4J4P: Ig epsilon chain C region

The complex of human IgE-Fc with two bound Fab fragments. Determined by X-ray diffraction at 2.91 Å resolution. Released 12 Mar 2014.

Method: X-ray diffraction
Resolution: 2.91 Å
Organism: Homo sapiens
Chains: 6
Atoms: 11,702
Mol. weight: 177.75 kDa
Released: 12 Mar 2014

Explore 4J4P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4J4P contains 40 α-helices and 156 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, 30 β-strands

Element	Residues	Length	Sheet
β-strand	233-239	7	1
β-strand	250-257	9	1
β-strand	265-270	6	2
β-strand	273-274	2	2
α-helix	277-279	3
β-strand	280-287	8	1
β-strand	290-300	11	1
α-helix	301-304	4
β-strand	310-316	7	2
β-strand	319-325	7	2
β-strand	326	1	3
α-helix	327-330	4
β-strand	333	1	4
β-strand	337-340	4	5
α-helix	341-344	4
α-helix	345	1
α-helix	346-350	5
β-strand	355-363	9	5
β-strand	371-376	6	6
β-strand	386-391	6	5
β-strand	397-404	8	5
β-strand	416-421	6	6
β-strand	429-433	5	6
α-helix	435-437	3
β-strand	441	1	7
β-strand	444-446	3	8
α-helix	450-452	3
β-strand	453	1	9
β-strand	456	1	9
β-strand	459-469	11	8
β-strand	470	1	7
β-strand	474-480	7	10
β-strand	483-484	2	10
α-helix	485-486	2
β-strand	491-492	2	8
β-strand	496-497	2	8
β-strand	503-512	10	8
α-helix	513-516	4
β-strand	522-528	7	10
β-strand	536-541	6	10

Chain B: 14 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	230-232	3
β-strand	233-239	7	1
β-strand	241	1	3
α-helix	246-248	3
β-strand	250-259	11	1
β-strand	265-270	6	11
β-strand	273-274	2	11
α-helix	277-279	3
β-strand	280-285	6	1
β-strand	291-300	10	1
α-helix	301-305	5
β-strand	310-316	7	11
β-strand	319-325	7	11
α-helix	327-330	4
β-strand	333	1	4
β-strand	337-340	4	12
α-helix	341-344	4
α-helix	345	1
α-helix	346-350	5
β-strand	355-363	9	12
β-strand	371-376	6	13
β-strand	386-391	6	12
β-strand	397-404	8	12
α-helix	407-411	5
β-strand	416-421	6	13
β-strand	429-433	5	13
α-helix	435-437	3
β-strand	441	1	14
β-strand	444-447	4	15
α-helix	450-452	3
β-strand	462-469	8	15
β-strand	470	1	14
β-strand	474-479	6	16
β-strand	484	1	16
α-helix	485-486	2
β-strand	491-492	2	15
α-helix	493-495	3
β-strand	496-497	2	15
β-strand	503-509	7	15
α-helix	513-518	6
β-strand	522-528	7	16
β-strand	536-537	2	16
β-strand	540-541	2	16

Chain C: 2 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	22-24	3	31
β-strand	30-31	2	32
β-strand	37-44	8	31
β-strand	53-61	9	33
β-strand	65-74	10	33
β-strand	78-82	5	33
β-strand	90-95	6	31
β-strand	100-105	6	31
α-helix	110-112	3
β-strand	114-123	10	33
β-strand	131-136	6	33
β-strand	140-142	3	33
β-strand	143-144	2	32
α-helix	150-152	3
β-strand	153-156	4	34
β-strand	169-171	3	35
β-strand	173-178	6	34
β-strand	184-187	4	36
β-strand	196-198	3	35
β-strand	202-203	2	34
β-strand	209-212	4	34
β-strand	213-217	5	35
β-strand	227-233	7	36
β-strand	238-239	2	36
β-strand	242-244	3	36

Chain D: 3 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	23	1	37
β-strand	24	1	38
β-strand	28-31	4	39
β-strand	37-42	6	38
α-helix	45-49	5
β-strand	53-58	6	39
β-strand	60	1	40
β-strand	62	1	40
α-helix	63-64	2
β-strand	65-68	4	39
β-strand	69	1	41
β-strand	73	1	41
β-strand	82-87	6	38
β-strand	90-95	6	38
β-strand	104-112	9	39
β-strand	117-120	4	39
β-strand	121	1	37
β-strand	124-128	5	39
β-strand	137-141	5	42
β-strand	153-160	8	42
β-strand	167	1	43
β-strand	172-173	2	44
β-strand	176-177	2	44
β-strand	182-184	3	42
β-strand	196-203	8	42
α-helix	205-208	4
β-strand	214-215	2	44
β-strand	220	1	43

Chain H: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	22-26	5	17
β-strand	30-31	2	18
β-strand	37-44	8	17
β-strand	54-61	8	19
β-strand	65-74	10	19
β-strand	78-82	5	19
α-helix	86-89	4
β-strand	90-95	6	17
β-strand	100-105	6	17
α-helix	110-112	3
β-strand	114-121	8	19
β-strand	133-136	4	19
β-strand	140-142	3	19
β-strand	143-144	2	18
β-strand	150	1	20
α-helix	151-152	2
β-strand	153-157	5	21
β-strand	170-178	9	21
β-strand	179	1	20
β-strand	184-187	4	22
β-strand	196-198	3	21
α-helix	199-200	2
β-strand	202-203	2	21
β-strand	209-216	8	21
β-strand	228-232	5	22
β-strand	233	1	23
α-helix	234-236	3
β-strand	238	1	23
β-strand	241-243	3	22

Chain L: 6 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	23	1	24
β-strand	24	1	25
β-strand	28-31	4	26
β-strand	36-42	7	25
α-helix	45-49	5
β-strand	53-58	6	26
β-strand	65-68	4	26
β-strand	69	1	27
β-strand	73	1	27
α-helix	74-75	2
β-strand	82-87	6	25
β-strand	90-96	7	25
β-strand	104-112	9	26
β-strand	117-120	4	26
β-strand	121	1	24
β-strand	124-128	5	26
α-helix	131-133	3
β-strand	134	1	28
β-strand	138-141	4	29
α-helix	142-144	3
β-strand	153-162	10	29
β-strand	163	1	28
β-strand	167-173	7	30
β-strand	176-177	2	30
β-strand	182-184	3	29
α-helix	185-187	3
β-strand	188-189	2	29
β-strand	195-203	9	29
α-helix	205-210	6
β-strand	214-220	7	30
β-strand	223-229	7	30

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ig epsilon chain C region	A, B	protein	323	Homo sapiens	P01854 (AlphaFold model)
Immunoglobulin G Fab Fragment Heavy Chain	C, H	protein	249	Homo sapiens
Immunoglobulin G Fab Fragment Light Chain	D, L	protein	235	Homo sapiens

Sequence of entity 1 (A, B), FASTA

>4J4P_1 Ig epsilon chain C region (chains A, B)
CSRDFTPPTVKILQSSCDGGGHFPPTIQLLCLVSGYTPGTIQITWLEDGQVMDVDLSTAS
TTQEGELASTQSELTLSQKHWLSDRTYTCQVTYQGHTFEDSTKKCADSNPRGVSAYLSRP
SPFDLFIRKSPTITCLVVDLAPSKGTVQLTWSRASGKPVNHSTRKEEKQRNGTLTVTSTL
PVGTRDWIEGETYQCRVTHPHLPRALMRSTTKTSGPRAAPEVYAFATPEWPGSRDKRTLA
CLIQNFMPEDISVQWLHNEVQLPDARHSTTQPRKTKGSGFFVFSRLEVTRAEWEQKDEFI
CRAVHEAASPSQTVQRAVSVNPG

Sequence of entity 2 (C, H), FASTA

>4J4P_2 Immunoglobulin G Fab Fragment Heavy Chain (chains C, H)
MEWIWIFLFLLSVTTGVHSQVQLQQSGPGLVKPSQTLSLTCGISGDSVSSNSAAWNWLRQ
SPSRGLEWLGRTYYRSKWYNDYAVSMKSRITINPDTSRNQFSLQLNSVTPEDTAVYYCAR
DGEISYDYYYYGMDVWGRGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFP
EPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKV
DKKVEPKSC

Sequence of entity 3 (D, L), FASTA

>4J4P_3 Immunoglobulin G Fab Fragment Light Chain (chains D, L)
MDWSPLLLTLLAHCTGSWAQSVLTQPPSASGTPGQRVTISCSGSSSNIGNNGVNWYQQVP
GKPPKLLIYYDDLLPSGVSDRFSGSKSGTSASLAISGLQSEDEADYYCEAWDDSLDGVVF
GGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKA
GVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Primary citation

Human immunoglobulin E flexes between acutely bent and extended conformations. Drinkwater, N., Cossins, B.P., Keeble, A.H. et al. Nat Struct Mol Biol (2014) 21:397-404. DOI 10.1038/nsmb.2795 · 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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