7SI0: IgE-Fc

IgE-Fc in complex with 813. 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: 14,043
Mol. weight: 226.33 kDa
Released: 15 Dec 2021

Explore 7SI0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7SI0 contains 62 α-helices and 173 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: 8 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	337-340	4	25
α-helix	341-344	4
α-helix	345-349	5
β-strand	355-362	8	25
β-strand	371-376	6	26
β-strand	386-391	6	25
β-strand	397-404	8	25
α-helix	407-411	5
β-strand	415-421	7	26
β-strand	429-434	6	26
β-strand	441	1	27
α-helix	442-443	2
β-strand	444-449	6	28
β-strand	453	1	29
β-strand	456	1	29
β-strand	459-469	11	28
β-strand	470	1	27
β-strand	475-480	6	30
β-strand	483-484	2	30
α-helix	485-486	2
α-helix	487-489	3
β-strand	490-492	3	28
α-helix	493-495	3
β-strand	496-497	2	28
β-strand	503-512	10	28
α-helix	513-518	6
β-strand	522-527	6	30
β-strand	536-541	6	30

Chain B: 10 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	337-340	4	1
α-helix	341-344	4
α-helix	345-349	5
β-strand	355-361	7	1
β-strand	371-376	6	2
α-helix	380-382	3
β-strand	386-391	6	1
β-strand	397-404	8	1
α-helix	407-411	5
β-strand	416-421	6	2
β-strand	429-433	5	2
β-strand	441	1	3
α-helix	442-443	2
β-strand	444-449	6	4
α-helix	452-453	2
β-strand	459-469	11	4
β-strand	470	1	3
β-strand	475-480	6	5
β-strand	483-484	2	5
α-helix	485-486	2
α-helix	487-489	3
β-strand	490-492	3	4
α-helix	493-495	3
β-strand	496-497	2	4
β-strand	503-512	10	4
α-helix	513-516	4
β-strand	522-527	6	5
β-strand	536-541	6	5

Chain C: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	31
β-strand	11-12	2	32
β-strand	18-25	8	31
β-strand	34-40	7	33
β-strand	47-52	6	33
β-strand	58-60	3	33
α-helix	62-64	3
β-strand	68-73	6	31
β-strand	78-83	6	31
α-helix	88-90	3
β-strand	92-102	11	33
β-strand	105-111	7	33
β-strand	115-117	3	33
β-strand	118-119	2	32

Chain D: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	34
β-strand	10-13	4	33
β-strand	19-25	7	34
β-strand	30-31	2	35
β-strand	34-35	2	35
β-strand	37-42	6	33
β-strand	49-53	5	33
β-strand	57-58	2	33
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	33
α-helix	100	1
β-strand	101-102	2	33
β-strand	106-110	5	33

Chain E: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	11-12	2	11
β-strand	17-25	9	10
α-helix	29-31	3
β-strand	34-40	7	12
β-strand	46-52	7	12
β-strand	58-60	3	12
β-strand	68-73	6	10
α-helix	74-76	3
β-strand	78-84	7	10
α-helix	88-90	3
β-strand	92-102	11	12
β-strand	105-111	7	12
β-strand	115-117	3	12
β-strand	118-119	2	11

Chains F and L: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	10-13	4	12
β-strand	19-25	7	13
β-strand	30-31	2	14
β-strand	34-35	2	14
β-strand	37-42	6	12
β-strand	48-53	6	12
β-strand	57-58	2	12
α-helix	59	1
β-strand	66-71	6	13
β-strand	74-79	6	13
α-helix	84-86	3
β-strand	89-94	6	12
α-helix	100	1
β-strand	101-102	2	12
β-strand	106-110	5	12

Chain G: 12 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	337-340	4	15
α-helix	342-344	3
α-helix	345	1
α-helix	346-350	5
β-strand	355-361	7	15
α-helix	369-370	2
β-strand	371-376	6	16
α-helix	383-385	3
β-strand	386-391	6	15
β-strand	397-404	8	15
α-helix	407-411	5
β-strand	415-421	7	16
β-strand	429-434	6	16
β-strand	441	1	17
α-helix	442-443	2
β-strand	444-449	6	18
α-helix	452-453	2
β-strand	459-469	11	18
β-strand	470	1	17
β-strand	475-480	6	19
β-strand	483-484	2	19
α-helix	485-486	2
α-helix	487-489	3
β-strand	490-492	3	18
α-helix	493-495	3
β-strand	496-497	2	18
β-strand	503-512	10	18
α-helix	513-518	6
β-strand	522-527	6	19
β-strand	536-541	6	19

Chain H: 9 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	337-340	4	20
α-helix	345-349	5
β-strand	355-361	7	20
α-helix	369-370	2
β-strand	371-376	6	21
α-helix	380-382	3
β-strand	386-391	6	20
β-strand	397-404	8	20
α-helix	407-411	5
β-strand	415-421	7	21
β-strand	429-434	6	21
β-strand	441	1	22
α-helix	442-443	2
β-strand	444-449	6	23
α-helix	450-453	4
β-strand	459-469	11	23
β-strand	470	1	22
β-strand	475-480	6	24
β-strand	483-484	2	24
α-helix	485-486	2
β-strand	490-492	3	23
α-helix	493-495	3
β-strand	496-497	2	23
β-strand	503-512	10	23
α-helix	513-518	6
β-strand	522-527	6	24
β-strand	536-541	6	24

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
IgE Fc	A, B, G, H	protein	247	Homo sapiens	P01854 (AlphaFold model)
813 Variable fragment Heavy chain	C, E, I, K	protein	123	Homo sapiens
813 Variable fragment Light chain	D, F, J, L	protein	134	Homo sapiens

Sequence of entity 1 (A, B, G, H), FASTA

>7SI0_1 IgE Fc (chains A, B, G, H)
APMAEGGGQNHHHHHHHHGGENLYFQGGSCADSNPRGVSAYLSRPSPFDLFIRKSPTITC
LVVDLAPSKGTVNLTWSRASGKPVNHSTRKEEKQRNGTLTVTSTLPVGTRDWIEGETYQC
RVTHPHLPRALMRSTTKTSGPRAAPEVYAFATPEWPGSRDKRTLACLIQNFMPEDISVQW
LHNEVQLPDARHSTTQPRKTKGSGFFVFSRLEVTRAEWEQKDEFICRAVHEAASPSQTVQ
RAVSVNP

Sequence of entity 2 (C, E, I, K), FASTA

>7SI0_2 813 Variable fragment Heavy chain (chains C, E, I, K)
SEVQLVESGGGLVQPDGSLRLSCAVSGYSITSGYSWNWIRQAPGKGLEWVASVTYDGSTN
YNPSVKGRITISRDDSKNTFYLQMNSLRAEDTAVYYCARGSHYFGHWHFAVWGQGTLVTV
SSG

Sequence of entity 3 (D, F, J, L), FASTA

>7SI0_3 813 Variable fragment Light chain (chains D, F, J, L)
GSDIQLTQSPSSLSASVGDRVTITCRASQSVDSDGDSYMNWYQQKPGKAPKLLIYAASYL
ESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSHEDPYTFGQGTKVEIKGGSENLY
FQGGSGHHHHHHHH

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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