9EQ3: IgE HMM5

Structure of IgE HMM5 bound to FceRIa cryo-EM class 8. Determined by electron microscopy at 6.9 Å resolution. Released 10 Apr 2024.

Method: Electron microscopy
Resolution: 6.9 Å
Organism: Homo sapiens
Chains: 5
Atoms: 13,588
Mol. weight: 195.24 kDa
Ligands: NAG
Released: 10 Apr 2024

Explore 9EQ3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9EQ3 contains 61 α-helices and 157 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: 20 helices, 48 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	1
β-strand	10	1	2
β-strand	17-24	8	1
β-strand	32-38	7	3
β-strand	45-50	6	3
β-strand	56-58	3	3
β-strand	66-70	5	1
β-strand	75-80	6	1
α-helix	85-87	3
β-strand	89-96	8	3
β-strand	106	1	3
β-strand	110-112	3	3
β-strand	113	1	2
β-strand	120	1	4
α-helix	121-122	2
β-strand	123-127	5	5
α-helix	131-133	3
β-strand	140-150	11	5
β-strand	151	1	4
β-strand	156-160	5	6
β-strand	166-170	5	5
α-helix	171-173	3
β-strand	174-175	2	5
β-strand	182-191	10	5
β-strand	199-204	6	6
β-strand	213-218	6	6
α-helix	226-228	3
β-strand	230-235	6	7
α-helix	236-237	2
α-helix	242-244	3
β-strand	246-256	11	7
β-strand	261-267	7	8
β-strand	270-271	2	8
α-helix	272-273	2
α-helix	274-276	3
β-strand	277-284	8	7
β-strand	287-297	11	7
α-helix	298-302	5
β-strand	307-313	7	8
β-strand	316-322	7	8
β-strand	334-337	4	9
α-helix	338-341	4
α-helix	342-346	5
β-strand	352-360	9	9
α-helix	366-367	2
β-strand	368-373	6	10
α-helix	377-382	6
β-strand	383-388	6	9
β-strand	394-401	8	9
α-helix	404-408	5
β-strand	413-418	6	10
β-strand	426-430	5	10
β-strand	438	1	11
α-helix	439-440	2
β-strand	441-446	6	12
α-helix	447-449	3
β-strand	456-466	11	12
β-strand	467	1	11
β-strand	471-477	7	13
β-strand	481	1	13
α-helix	484-486	3
β-strand	487-489	3	12
α-helix	490-492	3
β-strand	493-494	2	12
β-strand	500-509	10	12
α-helix	510-515	6
β-strand	518-525	8	13
β-strand	533-539	7	13

Chain L: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	14
β-strand	10	1	15
β-strand	18-25	8	14
α-helix	28-29	2
α-helix	30-32	3
β-strand	35-40	6	15
β-strand	47-51	5	15
β-strand	55-56	2	15
α-helix	57	1
β-strand	64-69	6	14
β-strand	72-78	7	14
α-helix	82-84	3
β-strand	87-94	8	15
β-strand	98-101	4	15
β-strand	106	1	15
β-strand	114	1	16
α-helix	115-116	2
β-strand	117-121	5	17
α-helix	122-124	3
α-helix	125-128	4
β-strand	132-142	11	17
β-strand	143	1	16
β-strand	148-153	6	18
β-strand	156-157	2	18
β-strand	162-166	5	17
α-helix	168-170	3
β-strand	176-185	10	17
α-helix	186-190	5
β-strand	194-200	7	18
β-strand	208-213	6	18

Chain R: 5 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	19
β-strand	15-17	3	20
β-strand	22-27	6	19
β-strand	38-42	5	21
β-strand	44-46	3	21
β-strand	52-55	4	19
α-helix	60-62	3
β-strand	64-69	6	21
β-strand	79-81	3	21
β-strand	82-84	3	20
β-strand	88-92	5	22
β-strand	96-98	3	23
β-strand	103-109	7	22
α-helix	110-112	3
α-helix	113-114	2
β-strand	115-122	8	24
β-strand	125-130	6	24
β-strand	135-138	4	22
α-helix	143-145	3
β-strand	147-155	9	24
β-strand	158-161	4	24
α-helix	162-164	3
β-strand	165-167	3	24
β-strand	168-170	3	23

Chain X: 17 helices, 48 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	25
β-strand	10-11	2	26
β-strand	17-24	8	25
β-strand	32-38	7	27
β-strand	45-50	6	27
β-strand	56-58	3	27
β-strand	66-70	5	25
β-strand	75-80	6	25
α-helix	85-87	3
β-strand	89-96	8	27
β-strand	106	1	27
β-strand	110-112	3	27
β-strand	113-114	2	26
β-strand	120	1	28
α-helix	121-122	2
β-strand	123-127	5	29
β-strand	140-150	11	29
β-strand	151	1	28
β-strand	156-160	5	30
β-strand	167-170	4	29
α-helix	171-173	3
β-strand	174-175	2	29
β-strand	182-191	10	29
β-strand	199-204	6	30
β-strand	213-218	6	30
β-strand	229-235	7	7
α-helix	236-237	2
α-helix	242-244	3
β-strand	246-256	11	7
β-strand	261-267	7	31
β-strand	270-271	2	31
α-helix	272-273	2
α-helix	274-276	3
β-strand	277-284	8	7
β-strand	287-297	11	7
α-helix	298-302	5
β-strand	307-313	7	31
β-strand	316-322	7	31
β-strand	334-337	4	32
α-helix	338-341	4
α-helix	342-346	5
β-strand	352-360	9	32
β-strand	368-373	6	33
β-strand	383-388	6	32
β-strand	394-401	8	32
α-helix	404-408	5
β-strand	413-418	6	33
β-strand	426-430	5	33
β-strand	438	1	34
α-helix	439-440	2
β-strand	441-446	6	35
α-helix	447-450	4
β-strand	456-466	11	35
β-strand	467	1	34
β-strand	471-477	7	36
β-strand	480-481	2	36
α-helix	482-483	2
α-helix	484-486	3
β-strand	487-489	3	35
α-helix	490-492	3
β-strand	493-494	2	35
β-strand	500-509	10	35
α-helix	510-515	6
β-strand	519-525	7	36
β-strand	533-538	6	36

Chain Y: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	37
β-strand	10-13	4	38
β-strand	19-25	7	37
α-helix	28-29	2
α-helix	30-32	3
β-strand	35-40	6	38
β-strand	47-51	5	38
β-strand	55-56	2	38
α-helix	57	1
β-strand	64-69	6	37
β-strand	72-77	6	37
α-helix	82-84	3
β-strand	87-94	8	38
β-strand	98-101	4	38
β-strand	105-109	5	38
β-strand	114	1	39
α-helix	115-116	2
β-strand	117-121	5	40
α-helix	122-124	3
α-helix	125-128	4
β-strand	132-142	11	40
β-strand	143	1	39
β-strand	147-153	7	41
β-strand	156-157	2	41
α-helix	158	1
β-strand	162-166	5	40
α-helix	167-170	4
β-strand	176-185	10	40
α-helix	186-190	5
β-strand	194-201	8	41
β-strand	208-213	6	41

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
IgE HMM5 heavy chain	H, X	protein	551	Homo sapiens
IgE HMM5 light chain	L, Y	protein	217	Homo sapiens
High affinity immunoglobulin epsilon receptor subunit alpha	R	protein	171	Homo sapiens	P12319 (AlphaFold model)

Sequence of entity 1 (H, X), FASTA

>9EQ3_1 IgE HMM5 heavy chain (chains H, X)
QSLEESGGRLVTPGTPLTLTCTVSGFSLSTYNIHWVRQAPGKGLEWIGVIDTGGGTYFAS
WAKGRFAISKTSSTTVDLKMTSLTAADTATYFCAKGFDYSASTNLWGPGTLVTISSASTQ
SPSVFPLTRCCKNIPSNATSVTLGCLATGYFPEPVMVTWDTGSLNGTTMTLPATTLTLSG
HYATISLLTVSGAWAKQMFTCRVAHTPSSTDWVDNKTFSVCSRDFTPPTVKILQSSCDGG
GHFPPTIQLLCLVSGYTPGTINITWLEDGQVMDVDLSTASTTQEGELASTQSELTLSQKH
WLSDRTYTCQVTYQGHTFEDSTKKCADSNPRGVSAYLSRPSPFDLFIRKSPTITCLVVDL
APSKGTVNLTWSRASGKPVNHSTRKEEKQRNGTLTVTSTLPVGTRDWIEGETYQCRVTHP
HLPRALMRSTTKTSGPRAAPEVYAFATPEWPGSRDKRTLACLIQNFMPEDISVQWLHNEV
QLPDARHSTTQPRKTKGSGFFVFSRLEVTRAEWEQKDEFICRAVHEAASPSQTVQRAVSS
VNPGKHHHHHH

Sequence of entity 2 (L, Y), FASTA

>9EQ3_2 IgE HMM5 light chain (chains L, Y)
ELDMTQTPSSVSAPVGGSVTINCQSSQSVYGNNYLAWYQQKAGQPPKLLIYRASTLASGA
PSRFKGSGSGTQFTLTISDLESDDAATYYCLGYYNGVINVFGGGTNVEIKRTVGAPSVFI
FPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSS
TLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (R), FASTA

>9EQ3_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	8

Primary citation

The dynamics of hinge flexibility in receptor bound immunoglobulin E revealed by electron microscopy. Jensen, R.K., Miehe, M., Gandini, R. et al. bioRxiv (2023). DOI 10.1101/2023.02.17.528943

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'…
8YWA 3.14 Å, The structure of IgE receptor binding to IgE
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

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