8D82: Soluble interleukin-6 receptor subunit alpha

Name: PDB 8D82: Cryo-EM structure of human IL-6 signaling complex in detergent: model containing full extracellular domains
Published: 2023-03-29
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: cytokine

Cryo-EM structure of human IL-6 signaling complex in detergent: model containing full extracellular domains. Determined by electron microscopy at 3.22 Å resolution. Released 29 Mar 2023.

Method: Electron microscopy
Resolution: 3.22 Å
Organism: Homo sapiens
Chains: 6
Atoms: 17,366
Mol. weight: 281.46 kDa
Ligands: NAG
Released: 29 Mar 2023

Explore 8D82 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8D82 contains 56 α-helices and 158 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.

Chains A and E: 9 helices, 52 β-strands

Element	Residues	Length	Sheet
β-strand	26-27	2	10
β-strand	29-32	4	11
β-strand	37	1	12
β-strand	44-50	7	11
α-helix	52-58	7
β-strand	66-68	3	12
β-strand	73	1	12
β-strand	80-81	2	11
β-strand	86-91	6	11
β-strand	98-105	8	12
β-strand	113-121	9	12
β-strand	130-137	8	13
β-strand	142-147	6	13
β-strand	157-163	7	14
α-helix	169-171	3
β-strand	172-173	2	14
α-helix	174-175	2
β-strand	183	1	13
β-strand	194-201	8	14
β-strand	206-208	3	14
β-strand	212-214	3	14
β-strand	220-221	2	13
α-helix	223-225	3
β-strand	226-231	6	15
β-strand	240-245	6	15
α-helix	248-251	4
β-strand	255-257	3	16
β-strand	260-262	3	17
β-strand	270-271	2	17
α-helix	274-277	4
β-strand	283-286	4	15
β-strand	294-298	5	17
β-strand	301-303	3	16
α-helix	310-313	4
β-strand	317-320	4	17
β-strand	332-335	4	18
β-strand	345-351	7	18
β-strand	365-372	8	19
β-strand	376-382	7	19
β-strand	386-391	6	18
β-strand	396-403	8	19
β-strand	408	1	19
β-strand	412-416	5	19
β-strand	430-432	3	20
β-strand	440-443	4	20
β-strand	452-459	8	21
β-strand	469-474	6	21
β-strand	479-481	3	20
β-strand	492-500	9	21
β-strand	503-504	2	21
β-strand	508-512	5	21
β-strand	526	1	22
β-strand	538	1	22
α-helix	541-543	3
α-helix	544-547	4
β-strand	553-559	7	23
β-strand	566-571	6	23
β-strand	576	1	22
β-strand	587-595	9	23
β-strand	600-602	3	23
β-strand	606-609	4	23

Chains C and G: 11 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	30-31	2
β-strand	34-37	4	1
β-strand	43-44	2	2
β-strand	57-63	7	1
β-strand	73-77	5	1
β-strand	82-83	2	2
α-helix	88-90	3
β-strand	92-97	6	1
β-strand	105-110	6	1
α-helix	112-115	4
β-strand	120-122	3	3
β-strand	123	1	4
α-helix	129	1
β-strand	130-134	5	3
β-strand	145-153	9	5
α-helix	157-158	2
β-strand	159-163	5	5
β-strand	166-167	2	3
β-strand	174-178	5	3
β-strand	187-195	9	5
β-strand	200-202	3	5
α-helix	203-205	3
β-strand	206-209	4	5
β-strand	214	1	4
α-helix	217-219	3
β-strand	220-226	7	6
α-helix	227	1
β-strand	234-239	6	6
β-strand	251-259	9	7
β-strand	266-269	4	7
α-helix	270-271	2
β-strand	276-279	4	6
α-helix	282-283	2
β-strand	288-296	9	7
α-helix	303-309	7
β-strand	310-312	3	7

Chains D and H: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	45-47	3
α-helix	49-74	26
β-strand	84	1	8
β-strand	86-88	3	9
α-helix	97-99	3
α-helix	109-129	21
α-helix	138-155	18
α-helix	166-168	3
α-helix	171-178	8
α-helix	184-210	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Soluble interleukin-6 receptor subunit alpha	C, G	protein	346	Homo sapiens	P08887 (AlphaFold model)
Interleukin-6	D, H	protein	183	Homo sapiens	P05231 (AlphaFold model)
Interleukin-6 receptor subunit beta	A, E	protein	678	Homo sapiens	P40189 (AlphaFold model)

Sequence of entity 1 (C, G), FASTA

>8D82_1 Soluble interleukin-6 receptor subunit alpha (chains C, G)
LAPRRCPAQEVARGVLTSLPGDSVTLTCPGVEPEDNATVHWVLRKPAAGSHPSRWAGMGR
RLLLRSVQLHDSGNYSCYRAGRPAGTVHLLVDVPPEEPQLSCFRKSPLSNVVCEWGPRST
PSLTTKAVLLVRKFQNSPAEDFQEPCQYSQESQKFSCQLAVPEGDSSFYIVSMCVASSVG
SKFSKTQTFQGCGILQPDPPANITVTAVARNPRWLSVTWQDPHSWNSSFYRLRFELRYRA
ERSKTFTTWMVKDLQHHCVIHDAWSGLRHVVQLRAQEEFGQGEWSEWSPEAMGTPWTESR
SPPAENEVSTPMGPGGEQKLISEEDLGGEQKLISEEDLSGHHHHHH

Sequence of entity 2 (D, H), FASTA

>8D82_2 Interleukin-6 (chains D, H)
VPPGEDSKDVAAPHRQPLTSSERIDKQIRYILDGISALRKETCNKSNMCESSKEALAENN
LNLPKMAEKDGCFQSGFNEETCLVKIITGLLEFEVYLEYLQNRFESSEEQARAVQMSTKV
LIQFLQKKAKNLDAITTPDPTTNASLLTKLQAQNQWLQDMTTHLILRSFKEFLQSSLRAL
RQM

Sequence of entity 3 (A, E), FASTA

>8D82_3 Interleukin-6 receptor subunit beta (chains A, E)
ELLDPCGYISPESPVVQLHSNFTAVCVLKEKCMDYFHVNANYIVWKTNHFTIPKEQYTII
NRTASSVTFTDIASLNIQLTCNILTFGQLEQNVYGITIISGLPPEKPKNLSCIVNEGKKM
RCEWDGGRETHLETNFTLKSEWATHKFADCKAKRDTPTSCTVDYSTVYFVNIEVWVEAEN
ALGKVTSDHINFDPVYKVKPNPPHNLSVINSEELSSILKLTWTNPSIKSVIILKYNIQYR
TKDASTWSQIPPEDTASTRSSFTVQDLKPFTEYVFRIRCMKEDGKGYWSDWSEEASGITY
EDRPSKAPSFWYKIDPSHTQGYRTVQLVWKTLPPFEANGKILDYEVTLTRWKSHLQNYTV
NATKLTVNLTNDRYLATLTVRNLVGKSDAAVLTIPACDFQATHPVMDLKAFPKDNMLWVE
WTTPRESVKKYILEWCVLSDKAPCITDWQQEDGTVHRTYLRGNLAESKCYLITVTPVYAD
GPGSPESIKAYLKQAPPSKGPTVRTKKVGKNEAVLEWDQLPVDVQNGFIRNYTIFYRTII
GNETAVNVDSSHTEYTLSSLTSDTLYMVRMAAYTDEGGKDGPEFTFTTPKFAQGEIEAIV
VPVCLAFLLTTLLGVLFCFNKRDLIKKHIWPNVPDPSKSHIAQWSPHTPPRHNFNSKDQM
YSDGNFTDVSVVEIEAND

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	18

Primary citation

Structural insights into the assembly of gp130 family cytokine signaling complexes. Zhou, Y., Stevis, P.E., Cao, J. et al. Sci Adv (2023) 9:eade4395-eade4395. DOI 10.1126/sciadv.ade4395 · PubMed

Other PDB entries of the same protein (UniProt P08887 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1N26 2.4 Å, Crystal Structure of the extra-cellular domains of Human Interleukin-6 Receptor alpha…
5FUC 2.7 Å, Biophysical and cellular characterisation of a junctional epitope antibody that locks…
7DC8 2.76 Å, Crystal structure of Switch Ab Fab and hIL6R in complex with ATP
8QY5 3.1 Å, Structure of interleukin 6.
8QY6 3.16 Å, Structure of interleukin 6 (gp130 P496L mutant).
8IOW 3.2 Å, Cryo-EM structure of the sarilumab Fab/IL-6R complex
8J6F 3.3 Å, Cryo-EM structure of the Tocilizumab Fab/IL-6R complex
1P9M 3.65 Å, Crystal structure of the hexameric human IL-6/IL-6 alpha receptor/gp130 complex
2ARW The solution structure of the membrane proximal cytokine receptor domain of the human…

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