5MOL: Human IgE-Fc crystal structure

Human IgE-Fc crystal structure. Determined by X-ray diffraction at 1.75 Å resolution. Released 10 Jan 2018.

Method: X-ray diffraction
Resolution: 1.75 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,750
Mol. weight: 75.75 kDa
Ligands: PG0, AE3
Released: 10 Jan 2018

Explore 5MOL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5MOL contains 37 α-helices and 52 β-strands across 2 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: 18 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	235-239	5	1
α-helix	240-241	2
α-helix	246-248	3
β-strand	250-259	11	1
β-strand	264-270	7	2
β-strand	273-274	2	2
α-helix	275-276	2
α-helix	277-279	3
β-strand	280-287	8	1
β-strand	290-300	11	1
α-helix	301-305	5
β-strand	310-316	7	2
β-strand	319-325	7	2
α-helix	327-330	4
α-helix	333-335	3
β-strand	337-340	4	3
α-helix	341-344	4
α-helix	345	1
α-helix	346-351	6
β-strand	355-363	9	3
α-helix	369-370	2
β-strand	371-376	6	4
β-strand	388-391	4	3
β-strand	397-404	8	3
α-helix	407-411	5
β-strand	416-421	6	4
β-strand	429-433	5	4
β-strand	441	1	5
α-helix	442-443	2
β-strand	444-449	6	6
α-helix	450-453	4
β-strand	459-469	11	6
β-strand	470	1	5
β-strand	475-480	6	7
β-strand	483-484	2	7
α-helix	485-486	2
α-helix	487-489	3
β-strand	490-492	3	6
α-helix	493-495	3
β-strand	496-497	2	6
β-strand	503-512	10	6
α-helix	513-518	6
β-strand	522-527	6	7
β-strand	536-541	6	7

Chain B: 19 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	226-228	3
β-strand	234-239	6	1
α-helix	240-241	2
α-helix	246-248	3
β-strand	250-259	11	1
β-strand	264-270	7	8
β-strand	273-274	2	8
α-helix	275-276	2
α-helix	277-279	3
β-strand	280-287	8	1
β-strand	290-300	11	1
α-helix	301-305	5
β-strand	310-316	7	8
β-strand	319-325	7	8
α-helix	327-330	4
α-helix	333-336	4
β-strand	337-340	4	9
α-helix	341-344	4
α-helix	345-349	5
β-strand	355-363	9	9
α-helix	364	1
α-helix	368-370	3
β-strand	371-376	6	10
α-helix	380-385	6
β-strand	386-391	6	9
β-strand	397-404	8	9
α-helix	407-411	5
β-strand	416-421	6	10
β-strand	429-433	5	10
β-strand	441	1	11
α-helix	442-443	2
β-strand	444-449	6	12
α-helix	450-452	3
β-strand	459-469	11	12
β-strand	470	1	11
β-strand	475-480	6	13
β-strand	483-484	2	13
α-helix	487-489	3
β-strand	490-492	3	12
α-helix	493-495	3
β-strand	496-497	2	12
β-strand	503-512	10	12
α-helix	513-518	6
β-strand	522-527	6	13
β-strand	536-541	6	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ig epsilon chain C region	A, B	protein	327	Homo sapiens	P01854 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5MOL_1 Ig epsilon chain C region (chains A, B)
DIVASRDFTPPTVKILQSSCDGGGHFPPTIQLLCLVSGYTPGTIQITWLEDGQVMDVDLS
TASTTQEGELASTQSELTLSQKHWLSDRTYTCQVTYQGHTFEDSTKKCADSNPRGVSAYL
SRPSPFDLFIRKSPTITCLVVDLAPSKGTVQLTWSRASGKPVNHSTRKEEKQRNGTLTVT
STLPVGTRDWIEGETYQCRVTHPHLPRALMRSTTKTSGPRAAPEVYAFATPEWPGSRDKR
TLACLIQNFMPEDISVQWLHNEVQLPDARHSTTQPRKTKGSGFFVFSRLEVTRAEWEQKD
EFICRAVHEAASPSQTVQRAVSVNPGK

Ligands and cofactors

ID	Name	Formula	Copies
PG0	2-(2-methoxyethoxy)ethanol	C5 H12 O3	2
AE3	2-(2-ethoxyethoxy)ethanol	C6 H14 O3	1

Water and common crystallization additives (EDO, PEG) are not listed.

Primary citation

Thermal sensitivity and flexibility of the C epsilon 3 domains in immunoglobulin E. Dore, K.A., Davies, A.M., Drinkwater, N. et al. Biochim Biophys Acta (2017) 1865:1336-1347. DOI 10.1016/j.bbapap.2017.08.005 · PubMed

Other PDB entries of the same protein (UniProt P01854 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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
4GT7 2.61 Å, An engineered disulfide bond reversibly traps the IgE-Fc3-4 in a closed, non-receptor…

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