7SHU: IgE-Fc

IgE-Fc in complex with omalizumab variant C02. Determined by X-ray diffraction at 2.75 Å resolution. Released 15 Dec 2021.

Method: X-ray diffraction
Resolution: 2.75 Å
Organism: Homo sapiens
Chains: 6
Atoms: 6,549
Mol. weight: 106.92 kDa
Ligands: NAG, PO4
Released: 15 Dec 2021

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

Secondary structure: helices and β-sheets

7SHU contains 29 α-helices and 87 β-strands across 6 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: 8 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	342-344	3
α-helix	345-346	2
α-helix	347-351	5
β-strand	355-357	3	19
β-strand	373-376	4	20
β-strand	402-404	3	19
α-helix	407-411	5
β-strand	415-419	5	20
β-strand	430-434	5	20
α-helix	435-437	3
β-strand	441	1	21
β-strand	444-447	4	22
β-strand	463-469	7	22
β-strand	470	1	21
β-strand	475-480	6	23
β-strand	483-484	2	23
α-helix	487-489	3
β-strand	491-492	2	22
α-helix	493-495	3
β-strand	496-497	2	22
β-strand	503-508	6	22
α-helix	513-518	6
β-strand	522-527	6	23
β-strand	537-540	4	23

Chain B: 13 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	340	1	7
α-helix	341-344	4
α-helix	345	1
α-helix	346-350	5
β-strand	355-358	4	7
α-helix	369-370	2
β-strand	371-376	6	8
α-helix	380-382	3
β-strand	386-390	5	7
β-strand	398-404	7	7
α-helix	407-411	5
β-strand	416-421	6	8
β-strand	429-433	5	8
α-helix	435-437	3
β-strand	441	1	9
α-helix	442-443	2
β-strand	444-449	6	10
α-helix	450-452	3
β-strand	453	1	11
β-strand	456	1	11
β-strand	459-469	11	10
β-strand	470	1	9
β-strand	475-480	6	12
β-strand	483-484	2	12
α-helix	485-486	2
α-helix	487-489	3
β-strand	490-492	3	10
α-helix	493-495	3
β-strand	496-497	2	10
β-strand	503-512	10	10
α-helix	513-518	6
β-strand	522-527	6	12
β-strand	536-541	6	12

Chain C: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	13
β-strand	11-12	2	14
β-strand	18-25	8	13
β-strand	34-40	7	15
β-strand	46-52	7	15
β-strand	58-60	3	15
β-strand	68-73	6	13
β-strand	78-83	6	13
α-helix	88-90	3
β-strand	92-102	11	15
β-strand	105-111	7	15
β-strand	115-117	3	15
β-strand	118-119	2	14

Chain D: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	16
β-strand	10-13	4	17
β-strand	19-24	6	16
β-strand	30-31	2	18
β-strand	34-35	2	18
β-strand	37-42	6	17
β-strand	49-53	5	17
β-strand	57-58	2	17
α-helix	59	1
β-strand	66-71	6	16
β-strand	74-79	6	16
α-helix	84-86	3
β-strand	89-94	6	17
α-helix	100	1
β-strand	101-102	2	17
β-strand	106-110	5	17

Chain E: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
β-strand	17-25	9	1
β-strand	34-40	7	3
β-strand	46-53	8	3
β-strand	58-60	3	3
β-strand	65	1	1
β-strand	68-73	6	1
β-strand	78-84	7	1
α-helix	88-90	3
β-strand	92-102	11	3
β-strand	105-111	7	3
β-strand	115-117	3	3
β-strand	118-119	2	2

Chain F: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	4
β-strand	10-12	3	5
β-strand	19-25	7	4
β-strand	30-31	2	6
β-strand	34-35	2	6
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	4
β-strand	74-79	6	4
α-helix	84-86	3
β-strand	89-94	6	5
α-helix	100	1
β-strand	101-102	2	5
β-strand	106-109	4	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
omalizumab variant C02 VH	C, E	protein	123	Homo sapiens
omalizumab variant C02 VL	D, F	protein	134	Homo sapiens
Immunoglobulin heavy constant epsilon	A, B	protein	220	Homo sapiens	P01854 (AlphaFold model)

Sequence of entity 1 (C, E), FASTA

>7SHU_1 omalizumab variant C02 VH (chains C, E)
SEVQLVESGGGLVQPDGSLRLSCAVSGYNITSGYSWNWIRQTPGKGLEWVASVTYDGSTN
YNPSVKGRITISRDGSKNTFYLQMNSLRAEDTAVYYCAKGNNYFGHWHFAVWGQGTLVTV
SSG

Sequence of entity 2 (D, F), FASTA

>7SHU_2 omalizumab variant C02 VL (chains D, F)
GSDIQLTQSPSSLSASVGDRVTITCRASKSVDSDGDSYMNWYQQKPGRAPKLLIYAASYL
ESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSHEDPYTFGQGTKVEIKGGSENLY
FQGGSGHHHHHHHH

Sequence of entity 3 (A, B), FASTA

>7SHU_3 Immunoglobulin heavy constant epsilon (chains A, B)
GSCADSNPRGVSAYLSRPSPFDLFIRKSPTITCLVVDLAPSKGTVNLTWSRASGKPVNHS
TRKEEKQRNGTLTVTSTLPVGTRDWIEGETYQCRVTHPHLPRALMRSTTKTSGPRAAPEV
YAFATPEWPGSRDKRTLACLIQNFMPEDISVQWLHNEVQLPDARHSTTQPRKTKGSGFFV
FSRLEVTRAEWEQKDEFICRAVHEAASPSQTVQRAVSVNP

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
PO4	Phosphate ion	O4 P	1

Water and common crystallization additives (EDO) 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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