7SHT: PDB entry 7SHT

Structure of a partially disrupted IgE high affinity receptor complex bound to an omalizumab variant. Determined by electron microscopy at 7.29 Å resolution. Released 15 Dec 2021.

Method: Electron microscopy
Resolution: 7.29 Å
Organism: Homo sapiens
Chains: 7
Atoms: 10,062
Mol. weight: 153.77 kDa
Ligands: NAG
Released: 15 Dec 2021

Explore 7SHT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7SHT contains 26 α-helices and 134 β-strands across 7 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: 2 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	10	1	1
β-strand	15-17	3	2
β-strand	22-25	4	1
β-strand	40-41	2	3
β-strand	44-45	2	3
β-strand	52-55	4	1
α-helix	60-62	3
β-strand	66-67	2	3
β-strand	79	1	3
β-strand	82-84	3	2
β-strand	88-92	5	4
β-strand	97	1	5
β-strand	103-109	7	4
β-strand	116-122	7	6
β-strand	125-130	6	6
β-strand	136-138	3	4
β-strand	147-149	3	7
β-strand	151-154	4	6
β-strand	155	1	8
β-strand	158	1	8
β-strand	161	1	6
α-helix	162-164	3
β-strand	165-167	3	7
β-strand	169	1	5

Chain B: 8 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	232-236	5	9
β-strand	237-238	2	10
α-helix	245-247	3
β-strand	249-257	9	9
β-strand	264-270	7	11
β-strand	273-274	2	11
α-helix	275-276	2
β-strand	280-287	8	9
β-strand	290-300	11	9
α-helix	301-304	4
β-strand	309-316	8	11
β-strand	321-326	6	11
β-strand	338-341	4	12
α-helix	346-350	5
β-strand	355-360	6	12
β-strand	363	1	12
α-helix	369-370	2
β-strand	373-376	4	13
β-strand	388-391	4	12
β-strand	397-404	8	12
α-helix	408-411	4
β-strand	416-419	4	13
β-strand	430-433	4	13
β-strand	441	1	14
β-strand	444-448	5	15
α-helix	451-453	3
β-strand	461-467	7	15
β-strand	470	1	14
β-strand	475-480	6	16
β-strand	483-484	2	16
β-strand	491-492	2	15
β-strand	496-497	2	17
β-strand	503-504	2	17
β-strand	506-510	5	15
α-helix	513-518	6
β-strand	522-527	6	16
β-strand	536-537	2	16

Chain D: 7 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	232-237	6	10
β-strand	249-259	11	10
β-strand	264-270	7	18
β-strand	273	1	18
β-strand	280-287	8	10
β-strand	290-300	11	10
α-helix	301-305	5
β-strand	310-316	7	18
β-strand	321-322	2	18
β-strand	325	1	18
β-strand	338-340	3	19
α-helix	345	1
α-helix	346-350	5
β-strand	355-363	9	19
β-strand	376	1	20
α-helix	380-382	3
β-strand	388-389	2	19
β-strand	397-404	8	19
α-helix	408-411	4
β-strand	416	1	20
β-strand	433	1	20
β-strand	441	1	21
β-strand	446-448	3	22
β-strand	461-462	2	23
β-strand	463-467	5	22
β-strand	470	1	21
β-strand	475-476	2	24
β-strand	479-480	2	25
β-strand	483-484	2	25
α-helix	487-489	3
β-strand	490-492	3	23
β-strand	496-497	2	22
β-strand	503-506	4	22
β-strand	507-510	4	23
α-helix	514-518	5
β-strand	523	1	25
β-strand	526-527	2	24
β-strand	537	1	24

Chain H: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	26
β-strand	11-12	2	27
β-strand	17-25	9	26
β-strand	35-40	6	28
β-strand	46-52	7	28
β-strand	58-60	3	28
β-strand	68-73	6	26
β-strand	78-84	7	26
α-helix	88-90	3
β-strand	92-98	7	28
β-strand	100-102	3	29
β-strand	105-107	3	29
β-strand	115-117	3	28
β-strand	118-119	2	27

Chain J: 2 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	30
β-strand	10	1	31
β-strand	17-19	3	32
β-strand	21-25	5	30
α-helix	29-31	3
β-strand	35-40	6	31
β-strand	46-52	7	31
β-strand	58-59	2	31
β-strand	71-73	3	30
β-strand	78-80	3	30
β-strand	82-84	3	32
α-helix	88-90	3
β-strand	92-98	7	31
β-strand	99-102	4	33
β-strand	105-108	4	33
β-strand	115-117	3	31

Chain K: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	34
β-strand	10-12	3	35
β-strand	19-24	6	34
β-strand	31	1	36
β-strand	34	1	36
β-strand	37-42	6	35
β-strand	48-50	3	35
β-strand	52-53	2	37
β-strand	57-58	2	37
α-helix	59	1
β-strand	66-71	6	34
β-strand	74-79	6	34
α-helix	84-86	3
β-strand	89-94	6	35
α-helix	100-101	2
β-strand	102	1	35
β-strand	106-109	4	35

Chain L: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	38
β-strand	10-12	3	39
β-strand	19-24	6	38
β-strand	37-42	6	39
β-strand	48-53	6	39
β-strand	57-58	2	39
α-helix	59	1
β-strand	66-71	6	38
β-strand	74-79	6	38
α-helix	84-86	3
β-strand	89-94	6	39
α-helix	100	1
β-strand	102	1	39
β-strand	106-109	4	39

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
High affinity immunoglobulin epsilon receptor subunit alpha	A	protein	197	Homo sapiens	P12319 (AlphaFold model)
Immunoglobulin heavy constant epsilon	B, D	protein	322	Homo sapiens	P01854 (AlphaFold model)
clone_7 Variable fragment heavy chain	H, J	protein	123	Homo sapiens
clone_7 Variable fragment light chain	K, L	protein	134	Homo sapiens

Sequence of entity 1 (A), FASTA

>7SHT_1 High affinity immunoglobulin epsilon receptor subunit alpha (chains A)
APMAEGGGQNHHHHHHHHGGENLYFQGGSPKVSLNPPWNRIFKGENVTLTCNGNNFFEVS
STKWFHNGSLSEETNSSLNIVNAKFEDSGEYKCQHQQVNESEPVYLEVFSDWLLLQASAE
VVMEGQPLFLRCHGWRNWDVYKVIYYKDGEALKYWYENHNISITNATVEDSGTYYCTGKV
CQLDYESEPLNITVIKA

Sequence of entity 2 (B, D), FASTA

>7SHT_2 Immunoglobulin heavy constant epsilon (chains B, D)
ASFTPPTVKILQSSCDGGGHFPPTIQLLCLVSGYTPGTINITWLEDGQVMDVDLSTASTT
QEGELASTQSELTLSQKHWLSDRTYTCQVTYQGHTFEDSTKKCADSNPRCVSAYLSRPSP
FDLFIRKSPTITCLVVDLAPSKGTVNLTWSRASGKPVNHSTRKEEKQRNGTLTVTSTLPV
GTRDWIEGETYQCRVTHPHLPRALMRSTTKTSGPRAAPEVYAFATPEWPGSRDKRTLACL
IQNFMPEDISVQWLHNEVQLPDARHSTTQPRKTKGSGFFVFSRLEVTRAEWEQKDEFICR
AVHEAASPSQTVQRAVSVNPGK

Sequence of entity 3 (H, J), FASTA

>7SHT_3 clone_7 Variable fragment heavy chain (chains H, J)
ASEVQLVESGGGLVQPDGSLRLSCAVSGYNITSGYSWNWIRQTPGKGLEWVASVTYDGST
NYNPSVKGRITISRDGSKNTFYLQMNSLRAEDTAVYYCAKGNNYFGHWHFAVWGQGTLVT
VSS

Sequence of entity 4 (K, L), FASTA

>7SHT_4 clone_7 Variable fragment light chain (chains K, L)
GSDIQLTQSPSSLSASVGDRVTITCRASKSVDSDGDSYMNWYQQKPGRAPKLLIYAASYL
ESGVPSRFSGSGSGTHFTLTISSLQPEDFATYYCQQSHEDPYTFGQGTKVEIKGGSENLY
FQGGSGHHHHHHHH

Ligands and cofactors

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

Primary citation

Directed evolution of and structural insights into antibody-mediated disruption of a stable receptor-ligand complex. Pennington, L.F., Gasser, P., Kleinboelting, S. et al. Nat Commun (2021) 12:7069-7069. DOI 10.1038/s41467-021-27397-z · 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'…
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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