8DPU: IL-11 signalling complex

Name: PDB 8DPU: The crystal structure of the IL-11 signalling complex
Published: 2023-11-29
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: cytokine

The crystal structure of the IL-11 signalling complex. Determined by X-ray diffraction at 3.78 Å resolution. Released 29 Nov 2023.

Method: X-ray diffraction
Resolution: 3.78 Å
Organism: Homo sapiens
Chains: 18
Atoms: 35,568
Mol. weight: 561.23 kDa
Ligands: NAG
Released: 29 Nov 2023

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

Secondary structure: helices and β-sheets

8DPU contains 174 α-helices and 298 β-strands across 18 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, D, G, J, M and P: 14 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	7-10	4	1
β-strand	15-17	3	2
β-strand	22-28	7	1
α-helix	30-36	7
α-helix	40-42	3
β-strand	43-47	5	2
β-strand	50-51	2	2
α-helix	52-53	2
α-helix	54-56	3
β-strand	57-61	5	1
β-strand	64-69	6	1
β-strand	76-83	8	2
α-helix	85-87	3
β-strand	91-101	11	2
α-helix	103-107	5
β-strand	108-113	6	3
β-strand	114-115	2	4
β-strand	121-125	5	3
β-strand	135-142	8	5
β-strand	145-146	2	5
α-helix	147-149	3
β-strand	150-151	2	5
α-helix	152-153	2
β-strand	159-161	3	3
β-strand	172-180	9	5
β-strand	183-186	4	5
β-strand	190-192	3	5
α-helix	194-196	3
β-strand	198-199	2	4
α-helix	200-203	4
β-strand	204-207	4	6
β-strand	217-223	7	6
α-helix	226-229	4
β-strand	233-241	9	7
β-strand	248-249	2	7
α-helix	252-255	4
β-strand	261-265	5	6
α-helix	267-268	2
β-strand	272-281	10	7
α-helix	288-291	4
β-strand	295-298	4	7

Chains B and Q: 8 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	16-42	27
β-strand	61	1	8
α-helix	62-66	5
α-helix	69-93	25
α-helix	96-101	6
α-helix	104-125	22
α-helix	128-132	5
α-helix	134-143	10
α-helix	146-177	32

Chains C and R: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	14-16	3	9
β-strand	22-25	4	10
β-strand	35-39	5	9
β-strand	42	1	9
α-helix	44-46	3
β-strand	56-59	4	10
α-helix	64-66	3
β-strand	68-74	7	9
β-strand	79-87	9	9
α-helix	90-94	5
β-strand	95-99	5	11
β-strand	106-111	6	11
β-strand	121-128	8	12
β-strand	146-147	2	12
β-strand	150	1	11
β-strand	157-160	4	11
β-strand	164	1	8
β-strand	168-177	10	12
β-strand	180-189	10	12
α-helix	190-193	4
α-helix	196-199	4
β-strand	200-206	7	13
β-strand	214-219	6	13
β-strand	232-240	9	14
β-strand	247-249	3	14
β-strand	255-258	4	13
α-helix	261-262	2
β-strand	267-275	9	14
α-helix	282-288	7
β-strand	289-291	3	14

Chains E, H, K and N: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	16-42	27
α-helix	62-66	5
α-helix	69-93	25
α-helix	96-101	6
α-helix	104-125	22
α-helix	128-132	5
α-helix	134-143	10
α-helix	146-177	32

Chains F, I, L and O: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	14-16	3	22
β-strand	22-25	4	23
β-strand	35-39	5	22
β-strand	42	1	22
α-helix	44-46	3
β-strand	56-59	4	23
α-helix	64-66	3
β-strand	68-74	7	22
β-strand	79-87	9	22
α-helix	90-94	5
β-strand	95-99	5	24
β-strand	106-111	6	24
β-strand	121-128	8	25
β-strand	146-147	2	25
β-strand	150	1	24
β-strand	157-160	4	24
β-strand	168-177	10	25
β-strand	180-189	10	25
α-helix	190-193	4
α-helix	196-199	4
β-strand	200-206	7	26
β-strand	214-219	6	26
β-strand	232-240	9	27
β-strand	247-249	3	27
β-strand	255-258	4	26
α-helix	261-262	2
β-strand	267-275	9	27
α-helix	282-288	7
β-strand	289-291	3	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Interleukin-6 receptor subunit beta	A, D, G, J, M, P	protein	303	Homo sapiens	P40189 (AlphaFold model)
Interleukin-11	B, E, H, K, N, Q	protein	179	Homo sapiens	P20809 (AlphaFold model)
Interleukin-11 receptor subunit alpha	C, F, I, L, O, R	protein	348	Homo sapiens	Q14626 (AlphaFold model)

Sequence of entity 1 (A, D, G, J, M, P), FASTA

>8DPU_1 Interleukin-6 receptor subunit beta (chains A, D, G, J, M, P)
GELLDPCGYISPESPVVQLHSNFTAVCVLKEKCMDYFHVNANYIVWKTNHFTIPKEQYTI
INRTASSVTFTDIASLNIQLTCNILTFGQLEQNVYGITIISGLPPEKPKNLSCIVNEGKK
MRCEWDGGRETHLETNFTLKSEWATHKFADCKAKRDTPTSCTVDYSTVYFVNIEVWVEAE
NALGKVTSDHINFDPVYKVKPNPPHNLSVINSEELSSILKLTWTNPSIKSVIILKYNIQY
RTKDASTWSQIPPEDTASTRSSFTVQDLKPFTEYVFRIRCMKEDGKGYWSDWSEEASGIT
YED

Sequence of entity 2 (B, E, H, K, N, Q), FASTA

>8DPU_2 Interleukin-11 (chains B, E, H, K, N, Q)
GPGPPPGPPRVSPDPRAELDSTVLLTRSLLADTRQLAAQLRDKFPADGDHNLDSLPTLAM
SAGALGALQLPGVLTRLRADLLSYLRHVQWLRRAGGSSLKTLEPELGTLQARLDRLLRRL
QLLMSRLALPQPPPDPPAPPLAPPSSAWGGIRAAHAILGGLHLTLDWAVRGLLLLKTRL

Sequence of entity 3 (C, F, I, L, O, R), FASTA

>8DPU_3 Interleukin-11 receptor subunit alpha (chains C, F, I, L, O, R)
SSPCPQAWGPPGVQYGQPGRSVKLCCPGVTAGDPVSWFRDGEPKLLQGPDSGLGHELVLA
QADSTDEGTYICQTLDGALGGTVTLQLGYPPARPVVSCQAADYENFSCTWSPSQISGLPT
RYLTSYRKKTVLGADSQRRSPSTGPWPCPQDPLGAARCVVHGAEFWSQYRINVTEVNPLG
ASTRLLDVSLQSILRPDPPQGLRVESVPGYPRRLRASWTYPASWPSQPHFLLKFRLQYRP
AQHPAWSTVEPAGLEEVITDAVAGLPHAVRVSARDFLDAGTWSTWSPEAWGTPSTGTIPK
EIPAWGQLHTQPEVEPQVDSPAPPRPSLQPHPRLLDHRDSVHHHHHHH

Ligands and cofactors

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

Primary citation

Structures of the interleukin 11 signalling complex reveal gp130 dynamics and the inhibitory mechanism of a cytokine variant. Metcalfe, R.D., Hanssen, E., Fung, K.Y. et al. Nat Commun (2023) 14:7543-7543. DOI 10.1038/s41467-023-42754-w · 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

Browse structure collections

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