8C1C: IgE

Structure of IgE bound to the ectodomain of FceRIa. Determined by electron microscopy at 4.1 Å resolution. Released 29 Mar 2023.

Method: Electron microscopy
Resolution: 4.1 Å
Organism: Homo sapiens
Chains: 5
Atoms: 9,983
Mol. weight: 142.43 kDa
Ligands: NAG
Released: 29 Mar 2023

Explore 8C1C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8C1C contains 47 α-helices and 111 β-strands across 5 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: 18 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	120	1	1
α-helix	121-122	2
β-strand	123-128	6	2
β-strand	140-148	9	2
β-strand	151	1	1
β-strand	156-160	5	3
β-strand	166-170	5	2
α-helix	171-173	3
β-strand	174-175	2	2
β-strand	182-191	10	2
β-strand	198-204	7	3
β-strand	213-219	7	3
α-helix	226-228	3
β-strand	230-235	6	4
α-helix	236-237	2
α-helix	242-244	3
β-strand	246-256	11	4
β-strand	261-267	7	5
β-strand	270-271	2	5
α-helix	272-273	2
α-helix	274-276	3
β-strand	277-284	8	4
β-strand	287-297	11	4
α-helix	298-302	5
β-strand	307-313	7	5
β-strand	316-322	7	5
β-strand	334-337	4	6
α-helix	338-341	4
α-helix	342-346	5
β-strand	352-360	9	6
α-helix	366-367	2
β-strand	368-373	6	7
α-helix	377-382	6
β-strand	383-388	6	6
β-strand	394-401	8	6
α-helix	404-408	5
β-strand	412-418	7	7
β-strand	426-431	6	7
β-strand	438	1	8
α-helix	439-440	2
β-strand	441-446	6	9
α-helix	447-449	3
β-strand	456-466	11	9
β-strand	467	1	8
β-strand	472-477	6	10
β-strand	480-481	2	10
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	518-524	7	10
β-strand	533-539	7	10

Chain L: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	114	1	11
β-strand	117-121	5	12
α-helix	122-124	3
α-helix	125-130	6
β-strand	132-142	11	12
β-strand	143	1	11
β-strand	148-153	6	13
β-strand	157	1	13
β-strand	162-166	5	12
β-strand	176-185	10	12
α-helix	186-190	5
β-strand	194-200	7	13
β-strand	208-213	6	13

Chain R: 5 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	14
β-strand	15-17	3	15
β-strand	22-27	6	14
β-strand	38-42	5	16
β-strand	44-46	3	16
β-strand	52-55	4	14
α-helix	60-62	3
β-strand	64-69	6	16
β-strand	79-81	3	16
β-strand	82-84	3	15
β-strand	88-92	5	17
β-strand	96-98	3	18
β-strand	103-109	7	17
α-helix	110-112	3
α-helix	113-114	2
β-strand	115-122	8	19
β-strand	125-130	6	19
β-strand	135-138	4	17
α-helix	143-145	3
β-strand	147-155	9	19
β-strand	158-161	4	19
α-helix	162-164	3
β-strand	165-167	3	19
β-strand	168-170	3	18

Chain X: 16 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	120	1	20
α-helix	121-122	2
β-strand	123-127	5	21
β-strand	140-150	11	21
β-strand	151	1	20
β-strand	156-160	5	22
β-strand	166-170	5	21
α-helix	171-173	3
β-strand	174-175	2	21
β-strand	182-191	10	21
β-strand	198-204	7	22
β-strand	213-219	7	22
β-strand	231-234	4	4
α-helix	235-237	3
α-helix	242-244	3
β-strand	246-256	11	4
β-strand	261-267	7	23
β-strand	270-271	2	23
α-helix	272-273	2
α-helix	274-276	3
β-strand	277-284	8	4
β-strand	287-297	11	4
α-helix	298-302	5
β-strand	307-313	7	23
β-strand	316-322	7	23
β-strand	334-337	4	24
α-helix	338-341	4
α-helix	342-346	5
β-strand	352-360	9	24
β-strand	368-373	6	25
β-strand	385-388	4	24
β-strand	394-401	8	24
α-helix	404-408	5
β-strand	412-418	7	25
β-strand	426-431	6	25
β-strand	438	1	26
α-helix	439-440	2
β-strand	441-446	6	27
α-helix	447-450	4
β-strand	456-466	11	27
β-strand	467	1	26
β-strand	471-477	7	28
β-strand	480-481	2	28
α-helix	482-483	2
α-helix	484-486	3
β-strand	487-489	3	27
α-helix	490-492	3
β-strand	493-494	2	27
β-strand	500-509	10	27
α-helix	510-515	6
β-strand	518-525	8	28
β-strand	533-539	7	28

Chain Y: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	114	1	29
β-strand	117-121	5	30
α-helix	122-124	3
α-helix	125-130	6
β-strand	132-142	11	30
β-strand	143	1	29
β-strand	148-153	6	31
β-strand	157-158	2	31
β-strand	162-166	5	30
β-strand	176-185	10	30
α-helix	186-191	6
β-strand	194-200	7	31
α-helix	207	1
β-strand	208-213	6	31
α-helix	214-216	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Immunoglobulin heavy constant epsilon	H, X	protein	426	Homo sapiens	P01854 (AlphaFold model)
Immunoglobulin kappa constant	L, Y	protein	107	Homo sapiens	P01834 (AlphaFold model)
High affinity immunoglobulin epsilon receptor subunit alpha	R	protein	171	Homo sapiens	P12319 (AlphaFold model)

Sequence of entity 1 (H, X), FASTA

>8C1C_1 Immunoglobulin heavy constant epsilon (chains H, X)
ASTQSPSVFPLTRCCKNIPSNATSVTLGCLATGYFPEPVMVTWDTGSLNGTTMTLPATTL
TLSGHYATISLLTVSGAWAKQMFTCRVAHTPSSTDWVDNKTFSVCSRDFTPPTVKILQSS
CDGGGHFPPTIQLLCLVSGYTPGTINITWLEDGQVMDVDLSTASTTQEGELASTQSELTL
SQKHWLSDRTYTCQVTYQGHTFEDSTKKCADSNPRGVSAYLSRPSPFDLFIRKSPTITCL
VVDLAPSKGTVNLTWSRASGKPVNHSTRKEEKQRNGTLTVTSTLPVGTRDWIEGETYQCR
VTHPHLPRALMRSTTKTSGPRAAPEVYAFATPEWPGSRDKRTLACLIQNFMPEDISVQWL
HNEVQLPDARHSTTQPRKTKGSGFFVFSRLEVTRAEWEQKDEFICRAVHEAASPSQTVQR
AVSSVA

Sequence of entity 2 (L, Y), FASTA

>8C1C_2 Immunoglobulin kappa constant (chains L, Y)
RTVGAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQD
SKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (R), FASTA

>8C1C_3 High affinity immunoglobulin epsilon receptor subunit alpha (chains R)
KPKVSLNPPWNRIFKGENVTLTCNGNNFFEVSSTKWFHNGSLSEETNSSLNIVNAKFEDS
GEYKCQHQQVNESEPVYLEVFSDWLLLQASAEVVMEGQPLFLRCHGWRNWDVYKVIYYKD
GEALKYWYENHNISITNATVEDSGTYYCTGKVWQLDYESEPLNITVIKAPR

Ligands and cofactors

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

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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