLLLWLSGARCVPQKPKVSLNPPWNRIFKGENVTLTCNGNNFFEVSSTK
WFHNGSLSEETNSSLNIVNAKFEDSGEYKCQHQQVNESEPVYLEVFSDWLLLQASAEVVM
EGQPLFLRCHGWRNWDVYKVIYYKDGEALKYWYENHNISITNATVEDSGTYYCTGKVWQL
DYESEPLNITVIKAPREKYWLQFFIPLLVVILFAVDTGLFISTQQQVTFLLKIKRTRKGF
RLLNPHPKPNPKNNGGGSMDYKDDDDK

Sequence of entity 4 (B), FASTA

>8YWA_4 High affinity immunoglobulin epsilon receptor subunit beta (chains B)
MGASSAWSHPQFEKGGGSGGGSGGSAWSHPQFEKGSAAAMDTESNRRANLALPQEPSSVP
AFEVLEISPQEVSSGRLLKSASSPPLHTWLTVLKKEQEFLGVTQILTAMICLCFGTVVCS
VLDISHIEGDIFSSFKAGYPFWGAIFFSISGMLSIISERRNATYLVRGSLGANTASSIAG
GTGITILIINLKKSLAYIHIHSCQKFFETKCFMASFSTEIVVMMLFLTILGLGSAVSLTI
CGAGEELKGNKVPEDRVYEELNIYSATYSELEDPGEMSPPIDL

Sequence of entity 5 (C, D), FASTA

>8YWA_5 High affinity immunoglobulin epsilon receptor subunit gamma (chains C, D)
MIPAVVLLLLLLVEQAAALGEPQLCYILDAILFLYGIVLTLLYCRLKIQVRKAAITSYEK
SDGVYTGLSTRNQETYETLKHEKPPQ

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	9

Primary citation

Molecular mechanism of IgE-mediated Fc epsilon RI activation. Chen, M., Su, Q., Shi, Y. Nature (2025) 637:453-460. DOI 10.1038/s41586-024-08229-8 · PubMed

Other PDB entries of the same protein (UniProt P12319 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1F2Q 2.4 Å, Crystal structure of the human high-affinity IgE receptor
1RPQ 3.0 Å, High Affinity IgE Receptor (alpha chain) Complexed with Tight-Binding E131 'zeta'…
1J86 3.2 Å, Human high affinity fc receptor fc(epsilon)ri(alpha), monoclinic crystal form 2
1J87 3.2 Å, Human high affinity fc receptor fc(epsilon)ri(alpha), hexagonal crystal form 1
1J88 3.2 Å, Human high affinity fc receptor fc(epsilon)ri(alpha), tetragonal crystal form 1
2Y7Q 3.4 Å, The high-affinity complex between IgE and its receptor fc epsilon ri
1F6A 3.5 Å, Structure of the human ige-fc bound to its high affinity receptor fc(epsilon)ri(alpha)
8K7R 3.56 Å, Human Fc epsilon RI in complex with hIgE Fc (TMD disordered)
8Z0T 3.58 Å, Structure of the human ige-fc bound to its high affinity receptor fc(epsilon)
8C1B 3.8 Å, Focused map for structure of IgE bound to the ectodomain of FceRIa
8YVU 3.9 Å, structure of Ige receptor
1J89 4.1 Å, Human high affinity fc receptor fc(epsilon)ri(alpha), tetragonal crystal form 2

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