8QY6: Interleukin 6 (gp130 P496L mutant)

Structure of interleukin 6 (gp130 P496L mutant). Determined by electron microscopy at 3.16 Å resolution. Released 21 Feb 2024.

Method: Electron microscopy
Resolution: 3.16 Å
Organisms: Mus musculus, Homo sapiens
Chains: 6
Atoms: 15,302
Mol. weight: 360.52 kDa
Ligands: NAG
Released: 21 Feb 2024

Explore 8QY6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8QY6 contains 84 α-helices and 148 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 D: 27 helices, 54 β-strands

Element	Residues	Length	Sheet
β-strand	25-27	3	1
β-strand	29-32	4	2
β-strand	37-39	3	3
β-strand	43-44	2	4
β-strand	47-50	4	2
α-helix	52-58	7
α-helix	62-64	3
β-strand	65-69	5	3
β-strand	72-73	2	3
α-helix	74-75	2
β-strand	79-83	5	2
β-strand	86-89	4	2
β-strand	91-92	2	4
β-strand	98-107	10	3
β-strand	111-123	13	3
α-helix	125-129	5
β-strand	130-135	6	5
β-strand	136-137	2	6
α-helix	141-142	2
β-strand	143-147	5	5
α-helix	151-152	2
β-strand	157-163	7	7
β-strand	168	1	7
α-helix	169-171	3
β-strand	172-173	2	7
β-strand	179-181	3	5
α-helix	185-186	2
β-strand	192-200	9	7
β-strand	203-206	4	7
α-helix	207-209	3
β-strand	210-212	3	7
α-helix	214-217	4
β-strand	218-219	2	6
α-helix	220-223	4
β-strand	224-230	7	8
β-strand	237-243	7	8
α-helix	246-249	4
β-strand	253-261	9	9
α-helix	267	1
β-strand	268-269	2	9
α-helix	270-271	2
α-helix	272-275	4
β-strand	281-285	5	8
α-helix	287-288	2
β-strand	292-301	10	9
α-helix	308-314	7
β-strand	315-318	4	9
α-helix	319-321	3
α-helix	327-328	2
β-strand	329-334	6	10
β-strand	342-350	9	10
α-helix	351-353	3
α-helix	354-357	4
β-strand	361-369	9	11
α-helix	374-375	2
β-strand	376-380	5	11
β-strand	384-390	7	10
β-strand	394-402	9	11
β-strand	406	1	11
α-helix	407-409	3
β-strand	410-414	5	11
β-strand	424	1	12
β-strand	426-433	8	13
β-strand	436-442	7	13
α-helix	443-444	2
β-strand	450-457	8	14
β-strand	467-472	6	14
β-strand	477-479	3	13
β-strand	489-498	10	14
β-strand	501-511	11	14
α-helix	520-522	3
β-strand	523-528	6	15
β-strand	533-537	5	15
α-helix	539-541	3
β-strand	551-557	7	16
β-strand	564-569	6	16
β-strand	574-577	4	15
α-helix	580-581	2
β-strand	586-594	9	16
β-strand	597-600	4	16
β-strand	604-606	3	16

Chains B and E: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	21-46	26
β-strand	55	1	17
β-strand	57-60	4	18
α-helix	69-71	3
α-helix	80-101	22
α-helix	109-128	20
α-helix	141-152	12
α-helix	156-182	27

Chains C and F: 9 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	101-103	3	19
β-strand	104	1	20
α-helix	110	1
β-strand	111-115	5	19
α-helix	120-122	3
β-strand	126-134	9	21
α-helix	139	1
β-strand	140-146	7	21
β-strand	147-149	3	19
β-strand	154-159	6	19
α-helix	161-162	2
β-strand	168-176	9	21
β-strand	182-183	2	21
α-helix	184-186	3
β-strand	187-190	4	21
β-strand	195	1	20
α-helix	197-200	4
β-strand	201-208	8	22
β-strand	211-220	10	22
β-strand	232-240	9	23
α-helix	245-246	2
β-strand	247-250	4	23
β-strand	257-260	4	22
α-helix	263-264	2
β-strand	269-277	9	23
α-helix	283-289	7
β-strand	291-293	3	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Interleukin-6 receptor subunit beta	A, D	protein	917	Mus musculus	Q00560 (AlphaFold model)
Interleukin-6	B, E	protein	212	Homo sapiens	P05231 (AlphaFold model)
Interleukin-6 receptor subunit alpha	C, F	protein	468	Homo sapiens	P08887 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>8QY6_1 Interleukin-6 receptor subunit beta (chains A, D)
MSAPRIWLAQALLFFLTTESIGQLLEPCGYIYPEFPVVQRGSNFTAICVLKEACLQHYYV
NASYIVWKTNHAAVPREQVTVINRTTSSVTFTDVVLPSVQLTCNILSFGQIEQNVYGVTM
LSGFPPDKPTNLTCIVNEGKNMLCQWDPGRETYLETNYTLKSEWATEKFPDCQSKHGTSC
MVSYMPTYYVNIEVWVEAENALGKVSSESINFDPVDKVKPTPPYNLSVTNSEELSSILKL
SWVSSGLGGLLDLKSDIQYRTKDASTWIQVPLEDTMSPRTSFTVQDLKPFTEYVFRIRSI
KDSGKGYWSDWSEEASGTTYEDRPSRPPSFWYKTNPSHGQEYRSVRLIWKALPLSEANGK
ILDYEVILTQSKSVSQTYTVTGTELTVNLTNDRYVASLAARNKVGKSAAAVLTIPSPHVT
AAYSVVNLKAFPKDNLLWVEWTPPPKPVSKYILEWCVLSENAPCVEDWQQEDATVNRTHL
RGRLLESKCYQITVTLVFATGPGGSESLKAYLKQAAPARGPTVRTKKVGKNEAVLAWDQI
PVDDQNGFIRNYSISYRTSVGKEMVVHVDSSHTEYTLSSLSSDTLYMVRMAAYTDEGGKD
GPEFTFTTPKFAQGEIEAIVVPVCLAFLLTTLLGVLFCFNKRDLIKKHIWPNVPDPSKSH
IAQWSPHTPPRHNFNSKDQMYSDGNFTDVSVVEIEANNKKPCPDDLKSVDLFKKEKVSTE
GHSSGIGGSSCMSSSRPSISSNEENESAQSTASTVQYSTVVHSGYRHQVPSVQVFSRSES
TQPLLDSEERPEDLQLVDSVDGGDEILPRQPYFKQNCSQPEACPEISHFERSNQVLSGNE
EDFVRLKQQQVSDHISQPYGSEQRRLFQEGSTADALGTGADGQMERFESVGMETTIDEEI
PKSYLPQTVRQGGYMPQ

Sequence of entity 2 (B, E), FASTA

>8QY6_2 Interleukin-6 (chains B, E)
MNSFSTSAFGPVAFSLGLLLVLPAAFPAPVPPGEDSKDVAAPHRQPLTSSERIDKQIRYI
LDGISALRKETCNKSNMCESSKEALAENNLNLPKMAEKDGCFQSGFNEETCLVKIITGLL
EFEVYLEYLQNRFESSEEQARAVQMSTKVLIQFLQKKAKNLDAITTPDPTTNASLLTKLQ
AQNQWLQDMTTHLILRSFKEFLQSSLRALRQM

Sequence of entity 3 (C, F), FASTA

>8QY6_3 Interleukin-6 receptor subunit alpha (chains C, F)
MLAVGCALLAALLAAPGAALAPRRCPAQEVARGVLTSLPGDSVTLTCPGVEPEDNATVHW
VLRKPAAGSHPSRWAGMGRRLLLRSVQLHDSGNYSCYRAGRPAGTVHLLVDVPPEEPQLS
CFRKSPLSNVVCEWGPRSTPSLTTKAVLLVRKFQNSPAEDFQEPCQYSQESQKFSCQLAV
PEGDSSFYIVSMCVASSVGSKFSKTQTFQGCGILQPDPPANITVTAVARNPRWLSVTWQD
PHSWNSSFYRLRFELRYRAERSKTFTTWMVKDLQHHCVIHDAWSGLRHVVQLRAQEEFGQ
GEWSEWSPEAMGTPWTESRSPPAENEVSTPMQALTTNKDDDNILFRDSANATSLPVQDSS
SVPLPTFLVAGGSLAFGTLLCIAIVLRFKKTWKLRALKEGKTSMHPPYSLGQLVPERPRP
TPVLVPLISPPVSPSSLGSDNTSSHNRPDARDPRSPYDISNTDYFFPR

Ligands and cofactors

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

Primary citation

Structural insights into IL-11-mediated signalling and human IL6ST variant-associated immunodeficiency. Gardner, S., Jin, Y., Fyfe, P.K. et al. Nat Commun (2024) 15:2071-2071. DOI 10.1038/s41467-024-46235-6 · PubMed

Other PDB entries of the same protein (UniProt Q00560 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2HMH 2.0 Å, Crystal structure of SOCS3 in complex with gp130(pTyr757) phosphopeptide.
8QY4 3.06 Å, Structure of interleukin 11 (gp130 P496L mutant).
8QY5 3.1 Å, Structure of interleukin 6.
6C5X 3.1 Å, Crystal Structure of SOCS1 in complex with ElonginB and ElonginC
8V2C 3.46 Å, Cryo-EM structure of mouse type II OSM receptor complex: model for assembly core region
8V2B 3.67 Å, Cryo-EM structure of mouse type II OSM receptor complex: model for full extracellular…
4GL9 3.9 Å, Crystal structure of inhibitory protein SOCS3 in complex with JAK2 kinase domain and…
7Z0L 4.0 Å, IL-27 signalling complex
2BBU solution structure of mouse socs3 in complex with a phosphopeptide from the gp130 receptor

Browse structure collections

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