8C1B: Focused map for structure of IgE

Focused map for structure of IgE bound to the ectodomain of FceRIa. Determined by electron microscopy at 3.8 Å resolution. Released 29 Mar 2023.

Method: Electron microscopy
Resolution: 3.8 Å
Organism: Homo sapiens
Chains: 3
Atoms: 6,569
Mol. weight: 93.59 kDa
Ligands: NAG
Released: 29 Mar 2023

Explore 8C1B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8C1B contains 36 α-helices and 74 β-strands across 3 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 H: 17 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	226-228	3
β-strand	230-235	6	1
α-helix	236-237	2
α-helix	242-244	3
β-strand	246-256	11	1
β-strand	261-267	7	2
β-strand	270-271	2	2
α-helix	272-273	2
α-helix	274-276	3
β-strand	277-284	8	1
β-strand	287-297	11	1
α-helix	298-302	5
β-strand	306-313	8	2
β-strand	316-323	8	2
β-strand	334-337	4	3
α-helix	338-341	4
α-helix	342	1
α-helix	343-347	5
β-strand	352-360	9	3
α-helix	366-367	2
β-strand	368-373	6	4
α-helix	377-382	6
β-strand	383-388	6	3
β-strand	394-401	8	3
α-helix	404-408	5
β-strand	412-418	7	4
β-strand	426-431	6	4
β-strand	438	1	5
α-helix	439-440	2
β-strand	441-446	6	6
α-helix	447-449	3
β-strand	456	1	7
β-strand	459-466	8	6
β-strand	467	1	5
β-strand	472-477	6	8
β-strand	480-481	2	8
α-helix	484-486	3
β-strand	487-489	3	6
α-helix	490-492	3
β-strand	493-494	2	6
β-strand	500-506	7	6
β-strand	509	1	7
α-helix	510-515	6
β-strand	518-524	7	8
β-strand	533-539	7	8

Chain R: 5 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	9
β-strand	15-17	3	10
β-strand	22-27	6	9
β-strand	38-42	5	11
β-strand	44-46	3	11
β-strand	52-55	4	9
α-helix	60-62	3
β-strand	64-66	3	12
β-strand	68-69	2	11
β-strand	79-81	3	12
β-strand	82-84	3	10
β-strand	88-92	5	13
β-strand	96-98	3	14
β-strand	103-109	7	13
α-helix	110-112	3
α-helix	113-115	3
β-strand	116-122	7	15
β-strand	125-130	6	15
β-strand	135-138	4	13
α-helix	143-145	3
β-strand	147-155	9	15
β-strand	158-161	4	15
α-helix	162-164	3
β-strand	165-167	3	15
β-strand	168-170	3	14

Chain X: 14 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	231-234	4	1
α-helix	235-237	3
α-helix	242-244	3
β-strand	246-256	11	1
β-strand	261-267	7	16
β-strand	270-271	2	16
α-helix	272-273	2
α-helix	274-276	3
β-strand	277-284	8	1
β-strand	287-297	11	1
α-helix	298-302	5
β-strand	307-313	7	16
β-strand	316-322	7	16
β-strand	334-337	4	17
α-helix	338-341	4
α-helix	342-346	5
β-strand	352-360	9	17
β-strand	368-373	6	18
β-strand	385-388	4	17
β-strand	394-401	8	17
α-helix	404-408	5
β-strand	412-418	7	18
β-strand	426-431	6	18
β-strand	438	1	19
α-helix	439-440	2
β-strand	441-446	6	20
α-helix	447-450	4
β-strand	456-466	11	20
β-strand	467	1	19
β-strand	471-477	7	21
β-strand	480-481	2	21
α-helix	482-483	2
α-helix	484-486	3
β-strand	487-489	3	20
α-helix	490-492	3
β-strand	493-494	2	20
β-strand	500-509	10	20
α-helix	510-515	6
β-strand	518-525	8	21
β-strand	533-539	7	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Immunoglobulin heavy constant epsilon	H, X	protein	319	Homo sapiens	P01854 (AlphaFold model)
High affinity immunoglobulin epsilon receptor subunit alpha	R	protein	169	Homo sapiens	P12319 (AlphaFold model)

Sequence of entity 1 (H, X), FASTA

>8C1B_1 Immunoglobulin heavy constant epsilon (chains H, X)
DFTPPTVKILQSSCDGGGHFPPTIQLLCLVSGYTPGTINITWLEDGQVMDVDLSTASTTQ
EGELASTQSELTLSQKHWLSDRTYTCQVTYQGHTFEDSTKKCADSNPRGVSAYLSRPSPF
DLFIRKSPTITCLVVDLAPSKGTVNLTWSRASGKPVNHSTRKEEKQRNGTLTVTSTLPVG
TRDWIEGETYQCRVTHPHLPRALMRSTTKTSGPRAAPEVYAFATPEWPGSRDKRTLACLI
QNFMPEDISVQWLHNEVQLPDARHSTTQPRKTKGSGFFVFSRLEVTRAEWEQKDEFICRA
VHEAASPSQTVQRAVSSVA

Sequence of entity 2 (R), FASTA

>8C1B_2 High affinity immunoglobulin epsilon receptor subunit alpha (chains R)
KPKVSLNPPWNRIFKGENVTLTCNGNNFFEVSSTKWFHNGSLSEETNSSLNIVNAKFEDS
GEYKCQHQQVNESEPVYLEVFSDWLLLQASAEVVMEGQPLFLRCHGWRNWDVYKVIYYKD
GEALKYWYENHNISITNATVEDSGTYYCTGKVWQLDYESEPLNITVIKA

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

Primary citation

Structure of IgE bound to the ectodomain of FceRIa. Andersen, G.R., Jensen, R.K. To be published.

Other PDB entries of the same protein (UniProt P01854 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5MOL 1.75 Å, Human IgE-Fc crystal structure
2WQR 1.9 Å, The high resolution crystal structure of IgE Fc
5MOK 2.0 Å, Crystal structure of human IgE-Fc epsilon 3-4
5MOI 2.2 Å, Crystal structure of human IgE-Fc epsilon 3-4
3H9Y 2.23 Å, Crystal structure of the IgE-Fc3-4 domains
5MOJ 2.26 Å, Crystal structure of IgE-Fc epsilon 3-4
1FP5 2.3 Å, Crystal structure analysis of the human IgE-fc CEPSILON3-CEPSILON4 fragment.
30AF 2.4 Å, Complex between IgE-Fc and anti-IgE Fab aeFab98
3H9Z 2.45 Å, Crystal structure of the IgE-Fc3-4 domains
5HYS 2.5 Å, Structure of IgE complexed with omalizumab
1O0V 2.6 Å, The crystal structure of IgE Fc reveals an asymmetrically bent conformation
5LGJ 2.6 Å, The crystal structure of IgE fc mutant - P333C

Browse structure collections

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