1P9M: Interleukin-6 receptor beta chain

Crystal structure of the hexameric human IL-6/IL-6 alpha receptor/gp130 complex. Determined by X-ray diffraction at 3.65 Å resolution. Released 1 Jul 2003.

Method: X-ray diffraction
Resolution: 3.65 Å
Organism: Homo sapiens
Chains: 3
Atoms: 5,322
Mol. weight: 78.25 kDa
Released: 1 Jul 2003

Explore 1P9M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1P9M contains 13 α-helices and 53 β-strands across 3 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: 6 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	7-10	4	1
β-strand	17	1	2
β-strand	22	1	3
β-strand	25-28	4	1
α-helix	30-35	6
β-strand	44-46	3	4
β-strand	58-59	2	1
β-strand	64-66	3	1
β-strand	69	1	3
β-strand	80-82	3	4
β-strand	92-95	4	4
β-strand	101	1	2
α-helix	103-107	5
β-strand	108-111	4	5
β-strand	114-115	2	6
β-strand	120	1	6
β-strand	121-122	2	7
β-strand	123-125	3	5
β-strand	135-142	8	8
β-strand	145-146	2	8
α-helix	147-149	3
β-strand	150-151	2	8
β-strand	160-161	2	7
β-strand	172-179	8	8
β-strand	185-186	2	8
β-strand	190-192	3	8
β-strand	198-199	2	6
α-helix	200-203	4
β-strand	207-209	3	9
β-strand	218-221	4	9
β-strand	233-241	9	10
β-strand	248-249	2	10
α-helix	250	1
β-strand	261-264	4	9
β-strand	273-281	9	10
α-helix	288-290	3
β-strand	295-297	3	10

Chain B: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	23-26	4
α-helix	28-43	16
α-helix	69-71	3
α-helix	80-101	22
α-helix	109-128	20
α-helix	143-151	9
α-helix	156-182	27

Chain C: 0 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	104	1	11
β-strand	111	1	12
β-strand	128-133	6	13
β-strand	140-145	6	13
β-strand	146-149	4	14
β-strand	154-157	4	14
β-strand	159	1	12
β-strand	169-174	6	13
β-strand	175-176	2	15
β-strand	181-182	2	15
β-strand	187-189	3	13
β-strand	195	1	11
β-strand	201-208	8	16
β-strand	211-220	10	16
β-strand	232-234	3	17
β-strand	235-240	6	18
β-strand	247-250	4	18
β-strand	258-260	3	16
β-strand	269-272	4	18
β-strand	275-277	3	17
β-strand	281	1	17
β-strand	291-293	3	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Interleukin-6 receptor beta chain	A	protein	299	Homo sapiens	P40189 (AlphaFold model)
Interleukin-6	B	protein	186	Homo sapiens	P05231 (AlphaFold model)
Interleukin-6 receptor alpha chain	C	protein	201	Homo sapiens	P08887 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1P9M_1 Interleukin-6 receptor beta chain (chains A)
ELLDPCGYISPESPVVQLHSNFTAVCVLKEKCMDYFHVNANYIVWKTNHFTIPKEQYTII
NRTASSVTFTDIASLNIQLTCNILTFGQLEQNVYGITIISGLPPEKPKNLSCIVNEGKKM
RCEWDGGRETHLETNFTLKSEWATHKFADCKAKRDTPTSCTVDYSTVYFVNIEVWVEAEN
ALGKVTSDHINFDPVYKVKPNPPHNLSVINSEELSSILKLTWTNPSIKSVIILKYNIQYR
TKDASTWSQIPPEDTASTRSSFTVQDLKPFTEYVFRIRCMKEDGKGYWSDWSEEASGIT

Sequence of entity 2 (B), FASTA

>1P9M_2 Interleukin-6 (chains B)
APPVPPGEDSKDVAAPHRQPLTSSERIDKQIRYILDGISALRKETCNKSNMCESSKEALA
ENNLNLPKMAEKDGCFQSGFNEETCLVKIITGLLEFEVYLEYLQNRFESSEEQARAVQMS
TKVLIQFLQKKAKNLDAITTPDPTTNASLLTKLQAQNQWLQDMTTHLILRSFKEFLQSSL
RALRQM

Sequence of entity 3 (C), FASTA

>1P9M_3 Interleukin-6 receptor alpha chain (chains C)
EEPQLSCFRKSPLSNVVCEWGPRSTPSLTTKAVLLVRKFQNSPAEDFQEPCQYSQESQKF
SCQLAVPEGDSSFYIVSMCVASSVGSKFSKTQTFQGCGILQPDPPANITVTAVARNPRWL
SVTWQDPHSWNSSFYRLRFELRYRAERSKTFTTWMVKDLQHHCVIHDAWSGLRHVVQLRA
QEEFGQGEWSEWSPEAMGTPW

Primary citation

Hexameric Structure and Assembly of the Interleukin-6/IL-6 alpha-Receptor/gp130 Complex. Boulanger, M.J., Chow, D.C., Brevnova, E.E. et al. Science (2003) 300:2101-2104. DOI 10.1126/science.1083901 · PubMed

Other PDB entries of the same protein (UniProt P40189 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3L5I 1.9 Å, Crystal structure of FnIII domains of human GP130 (Domains 4-6)
1BQU 2.0 Å, Cytokyne-binding region of GP130
1I1R 2.4 Å, Crystal structure of a cytokine/receptor complex
1PVH 2.5 Å, Crystal structure of leukemia inhibitory factor in complex with gp130
8D74 3.03 Å, Cryo-EM structure of human CNTF signaling complex: model containing the interaction core…
3L5J 3.04 Å, Crystal structure of FnIII domains of human GP130 (Domains 4-6)
8D82 3.22 Å, Cryo-EM structure of human IL-6 signaling complex in detergent: model containing full…
8UPA 3.3 Å, Structure of gp130 in complex with a de novo designed IL-6 mimetic
7U7N 3.47 Å, IL-27 quaternary receptor signaling complex
8DPS 3.47 Å, The structure of the interleukin 11 signalling complex, truncated gp130
8D6A 3.54 Å, Cryo-EM structure of human LIF signaling complex: model containing the interaction core…
8V2A 3.59 Å, Cryo-EM structure of human type I OSM receptor complex: model for assembly core region

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