8DPT: Interleukin-6 receptor subunit beta

Name: PDB 8DPT: The structure of the IL-11 signalling complex, with full-length extracellular gp130
Published: 2023-11-29
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: cytokine

The structure of the IL-11 signalling complex, with full-length extracellular gp130. Determined by electron microscopy at 4.0 Å resolution. Released 29 Nov 2023.

Method: Electron microscopy
Resolution: 4.0 Å
Organism: Homo sapiens
Chains: 6
Atoms: 13,550
Mol. weight: 238.27 kDa
Ligands: NAG
Released: 29 Nov 2023

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

Secondary structure: helices and β-sheets

8DPT contains 70 α-helices and 114 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: 19 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	8-10	3	1
β-strand	15-17	3	2
β-strand	22-27	6	1
α-helix	30-36	7
α-helix	40-42	3
β-strand	43-47	5	3
β-strand	50-51	2	3
α-helix	52-53	2
α-helix	54-56	3
β-strand	57-61	5	1
β-strand	64-69	6	1
β-strand	78-83	6	3
β-strand	91-97	7	3
β-strand	99-101	3	2
α-helix	103-107	5
β-strand	108-113	6	4
β-strand	114-115	2	5
β-strand	121-125	5	4
β-strand	135-142	8	6
β-strand	145-146	2	6
α-helix	147-149	3
β-strand	150-151	2	6
α-helix	152-153	2
β-strand	159-161	3	4
β-strand	172-180	9	6
β-strand	183-186	4	6
α-helix	187-189	3
β-strand	190-192	3	6
α-helix	194-197	4
β-strand	198-199	2	5
α-helix	200-203	4
β-strand	204-209	6	7
β-strand	218-223	6	7
α-helix	226-229	4
β-strand	233-241	9	8
β-strand	248-249	2	8
α-helix	252-255	4
β-strand	261-264	4	7
α-helix	267-268	2
β-strand	272-281	10	8
α-helix	288-291	4
β-strand	295-298	4	8
α-helix	299-301	3
α-helix	307-309	3
β-strand	310-316	7	9
β-strand	323-329	7	9
α-helix	331-333	3
α-helix	334-337	4
β-strand	343-350	8	10
β-strand	356-360	5	10
β-strand	364-369	6	9
β-strand	374-381	8	10
β-strand	386	1	10
α-helix	387-389	3
β-strand	390-393	4	10

Chains B and E: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	16-42	27
α-helix	55-56	2
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	146-175	30

Chains C and F: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	14-16	3	11
β-strand	22-25	4	12
β-strand	35-39	5	11
β-strand	42	1	11
α-helix	44-46	3
β-strand	56-59	4	12
α-helix	64-66	3
β-strand	68-74	7	11
β-strand	79-87	9	11
α-helix	90-94	5
β-strand	95-99	5	13
β-strand	107-111	5	13
β-strand	121-128	8	14
β-strand	157-159	3	13
β-strand	168-177	10	14
β-strand	180-181	2	14
β-strand	184-189	6	14
α-helix	190-193	4
α-helix	196-199	4
β-strand	200-206	7	15
β-strand	214-219	6	15
β-strand	232-240	9	16
β-strand	247-249	3	16
β-strand	255-258	4	15
α-helix	261-262	2
β-strand	267-275	9	16
α-helix	282-288	7
β-strand	289-291	3	16
α-helix	293-295	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Interleukin-6 receptor subunit beta	A, D	protein	591	Homo sapiens	P40189 (AlphaFold model)
Interleukin-11	B, E	protein	169	Homo sapiens	P20809 (AlphaFold model)
Interleukin-11 receptor subunit alpha	C, F	protein	298	Homo sapiens	Q14626 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>8DPT_1 Interleukin-6 receptor subunit beta (chains A, D)
GELLDPCGYISPESPVVQLHSNFTAVCVLKEKCMDYFHVNANYIVWKTNHFTIPKEQYTI
INRTASSVTFTDIASLNIQLTCNILTFGQLEQNVYGITIISGLPPEKPKNLSCIVNEGKK
MRCEWDGGRETHLETNFTLKSEWATHKFADCKAKRDTPTSCTVDYSTVYFVNIEVWVEAE
NALGKVTSDHINFDPVYKVKPNPPHNLSVINSEELSSILKLTWTNPSIKSVIILKYNIQY
RTKDASTWSQIPPEDTASTRSSFTVQDLKPFTEYVFRIRCMKEDGKGYWSDWSEEASGIT
YEDRPSKAPSFWYKIDPSHTQGYRTVQLVWKTLPPFEANGKILDYEVTLTRWKSHLQNYT
VNATKLTVNLTNDRYLATLTVRNLVGKSDAAVLTIPACDFQATHPVMDLKAFPKDNMLWV
EWTTPRESVKKYILEWCVLSDKAPCITDWQQEDGTVHRTYLRGNLAESKCYLITVTPVYA
DGPGSPESIKAYLKQAPPSKGPTVRTKKVGKNEAVLEWDQLPVDVQNGFIRNYTIFYRTI
IGNETAVNVDSSHTEYTLSSLTSDTLYMVRMAAYTDEGGKDGPEFTFTTPK

Sequence of entity 2 (B, E), FASTA

>8DPT_2 Interleukin-11 (chains B, E)
GSPDPRAELDSTVLLTRSLLADTRQLAAQLRDKFPADGDHNLDSLPTLAMSAGALGALQL
PGVLTRLRADLLSYLRHVQWLRRAGGSSLKTLEPELGTLQARLDRLLRRLQLLMSRLALP
QPPPDPPAPPLAPPSSAWGGIRAAHAILGGLHLTLDWAVRGLLLLKTRL

Sequence of entity 3 (C, F), FASTA

>8DPT_3 Interleukin-11 receptor subunit alpha (chains C, F)
GSSPCPQAWGPPGVQYGQPGRSVKLCCPGVTAGDPVSWFRDGEPKLLQGPDSGLGHELVL
AQADSTDEGTYICQTLDGALGGTVTLQLGYPPARPVVSCQAADYENFSCTWSPSQISGLP
TRYLTSYRKKTVLGADSQRRSPSTGPWPCPQDPLGAARCVVHGAEFWSQYRINVTEVNPL
GASTRLLDVSLQSILRPDPPQGLRVESVPGYPRRLRASWTYPASWPSQPHFLLKFRLQYR
PAQHPAWSTVEPAGLEEVITDAVAGLPHAVRVSARDFLDAGTWSTWSPEAWGTPSTGT

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

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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