3H9Z: IgE-Fc3-4 domains

Crystal structure of the IgE-Fc3-4 domains. Determined by X-ray diffraction at 2.45 Å resolution. Released 8 Sept 2009.

Method: X-ray diffraction
Resolution: 2.45 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,954
Mol. weight: 102.43 kDa
Released: 8 Sept 2009

Explore 3H9Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3H9Z contains 40 α-helices and 72 β-strands across 4 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, 18 β-strands

Element	Residues	Length	Sheet
β-strand	337-341	5	1
α-helix	342-344	3
α-helix	345	1
α-helix	346-350	5
β-strand	355-362	8	1
β-strand	371-376	6	2
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
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
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	337-340	4	6
α-helix	341-344	4
α-helix	345	1
α-helix	346-350	5
β-strand	355-361	7	6
β-strand	371-376	6	7
α-helix	380-382	3
β-strand	386-392	7	6
β-strand	396-404	9	6
α-helix	407-411	5
β-strand	416-421	6	7
β-strand	429-433	5	7
β-strand	441	1	8
α-helix	442-443	2
β-strand	444-449	6	9
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, 18 β-strands

Element	Residues	Length	Sheet
β-strand	337-340	4	11
α-helix	341-344	4
α-helix	345	1
α-helix	346-350	5
β-strand	355-362	8	11
β-strand	371-376	6	12
α-helix	380-382	3
β-strand	386-391	6	11
β-strand	397-404	8	11
α-helix	407-412	6
β-strand	415-421	7	12
β-strand	429-434	6	12
β-strand	441	1	13
α-helix	442-443	2
β-strand	444-449	6	14
α-helix	450-453	4
β-strand	459-469	11	14
β-strand	470	1	13
β-strand	475-480	6	15
β-strand	483-484	2	15
α-helix	485-486	2
α-helix	487-489	3
β-strand	490-492	3	14
α-helix	493-495	3
β-strand	496-497	2	14
β-strand	503-512	10	14
α-helix	513-518	6
β-strand	522-527	6	15
β-strand	536-541	6	15

Chain D: 11 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	337-341	5	1
α-helix	342-344	3
α-helix	345	1
α-helix	346-350	5
β-strand	355-362	8	1
β-strand	371-376	6	16
α-helix	384-385	2
β-strand	386-391	6	1
β-strand	397-404	8	1
α-helix	407-411	5
β-strand	416-421	6	16
β-strand	429-433	5	16
β-strand	441	1	17
α-helix	442-443	2
β-strand	444-449	6	18
α-helix	450-453	4
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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ig epsilon chain C region	A, B, C, D	protein	223	Homo sapiens	P01854 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>3H9Z_1 Ig epsilon chain C region (chains A, B, C, D)
ADPCADSNPRGVSAYLSRPSPFDLFIRKSPTITCLVVDLAPSKGTVQLTWSRASGKPVQH
STRKEEKQRNGTLTVTSTLPVGTRDWIEGETYQCRVTHPHLPRALMRSTTKTSGPRAAPE
VYAFATPEWPGSRDKRTLACLIQNFMPEDISVQWLHNEVQLPDARHSTTQPRKTKGSGFF
VFSRLEVTRAEWEQKDEFICRAVHEAASPSQTVQRAVSVNPGK

Primary citation

Conformational flexibility in immunoglobulin E-Fc 3-4 revealed in multiple crystal forms. Wurzburg, B.A., Jardetzky, T.S. J Mol Biol (2009) 393:176-190. DOI 10.1016/j.jmb.2009.08.012 · 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
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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