7MXI: IgE-Fc

IgE-Fc in complex with DARPins E2_79 and E3_53. Determined by X-ray diffraction at 2.8 Å resolution. Released 28 Jul 2021.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: Homo sapiens, synthetic construct
Chains: 6
Atoms: 7,485
Mol. weight: 125.46 kDa
Released: 28 Jul 2021

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

Secondary structure: helices and β-sheets

7MXI contains 57 α-helices and 38 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: 10 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	336-340	5	1
α-helix	342-344	3
α-helix	345	1
α-helix	346-350	5
β-strand	355-362	8	1
α-helix	369-370	2
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
β-strand	444-449	6	4
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	513-518	6
β-strand	522-527	6	5
β-strand	536-541	6	5

Chain B: 10 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	336-340	5	6
α-helix	341-344	4
α-helix	345	1
α-helix	346-350	5
β-strand	355-362	8	6
α-helix	365-366	2
β-strand	371-376	6	7
β-strand	386-391	6	6
β-strand	397-404	8	6
α-helix	407-411	5
β-strand	416-421	6	7
β-strand	429-433	5	7
β-strand	441	1	8
β-strand	444-449	6	9
α-helix	450-452	3
β-strand	459-469	11	9
β-strand	470	1	8
β-strand	475-480	6	10
β-strand	483-484	2	10
α-helix	485-486	2
α-helix	487-489	3
β-strand	490-492	3	9
α-helix	493-495	3
β-strand	496-497	2	9
β-strand	503-512	10	9
α-helix	513-518	6
β-strand	522-527	6	10
β-strand	536-541	6	10

Chain C: 11 helices, 0 β-strands

Element	Residues	Length
α-helix	14-24	11
α-helix	27-35	9
α-helix	50-57	8
α-helix	60-68	9
α-helix	83-90	8
α-helix	93-101	9
α-helix	116-123	8
α-helix	126-134	9
α-helix	141-143	3
α-helix	149-155	7
α-helix	159-165	7

Chain D: 10 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	14-24	11
α-helix	27-35	9
α-helix	50-57	8
α-helix	60-68	9
α-helix	83-89	7
α-helix	93-101	9
α-helix	116-122	7
α-helix	126-134	9
β-strand	142	1	11
β-strand	148	1	11
α-helix	149-155	7
α-helix	159-162	4

Chain E: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	17-24	8
α-helix	27-35	9
α-helix	50-57	8
α-helix	60-68	9
α-helix	83-89	7
α-helix	93-101	9
α-helix	116-123	8
α-helix	126-133	8

Chain F: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	17-24	8
α-helix	27-35	9
α-helix	50-56	7
α-helix	60-68	9
α-helix	83-89	7
α-helix	93-101	9
α-helix	116-123	8
α-helix	126-133	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
IgE Fc	A, B	protein	247	Homo sapiens	P01854 (AlphaFold model)
DARPin E3_53	C, D	protein	173	synthetic construct
Anti-IgE Inhibitor E2_79	E, F	protein	143	synthetic construct	L7MTK7

Sequence of entity 1 (A, B), FASTA

>7MXI_1 IgE Fc (chains A, B)
APMAEGGGQNHHHHHHHHGGENLYFQGGSCADSNPRGVSAYLSRPSPFDLFIRKSPTITC
LVVDLAPSKGTVNLTWSRASGKPVNHSTRKEEKQRNGTLTVTSTLPVGTRDWIEGETYQC
RVTHPHLPRALMRSTTKTSGPRAAPEVYAFATPEWPGSRDKRTLACLIQNFMPEDISVQW
LHNEVQLPDARHSTTQPRKTKGSGFFVFSRLEVTRAEWEQKDEFICRAVHEAASPSQTVQ
RAVSVNP

Sequence of entity 2 (C, D), FASTA

>7MXI_2 DARPin E3_53 (chains C, D)
MRGSHHHHHHGSDDDDKSSDLGKKLLEAARAGQDDEVRILMANGADVNAIDHNGTTPLHL
AAYAGHLEIVEVLLKHGADVNARDLRGFTPLHLAAIDGHLEIVEVLLKYGADVNADDDYG
TTPLHLAAQYGHMEIVEVLLKYGADVNAQDKFGKTAFDISIDNGNEDLAEILQ

Sequence of entity 3 (E, F), FASTA

>7MXI_3 Anti-IgE Inhibitor E2_79 (chains E, F)
MRGSHHHHHHGSDDDDKSSDLGKKLLEAARAGQDDEVRILTANGADVNANDYWGHTPLHL
AAMLGHLEIVEVLLKNGADVNATGNTGRTPLHLAAWADHLEIVEVLLKHGADVNAQDKFG
KTAFDISIDNGNEDLAEILQKLN

Primary citation

Structure-guided design of ultrapotent disruptive IgE inhibitors to rapidly terminate acute allergic reactions. Pennington, L.F., Gasser, P., Brigger, D. et al. J Allergy Clin Immunol (2021) 148:1049-1060. DOI 10.1016/j.jaci.2021.03.050 · 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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