7SHY: IgE-Fc

IgE-Fc in complex with omalizumab scFv. Determined by X-ray diffraction at 3.0 Å resolution. Released 15 Dec 2021.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 12
Atoms: 14,125
Mol. weight: 227.37 kDa
Ligands: NAG, MAN
Released: 15 Dec 2021

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

Secondary structure: helices and β-sheets

7SHY contains 65 α-helices and 176 β-strands across 12 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: 10 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	337-340	4	13
α-helix	341-344	4
α-helix	345-349	5
β-strand	355-363	9	13
α-helix	368-370	3
β-strand	371-376	6	14
β-strand	386-391	6	13
β-strand	397-404	8	13
α-helix	407-412	6
β-strand	416-421	6	14
β-strand	429-433	5	14
β-strand	441	1	15
α-helix	442-443	2
β-strand	444-449	6	16
α-helix	450-452	3
β-strand	459-469	11	16
β-strand	470	1	15
β-strand	475-479	5	17
β-strand	484	1	17
α-helix	485-486	2
α-helix	487-489	3
β-strand	490-492	3	16
α-helix	493-495	3
β-strand	496-497	2	16
β-strand	503-512	10	16
α-helix	513-518	6
β-strand	522-527	6	17
β-strand	536-541	6	17

Chain B: 10 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	337-340	4	33
α-helix	341-344	4
α-helix	345-349	5
β-strand	355-363	9	33
α-helix	368-370	3
β-strand	371-376	6	34
β-strand	386-391	6	33
β-strand	397-404	8	33
α-helix	407-411	5
β-strand	416-421	6	34
α-helix	428	1
β-strand	429-433	5	34
β-strand	441	1	35
α-helix	442-443	2
β-strand	444-449	6	36
α-helix	450-453	4
β-strand	459-469	11	36
β-strand	470	1	35
β-strand	475-480	6	37
β-strand	483-484	2	37
α-helix	485-486	2
β-strand	490-492	3	36
α-helix	493-495	3
β-strand	496-497	2	36
β-strand	503-512	10	36
α-helix	513-518	6
β-strand	522-527	6	37
β-strand	536-541	6	37

Chain C: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	6
β-strand	10-12	3	2
β-strand	18-25	8	6
β-strand	34-40	7	2
β-strand	46-53	8	2
β-strand	58-60	3	2
β-strand	68-73	6	6
α-helix	74-76	3
β-strand	78-83	6	6
α-helix	88-90	3
β-strand	92-102	11	2
β-strand	105-111	7	2
β-strand	115-119	5	2

Chains D and L: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-7	4	11
β-strand	10-13	4	2
β-strand	19-25	7	11
β-strand	30-31	2	12
β-strand	34-35	2	12
β-strand	37-42	6	2
β-strand	49-53	5	2
β-strand	57-58	2	2
α-helix	59	1
β-strand	66-71	6	11
β-strand	74-79	6	11
α-helix	84-86	3
β-strand	88-94	7	2
α-helix	100	1
β-strand	101-102	2	2
β-strand	106-110	5	2

Chain E: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	29
β-strand	6-7	2	30
β-strand	10-12	3	5
β-strand	18-23	6	30
β-strand	25	1	29
β-strand	34-40	7	5
β-strand	46-53	8	5
β-strand	58-60	3	5
β-strand	68-73	6	30
α-helix	74-76	3
β-strand	78-83	6	30
α-helix	88-90	3
β-strand	92-102	11	5
β-strand	105-110	6	5
β-strand	115-119	5	5

Chain F: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	31
β-strand	10-13	4	5
β-strand	19-25	7	31
β-strand	30-31	2	32
β-strand	34-35	2	32
β-strand	37-42	6	5
β-strand	49-53	5	5
β-strand	57-58	2	5
α-helix	59	1
β-strand	66-71	6	31
β-strand	74-79	6	31
α-helix	84-86	3
β-strand	88-94	7	5
α-helix	100	1
β-strand	101-102	2	5
β-strand	106-110	5	5

Chain G: 12 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	337-340	4	18
α-helix	341-344	4
α-helix	345-349	5
β-strand	355-363	9	18
α-helix	369-370	2
β-strand	371-376	6	19
α-helix	380-382	3
β-strand	386-391	6	18
β-strand	397-404	8	18
α-helix	407-412	6
β-strand	415-421	7	19
β-strand	429-434	6	19
α-helix	435-437	3
β-strand	441	1	20
α-helix	442-443	2
β-strand	444-449	6	21
α-helix	450-452	3
β-strand	453	1	22
β-strand	456	1	22
β-strand	459-469	11	21
β-strand	470	1	20
β-strand	475-479	5	23
β-strand	484	1	23
α-helix	485-486	2
α-helix	487-489	3
β-strand	490-492	3	21
α-helix	493-495	3
β-strand	496-497	2	21
β-strand	503-512	10	21
α-helix	513-518	6
β-strand	522-527	6	23
β-strand	536-541	6	23

Chain H: 11 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	337-340	4	24
α-helix	341-344	4
α-helix	345-349	5
β-strand	355-363	9	24
α-helix	368-370	3
β-strand	371-376	6	25
α-helix	380-385	6
β-strand	386-391	6	24
β-strand	397-404	8	24
α-helix	407-411	5
β-strand	416-421	6	25
β-strand	429-433	5	25
β-strand	441	1	26
α-helix	442-443	2
β-strand	444-449	6	27
α-helix	450-452	3
β-strand	460-469	10	27
β-strand	470	1	26
β-strand	475-479	5	28
β-strand	484	1	28
α-helix	485-486	2
α-helix	487-489	3
β-strand	490-492	3	27
α-helix	493-495	3
β-strand	496-497	2	27
β-strand	503-511	9	27
α-helix	513-518	6
β-strand	522-527	6	28
β-strand	536-541	6	28

3 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Omalizumab VH	C, E, I, K	protein	122	Homo sapiens
Omalizumab VL	D, F, J, L	protein	134	Homo sapiens
IgE Fc	A, B, G, H	protein	247	Homo sapiens	P01854 (AlphaFold model)

Sequence of entity 1 (C, E, I, K), FASTA

>7SHY_1 Omalizumab VH (chains C, E, I, K)
SEVQLVESGGGLVQPGGSLRLSCAVSGYSITSGYSWNWIRQAPGKGLEWVASITYDGSTN
YNPSVKGRITISRDDSKNTFYLQMNSLRAEDTAVYYCARGSHYFGHWHFAVWGQGTLVTV
SS

Sequence of entity 2 (D, F, J, L), FASTA

>7SHY_2 Omalizumab VL (chains D, F, J, L)
GSDIQLTQSPSSLSASVGDRVTITCRASQSVDYDGDSYMNWYQQKPGKAPKLLIYAASYL
ESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSHEDPYTFGQGTKVEIKGGSENLY
FQGGSGHHHHHHHH

Sequence of entity 3 (A, B, G, H), FASTA

>7SHY_3 IgE Fc (chains A, B, G, H)
APMAEGGGQNHHHHHHHHGGENLYFQGGSCADSNPRGVSAYLSRPSPFDLFIRKSPTITC
LVVDLAPSKGTVNLTWSRASGKPVNHSTRKEEKQRNGTLTVTSTLPVGTRDWIEGETYQC
RVTHPHLPRALMRSTTKTSGPRAAPEVYAFATPEWPGSRDKRTLACLIQNFMPEDISVQW
LHNEVQLPDARHSTTQPRKTKGSGFFVFSRLEVTRAEWEQKDEFICRAVHEAASPSQTVQ
RAVSVNP

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3
MAN	alpha-D-mannopyranose	C6 H12 O6	1

Water and common crystallization additives (GOL) are not listed.

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 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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