8D74: Interleukin-6 receptor subunit beta

Name: PDB 8D74: Cryo-EM structure of human CNTF signaling complex: model containing the interaction core region
Published: 2023-03-29
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: cytokine

Cryo-EM structure of human CNTF signaling complex: model containing the interaction core region. Determined by electron microscopy at 3.03 Å resolution. Released 29 Mar 2023.

Method: Electron microscopy
Resolution: 3.03 Å
Organism: Homo sapiens
Chains: 4
Atoms: 9,639
Mol. weight: 228.5 kDa
Ligands: NAG
Released: 29 Mar 2023

Explore 8D74 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8D74 contains 26 α-helices and 88 β-strands across 4 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.

Chain A: 11 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	133-137	5	1
β-strand	142-145	4	1
β-strand	157-163	7	2
β-strand	168	1	2
β-strand	172-173	2	2
α-helix	174-175	2
β-strand	181-183	3	1
β-strand	194-202	9	2
β-strand	205-208	4	2
β-strand	212-214	3	2
α-helix	216-218	3
β-strand	220-221	2	1
α-helix	222-225	4
β-strand	226-231	6	3
β-strand	240-245	6	3
α-helix	248-251	4
β-strand	255-263	9	4
β-strand	270-271	2	4
β-strand	283-286	4	3
α-helix	289-290	2
β-strand	294-303	10	4
α-helix	310-316	7
β-strand	317-320	4	4
α-helix	329-331	3
β-strand	333-334	2	5
β-strand	345-350	6	5
α-helix	352-355	4
α-helix	356-359	4
β-strand	365-371	7	6
β-strand	377-380	4	6
β-strand	387-391	5	5
α-helix	395	1
β-strand	396-398	3	7
β-strand	399-403	5	6
β-strand	411	1	6
β-strand	414-416	3	7
β-strand	431-434	4	8
β-strand	439-442	4	8
β-strand	452-460	9	9
α-helix	467-468	2
β-strand	469-474	6	9
β-strand	479-481	3	8
β-strand	491-500	10	9
β-strand	503-504	2	9
β-strand	508-512	5	9

Chain B: 9 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	133-134	2	18
α-helix	136-139	4
β-strand	141-147	7	19
β-strand	152-157	6	19
α-helix	161-163	3
β-strand	169-178	10	20
β-strand	186-192	7	20
β-strand	201-206	6	19
α-helix	211-213	3
β-strand	216-225	10	20
β-strand	232-233	2	18
α-helix	235-241	7
β-strand	242-244	3	20
β-strand	254-255	2	21
β-strand	259-262	4	22
β-strand	267-271	5	21
β-strand	277-281	5	22
β-strand	287	1	22
β-strand	290-291	2	21
β-strand	297-301	5	21
α-helix	304-307	4
α-helix	311	1
β-strand	312-318	7	22
β-strand	322-330	9	22
α-helix	332-336	5
β-strand	337-342	6	23
β-strand	343	1	24
β-strand	348-354	7	23
β-strand	368-373	6	25
β-strand	379-381	3	25
α-helix	382-384	3
β-strand	393-398	6	23
β-strand	405-413	9	25
β-strand	418-426	9	25
α-helix	427-429	3
β-strand	431	1	24
β-strand	437-440	4	26
β-strand	452-454	3	26
β-strand	464-471	8	27
β-strand	477-484	8	27
β-strand	491	1	26
β-strand	508	1	27
β-strand	513	1	27

Chain C: 1 helix, 19 β-strands

Element	Residues	Length	Sheet
β-strand	113-117	5	11
β-strand	118	1	12
β-strand	125	1	13
β-strand	126-130	5	11
β-strand	140-145	6	14
β-strand	166	1	13
β-strand	171	1	10
β-strand	177-184	8	14
β-strand	189-196	8	14
β-strand	202	1	12
α-helix	205-207	3
β-strand	211-214	4	15
β-strand	222-225	4	15
β-strand	240-241	2	16
β-strand	243-248	6	17
β-strand	255-258	4	17
β-strand	264-267	4	15
β-strand	276-280	5	17
β-strand	283-284	2	16
β-strand	299	1	17

Chain D: 5 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	13-42	30
β-strand	61	1	10
α-helix	69-93	25
α-helix	94-98	5
α-helix	103-129	27
α-helix	150-182	33

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Interleukin-6 receptor subunit beta	A	protein	625	Homo sapiens	P40189 (AlphaFold model)
Ciliary neurotrophic factor	D	protein	214	Homo sapiens	P26441 (AlphaFold model)
Ciliary neurotrophic factor receptor subunit alpha	C	protein	320	Homo sapiens	P26992 (AlphaFold model)
Leukemia inhibitory factor receptor	B	protein	817	Homo sapiens	P42702 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8D74_1 Interleukin-6 receptor subunit beta (chains A)
ELLDPCGYISPESPVVQLHSNFTAVCVLKEKCMDYFHVNANYIVWKTNHFTIPKEQYTII
NRTASSVTFTDIASLNIQLTCNILTFGQLEQNVYGITIISGLPPEKPKNLSCIVNEGKKM
RCEWDGGRETHLETNFTLKSEWATHKFADCKAKRDTPTSCTVDYSTVYFVNIEVWVEAEN
ALGKVTSDHINFDPVYKVKPNPPHNLSVINSEELSSILKLTWTNPSIKSVIILKYNIQYR
TKDASTWSQIPPEDTASTRSSFTVQDLKPFTEYVFRIRCMKEDGKGYWSDWSEEASGITY
EDRPSKAPSFWYKIDPSHTQGYRTVQLVWKTLPPFEANGKILDYEVTLTRWKSHLQNYTV
NATKLTVNLTNDRYLATLTVRNLVGKSDAAVLTIPACDFQATHPVMDLKAFPKDNMLWVE
WTTPRESVKKYILEWCVLSDKAPCITDWQQEDGTVHRTYLRGNLAESKCYLITVTPVYAD
GPGSPESIKAYLKQAPPSKGPTVRTKKVGKNEAVLEWDQLPVDVQNGFIRNYTIFYRTII
GNETAVNVDSSHTEYTLSSLTSDTLYMVRMAAYTDEGGKDGPEFTFTTPKFAQGEIEEQK
LISEEDLGGEQKLISEEDLHHHHHH

Sequence of entity 2 (D), FASTA

>8D74_2 Ciliary neurotrophic factor (chains D)
MAFTEHSPLTPHRRDLCSRSIWLARKIRSDLTALTESYVKHQGLNKNINLDSADGMPVAS
TDQWSELTEAERLQENLQAYRTFHVLLARLLEDQQVHFTPTEGDFHQAIHTLLLQVAAFA
YQIEELMILLEYKIPRNEADGMPINVGDGGLFEKKLWGLKVLQELSQWTVRSIHDLRFIS
SHQTGIEQKLISEEDLGGEQKLISEEDLHHHHHH

Sequence of entity 3 (C), FASTA

>8D74_3 Ciliary neurotrophic factor receptor subunit alpha (chains C)
QRHSPQEAPHVQYERLGSDVTLPCGTANWDAAVTWRVNGTDLAPDLLNGSQLVLHGLELG
HSGLYACFHRDSWHLRHQVLLHVGLPPREPVLSCRSNTYPKGFYCSWHLPTPTYIPNTFN
VTVLHGSKIMVCEKDPALKNRCHIRYMHLFSTIKYKVSISVSNALGHNATAITFDEFTIV
KPDPPENVVARPVPSNPRRLEVTWQTPSTWPDPESFPLKFFLRYRPLILDQWQHVELSDG
TAHTITDAYAGKEYIIQVAAKDNEIGTWSDWSVAAHATPWTEEPRHLTTEAQAAETTTST
TSSLAPPPTTKICDPGELGS

Sequence of entity 4 (B), FASTA

>8D74_4 Leukemia inhibitory factor receptor (chains B)
QKKGAPHDLKCVTNNLQVWNCSWKAPSGTGRGTDYEVCIENRSRSCYQLEKTSIKIPALS
HGDYEITINSLHDFGSSTSKFTLNEQNVSLIPDTPEILNLSADFSTSTLYLKWNDRGSVF
PHRSNVIWEIKVLRKESMELVKLVTHNTTLNGKDTLHHWSWASDMPLECAIHFVEIRCYI
DNLHFSGLEEWSDWSPVKNISWIPDSQTKVFPQDKVILVGSDITFCCVSQEKVLSALIGH
TNCPLIHLDGENVAIKIRNISVSASSGTNVVFTTEDNIFGTVIFAGYPPDTPQQLNCETH
DLKEIICSWNPGRVTALVGPRATSYTLVESFSGKYVRLKRAEAPTNESYQLLFQMLPNQE
IYNFTLNAHNPLGRSQSTILVNITEKVYPHTPTSFKVKDINSTAVKLSWHLPGNFAKINF
LCEIEIKKSNSVQEQRNVTIKGVENSSYLVALDKLNPYTLYTFRIRCSTETFWKWSKWSN
KKQHLTTEASPSKGPDTWREWSSDGKNLIIYWKPLPINEANGKILSYNVSCSSDEETQSL
SEIPDPQHKAEIRLDKNDYIISVVAKNSVGSSPPSKIASMEIPNDDLKIEQVVGMGKGIL
LTWHYDPNMTCDYVIKWCNSSRSEPCLMDWRKVPSNSTETVIESDEFRPGIRYNFFLYGC
RNQGYQLLRSMIGYIEELAPIVAPNFTVEDTSADSILVKWEDIPVEELRGFLRGYLFYFG
KGERDTSKMRVLESGRSDIKVKNITDISQKTLRIADLQGKTSYHLVLRAYTDGGVGPEKS
MYVVTKENSEQKLISEEDLGGEQKLISEEDLHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6

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 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
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
3L5H 3.6 Å, Crystal structure of the full ectodomain of human gp130: New insights into the molecular…

Browse structure collections

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