8QY4: Interleukin 11 (gp130 P496L mutant)

Structure of interleukin 11 (gp130 P496L mutant). Determined by electron microscopy at 3.06 Å resolution. Released 21 Feb 2024.

Method: Electron microscopy
Resolution: 3.06 Å
Organisms: Homo sapiens, Mus musculus
Chains: 6
Atoms: 15,132
Mol. weight: 343.34 kDa
Ligands: NAG
Released: 21 Feb 2024

Explore 8QY4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8QY4 contains 70 α-helices and 136 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: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	36-63	28
α-helix	82-85	4
α-helix	90-114	25
α-helix	117-122	6
α-helix	125-147	23
α-helix	149-153	5
α-helix	155-164	10
α-helix	167-198	32

Chains B and E: 4 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	113-116	4
β-strand	117-121	5	29
β-strand	122	1	30
β-strand	127-133	7	29
β-strand	143-150	8	31
β-strand	168-169	2	31
β-strand	172	1	29
β-strand	179-183	5	29
β-strand	191-198	8	31
β-strand	204-210	7	31
α-helix	212-215	4
β-strand	216	1	30
α-helix	218-221	4
β-strand	222-228	7	32
β-strand	236-241	6	32
β-strand	254-262	9	33
β-strand	269-271	3	33
β-strand	277-280	4	32
β-strand	289-297	9	33
α-helix	304-310	7
β-strand	311-313	3	33

Chains C and F: 23 helices, 51 β-strands

Element	Residues	Length	Sheet
β-strand	29-32	4	1
β-strand	37-39	3	2
β-strand	44-50	7	1
α-helix	52-58	7
α-helix	62-64	3
β-strand	65-69	5	2
β-strand	72-73	2	2
β-strand	79-83	5	1
β-strand	86-91	6	1
β-strand	98-107	10	2
β-strand	111-123	13	2
α-helix	125-127	3
β-strand	130-135	6	3
β-strand	136-137	2	4
α-helix	141-142	2
β-strand	143-147	5	3
β-strand	159-164	6	5
β-strand	167-168	2	5
α-helix	169-171	3
β-strand	172-173	2	5
β-strand	179-181	3	3
α-helix	185-186	2
β-strand	192-200	9	5
β-strand	203-206	4	5
α-helix	207-209	3
β-strand	210-212	3	5
α-helix	214-217	4
β-strand	218-219	2	4
α-helix	220-223	4
β-strand	224-230	7	6
β-strand	238-243	6	6
α-helix	246-249	4
β-strand	253-261	9	7
β-strand	268-269	2	7
α-helix	272-275	4
β-strand	281-284	4	6
β-strand	292-301	10	7
α-helix	308-314	7
β-strand	315-318	4	7
α-helix	319-321	3
α-helix	327-328	2
β-strand	329-334	6	8
β-strand	342-350	9	8
α-helix	351-353	3
α-helix	354-357	4
β-strand	361-369	9	9
α-helix	374	1
β-strand	375-380	6	9
β-strand	384-390	7	8
β-strand	394-402	9	9
β-strand	406	1	9
α-helix	407-409	3
β-strand	410-414	5	9
β-strand	424	1	10
β-strand	426-433	8	11
β-strand	436-442	7	11
α-helix	443-444	2
β-strand	450-457	8	12
β-strand	466-472	7	12
β-strand	477-479	3	11
β-strand	489-498	10	12
β-strand	501-511	11	12
α-helix	520-521	2
β-strand	522-528	7	13
β-strand	533-538	6	13
α-helix	539-541	3
β-strand	551-558	8	14
α-helix	562-563	2
β-strand	564-569	6	14
β-strand	574-577	4	13
α-helix	580-581	2
β-strand	586-594	9	14
β-strand	597-600	4	14
β-strand	604-606	3	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Interleukin-11	A, D	protein	199	Homo sapiens	P20809 (AlphaFold model)
Interleukin-6 receptor subunit beta	C, F	protein	917	Mus musculus	Q00560 (AlphaFold model)
Interleukin-11 receptor subunit alpha	B, E	protein	422	Homo sapiens	Q14626 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>8QY4_1 Interleukin-11 (chains A, D)
MNCVCRLVLVVLSLWPDTAVAPGPPPGPPRVSPDPRAELDSTVLLTRSLLADTRQLAAQL
RDKFPADGDHNLDSLPTLAMSAGALGALQLPGVLTRLRADLLSYLRHVQWLRRAGGSSLK
TLEPELGTLQARLDRLLRRLQLLMSRLALPQPPPDPPAPPLAPPSSAWGGIRAAHAILGG
LHLTLDWAVRGLLLLKTRL

Sequence of entity 2 (C, F), FASTA

>8QY4_2 Interleukin-6 receptor subunit beta (chains C, F)
MSAPRIWLAQALLFFLTTESIGQLLEPCGYIYPEFPVVQRGSNFTAICVLKEACLQHYYV
NASYIVWKTNHAAVPREQVTVINRTTSSVTFTDVVLPSVQLTCNILSFGQIEQNVYGVTM
LSGFPPDKPTNLTCIVNEGKNMLCQWDPGRETYLETNYTLKSEWATEKFPDCQSKHGTSC
MVSYMPTYYVNIEVWVEAENALGKVSSESINFDPVDKVKPTPPYNLSVTNSEELSSILKL
SWVSSGLGGLLDLKSDIQYRTKDASTWIQVPLEDTMSPRTSFTVQDLKPFTEYVFRIRSI
KDSGKGYWSDWSEEASGTTYEDRPSRPPSFWYKTNPSHGQEYRSVRLIWKALPLSEANGK
ILDYEVILTQSKSVSQTYTVTGTELTVNLTNDRYVASLAARNKVGKSAAAVLTIPSPHVT
AAYSVVNLKAFPKDNLLWVEWTPPPKPVSKYILEWCVLSENAPCVEDWQQEDATVNRTHL
RGRLLESKCYQITVTLVFATGPGGSESLKAYLKQAAPARGPTVRTKKVGKNEAVLAWDQI
PVDDQNGFIRNYSISYRTSVGKEMVVHVDSSHTEYTLSSLSSDTLYMVRMAAYTDEGGKD
GPEFTFTTPKFAQGEIEAIVVPVCLAFLLTTLLGVLFCFNKRDLIKKHIWPNVPDPSKSH
IAQWSPHTPPRHNFNSKDQMYSDGNFTDVSVVEIEANNKKPCPDDLKSVDLFKKEKVSTE
GHSSGIGGSSCMSSSRPSISSNEENESAQSTASTVQYSTVVHSGYRHQVPSVQVFSRSES
TQPLLDSEERPEDLQLVDSVDGGDEILPRQPYFKQNCSQPEACPEISHFERSNQVLSGNE
EDFVRLKQQQVSDHISQPYGSEQRRLFQEGSTADALGTGADGQMERFESVGMETTIDEEI
PKSYLPQTVRQGGYMPQ

Sequence of entity 3 (B, E), FASTA

>8QY4_3 Interleukin-11 receptor subunit alpha (chains B, E)
MSSSCSGLSRVLVAVATALVSASSPCPQAWGPPGVQYGQPGRSVKLCCPGVTAGDPVSWF
RDGEPKLLQGPDSGLGHELVLAQADSTDEGTYICQTLDGALGGTVTLQLGYPPARPVVSC
QAADYENFSCTWSPSQISGLPTRYLTSYRKKTVLGADSQRRSPSTGPWPCPQDPLGAARC
VVHGAEFWSQYRINVTEVNPLGASTRLLDVSLQSILRPDPPQGLRVESVPGYPRRLRASW
TYPASWPCQPHFLLKFRLQYRPAQHPAWSTVEPAGLEEVITDAVAGLPHAVRVSARDFLD
AGTWSTWSPEAWGTPSTGTIPKEIPAWGQLHTQPEVEPQVDSPAPPRPSLQPHPRLLDHR
DSVEQVAVLASLGILSFLGLVAGALALGLWLRLRRGGKDGSPKPGFLASVIPVDRRPGAP
NL

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	10

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 P20809 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8DPV 1.48 Å, The crystal structure of Interleukin-11, W147A mutant
6O4O 1.62 Å, The structure of human interleukin 11
8DPW 1.8 Å, The structure of Interleukin-11 Mutein
4MHL 2.09 Å, The crystal structure of human interleukin-11
8DPS 3.47 Å, The structure of the interleukin 11 signalling complex, truncated gp130
8DPU 3.78 Å, The crystal structure of the IL-11 signalling complex
8DPT 4.0 Å, The structure of the IL-11 signalling complex, with full-length extracellular gp130

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