8D7R: Cardiotrophin-like cytokine factor 1

Name: PDB 8D7R: Cryo-EM structure of human CLCF1 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 CLCF1 signaling complex: model containing the interaction core region. Determined by electron microscopy at 3.9 Å resolution. Released 29 Mar 2023.

Method: Electron microscopy
Resolution: 3.9 Å
Organism: Homo sapiens
Chains: 4
Atoms: 9,627
Mol. weight: 226.76 kDa
Ligands: NAG
Released: 29 Mar 2023

Explore 8D7R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8D7R contains 22 α-helices and 100 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: 8 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	136-137	2	24
β-strand	143	1	25
β-strand	159-161	3	26
α-helix	168-171	4
β-strand	183	1	25
β-strand	194-196	3	27
β-strand	197-199	3	26
β-strand	200-201	2	28
β-strand	206-207	2	28
β-strand	212-214	3	27
β-strand	220-221	2	24
α-helix	223-225	3
β-strand	226-231	6	29
β-strand	239-245	7	29
β-strand	255-263	9	30
β-strand	270-271	2	30
α-helix	272-273	2
α-helix	274-276	3
β-strand	283-287	5	29
β-strand	295-303	9	30
α-helix	315-316	2
β-strand	317	1	30
α-helix	329-331	3
β-strand	333	1	31
β-strand	347-349	3	32
β-strand	350	1	31
α-helix	352-355	4
α-helix	356-359	4
β-strand	365-371	7	33
β-strand	377-378	2	33
β-strand	387-389	3	32
β-strand	396-403	8	33
β-strand	408	1	33
β-strand	415-416	2	33
β-strand	431-432	2	34
β-strand	441-442	2	34
β-strand	452-457	6	35
β-strand	459-460	2	35
β-strand	469-474	6	35
β-strand	479	1	34
β-strand	491-500	10	35
β-strand	503-504	2	35
β-strand	508-512	5	35

Chain B: 5 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	133-134	2	10
α-helix	136-139	4
β-strand	143-147	5	11
β-strand	152-158	7	11
β-strand	169-178	10	12
β-strand	186-192	7	12
β-strand	194	1	13
β-strand	197	1	13
β-strand	200-206	7	11
β-strand	216-225	10	12
β-strand	232-233	2	10
α-helix	235-241	7
β-strand	242-244	3	12
β-strand	254-255	2	14
β-strand	260-262	3	15
β-strand	267-272	6	14
β-strand	277-281	5	16
β-strand	287	1	16
β-strand	290-291	2	14
β-strand	296-301	6	14
α-helix	311	1
β-strand	312-318	7	16
β-strand	322-327	6	16
β-strand	328-330	3	15
α-helix	331-336	6
β-strand	337-342	6	17
β-strand	343	1	18
β-strand	348-349	2	19
β-strand	350-354	5	17
β-strand	368-372	5	20
β-strand	379-381	3	20
β-strand	394	1	17
β-strand	397-398	2	19
α-helix	399-400	2
β-strand	406-413	8	20
β-strand	419-425	7	20
β-strand	431	1	18
β-strand	437	1	21
β-strand	454	1	21
β-strand	464	1	22
β-strand	467-471	5	23
β-strand	477-481	5	23
β-strand	484	1	22
β-strand	491	1	21
β-strand	506-510	5	23
β-strand	513	1	22
β-strand	526	1	23

Chain C: 2 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	113	1	2
β-strand	117	1	3
β-strand	118	1	4
β-strand	125	1	5
β-strand	126	1	3
β-strand	130	1	2
β-strand	144-145	2	6
β-strand	152	1	6
β-strand	166	1	5
α-helix	167-168	2
β-strand	171	1	1
β-strand	178-182	5	6
β-strand	191-195	5	6
β-strand	202	1	4
α-helix	205-207	3
β-strand	211-214	4	7
β-strand	222-225	4	7
β-strand	240	1	8
β-strand	243-248	6	9
β-strand	256-258	3	9
β-strand	265-267	3	7
β-strand	276-280	5	9
β-strand	284	1	8
β-strand	299	1	9

Chain D: 7 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	36-64	29
α-helix	67-70	4
α-helix	85-86	2
β-strand	89	1	1
α-helix	91-96	6
α-helix	101-123	23
α-helix	127-153	27
α-helix	177-209	33

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cardiotrophin-like cytokine factor 1	D	protein	204	Homo sapiens	Q9UBD9 (AlphaFold model)
Ciliary neurotrophic factor receptor subunit alpha	C	protein	324	Homo sapiens	P26992 (AlphaFold model)
Leukemia inhibitory factor receptor	B	protein	817	Homo sapiens	P42702 (AlphaFold model)
Interleukin-6 receptor subunit beta	A	protein	625	Homo sapiens	P40189 (AlphaFold model)

Sequence of entity 1 (D), FASTA

>8D7R_1 Cardiotrophin-like cytokine factor 1 (chains D)
LNRTGDPGPGPSIQKTYDLTRYLEHQLRSLAGTYLNYLGPPFNEPDFNPPRLGAETLPRA
TVDLEVWRSLNDKLRLTQNYEAYSHLLCYLRGLNRQAATAELRRSLAHFCTSLQGLLGSI
AGVMAALGYPLPQPLPGTEPTWTPGPAHSDFLQKMDDFWLLKELQTWLWRSAKDFNRLKK
KMQPPAAAVTLHLGAHGFHHHHHH

Sequence of entity 2 (C), FASTA

>8D7R_2 Ciliary neurotrophic factor receptor subunit alpha (chains C)
QRHSPQEAPHVQYERLGSDVTLPCGTANWDAAVTWRVNGTDLAPDLLNGSQLVLHGLELG
HSGLYACFHRDSWHLRHQVLLHVGLPPREPVLSCRSNTYPKGFYCSWHLPTPTYIPNTFN
VTVLHGSKIMVCEKDPALKNRCHIRYMHLFSTIKYKVSISVSNALGHNATAITFDEFTIV
KPDPPENVVARPVPSNPRRLEVTWQTPSTWPDPESFPLKFFLRYRPLILDQWQHVELSDG
TAHTITDAYAGKEYIIQVAAKDNEIGTWSDWSVAAHATPWTEEPRHLTTEAQAAETTTST
TSSLAPPPTTKICDPGELGSGGGP

Sequence of entity 3 (B), FASTA

>8D7R_3 Leukemia inhibitory factor receptor (chains B)
QKKGAPHDLKCVTNNLQVWNCSWKAPSGTGRGTDYEVCIENRSRSCYQLEKTSIKIPALS
HGDYEITINSLHDFGSSTSKFTLNEQNVSLIPDTPEILNLSADFSTSTLYLKWNDRGSVF
PHRSNVIWEIKVLRKESMELVKLVTHNTTLNGKDTLHHWSWASDMPLECAIHFVEIRCYI
DNLHFSGLEEWSDWSPVKNISWIPDSQTKVFPQDKVILVGSDITFCCVSQEKVLSALIGH
TNCPLIHLDGENVAIKIRNISVSASSGTNVVFTTEDNIFGTVIFAGYPPDTPQQLNCETH
DLKEIICSWNPGRVTALVGPRATSYTLVESFSGKYVRLKRAEAPTNESYQLLFQMLPNQE
IYNFTLNAHNPLGRSQSTILVNITEKVYPHTPTSFKVKDINSTAVKLSWHLPGNFAKINF
LCEIEIKKSNSVQEQRNVTIKGVENSSYLVALDKLNPYTLYTFRIRCSTETFWKWSKWSN
KKQHLTTEASPSKGPDTWREWSSDGKNLIIYWKPLPINEANGKILSYNVSCSSDEETQSL
SEIPDPQHKAEIRLDKNDYIISVVAKNSVGSSPPSKIASMEIPNDDLKIEQVVGMGKGIL
LTWHYDPNMTCDYVIKWCNSSRSEPCLMDWRKVPSNSTETVIESDEFRPGIRYNFFLYGC
RNQGYQLLRSMIGYIEELAPIVAPNFTVEDTSADSILVKWEDIPVEELRGFLRGYLFYFG
KGERDTSKMRVLESGRSDIKVKNITDISQKTLRIADLQGKTSYHLVLRAYTDGGVGPEKS
MYVVTKENSEQKLISEEDLGGEQKLISEEDLHHHHHH

Sequence of entity 4 (A), FASTA

>8D7R_4 Interleukin-6 receptor subunit beta (chains A)
ELLDPCGYISPESPVVQLHSNFTAVCVLKEKCMDYFHVNANYIVWKTNHFTIPKEQYTII
NRTASSVTFTDIASLNIQLTCNILTFGQLEQNVYGITIISGLPPEKPKNLSCIVNEGKKM
RCEWDGGRETHLETNFTLKSEWATHKFADCKAKRDTPTSCTVDYSTVYFVNIEVWVEAEN
ALGKVTSDHINFDPVYKVKPNPPHNLSVINSEELSSILKLTWTNPSIKSVIILKYNIQYR
TKDASTWSQIPPEDTASTRSSFTVQDLKPFTEYVFRIRCMKEDGKGYWSDWSEEASGITY
EDRPSKAPSFWYKIDPSHTQGYRTVQLVWKTLPPFEANGKILDYEVTLTRWKSHLQNYTV
NATKLTVNLTNDRYLATLTVRNLVGKSDAAVLTIPACDFQATHPVMDLKAFPKDNMLWVE
WTTPRESVKKYILEWCVLSDKAPCITDWQQEDGTVHRTYLRGNLAESKCYLITVTPVYAD
GPGSPESIKAYLKQAPPSKGPTVRTKKVGKNEAVLEWDQLPVDVQNGFIRNYTIFYRTII
GNETAVNVDSSHTEYTLSSLTSDTLYMVRMAAYTDEGGKDGPEFTFTTPKFAQGEIEEQK
LISEEDLGGEQKLISEEDLHHHHHH

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 Q9UBD9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8D7H 3.4 Å, Cryo-EM structure of human CLCF1 in complex with CRLF1 and CNTFR alpha

Browse structure collections

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