8D7H: Human CLCF1

Name: PDB 8D7H: Cryo-EM structure of human CLCF1 in complex with CRLF1 and CNTFR alpha
Published: 2023-03-29
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: cytokine

Cryo-EM structure of human CLCF1 in complex with CRLF1 and CNTFR alpha. Determined by electron microscopy at 3.4 Å resolution. Released 29 Mar 2023.

Method: Electron microscopy
Resolution: 3.4 Å
Organism: Homo sapiens
Chains: 6
Atoms: 12,540
Mol. weight: 219.47 kDa
Ligands: NAG
Released: 29 Mar 2023

Explore 8D7H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8D7H contains 41 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 E: 7 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	42-44	3	12
β-strand	49-51	3	13
β-strand	56-61	6	12
α-helix	70-73	4
β-strand	75-78	4	14
β-strand	81-82	2	14
α-helix	83-84	2
β-strand	88-92	5	12
β-strand	95-100	6	12
β-strand	112-117	6	14
β-strand	123-129	7	14
β-strand	130-132	3	13
β-strand	139-146	8	15
β-strand	151-156	6	15
β-strand	168-175	8	16
β-strand	182-183	2	16
β-strand	186-187	2	15
β-strand	194-197	4	15
β-strand	207-214	8	16
β-strand	219-221	3	16
α-helix	222-224	3
β-strand	225-227	3	16
α-helix	229-231	3
β-strand	233-234	2	15
α-helix	236-238	3
β-strand	242-244	3	17
β-strand	254-256	3	17
β-strand	270-278	9	18
β-strand	284-286	3	18
β-strand	295-296	2	17
α-helix	301-302	2
β-strand	306-315	10	18
α-helix	326-330	5
β-strand	334-337	4	18

Chain C: 5 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	30-31	2
β-strand	32-36	5	1
β-strand	41-45	5	2
β-strand	55-59	5	1
β-strand	62-63	2	1
α-helix	64-65	2
α-helix	66-68	3
β-strand	69-70	2	2
β-strand	73-77	5	2
α-helix	81-83	3
β-strand	85-91	7	1
β-strand	97-105	9	1
β-strand	113-114	2	3
β-strand	117	1	4
β-strand	118	1	5
β-strand	125	1	6
β-strand	126	1	4
β-strand	129-130	2	3
β-strand	140-145	6	7
β-strand	166	1	6
β-strand	171	1	8
β-strand	177-184	8	7
β-strand	189-196	8	7
β-strand	202	1	5
α-helix	205-207	3
β-strand	211-214	4	9
β-strand	222-225	4	9
β-strand	240	1	10
β-strand	243-248	6	11
β-strand	255-258	4	11
β-strand	264-267	4	9
β-strand	276-281	6	11
β-strand	284	1	10
β-strand	299	1	11

Chains D and H: 9 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	36-65	30
α-helix	68-70	3
α-helix	85-86	2
β-strand	89	1	8
α-helix	91-96	6
α-helix	101-119	19
α-helix	120-122	3
α-helix	127-153	27
α-helix	177-204	28
α-helix	205-209	5

Chain G: 4 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	30-31	2
β-strand	32-36	5	19
β-strand	41-45	5	20
β-strand	55-59	5	19
β-strand	62-63	2	19
α-helix	66-68	3
β-strand	69-70	2	20
β-strand	73-77	5	20
α-helix	81-83	3
β-strand	85-91	7	19
β-strand	97-105	9	19
β-strand	113-114	2	21
β-strand	117	1	22
β-strand	118	1	23
β-strand	125	1	24
β-strand	126	1	22
β-strand	129-130	2	21
β-strand	140-145	6	25
β-strand	166	1	24
β-strand	171	1	26
β-strand	177-184	8	25
β-strand	189-196	8	25
β-strand	202	1	23
α-helix	205-207	3
β-strand	211-214	4	27
β-strand	222-225	4	27
β-strand	240	1	28
β-strand	243-248	6	29
β-strand	255-258	4	29
β-strand	264-267	4	27
β-strand	276-281	6	29
β-strand	284	1	28
β-strand	299	1	29

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ciliary neurotrophic factor receptor subunit alpha	C, G	protein	348	Homo sapiens	P26992 (AlphaFold model)
Cardiotrophin-like cytokine factor 1	D, H	protein	204	Homo sapiens	Q9UBD9 (AlphaFold model)
Cytokine receptor-like factor 1	A, E	protein	395	Homo sapiens	O75462 (AlphaFold model)

Sequence of entity 1 (C, G), FASTA

>8D7H_1 Ciliary neurotrophic factor receptor subunit alpha (chains C, G)
QRHSPQEAPHVQYERLGSDVTLPCGTANWDAAVTWRVNGTDLAPDLLNGSQLVLHGLELG
HSGLYACFHRDSWHLRHQVLLHVGLPPREPVLSCRSNTYPKGFYCSWHLPTPTYIPNTFN
VTVLHGSKIMVCEKDPALKNRCHIRYMHLFSTIKYKVSISVSNALGHNATAITFDEFTIV
KPDPPENVVARPVPSNPRRLEVTWQTPSTWPDPESFPLKFFLRYRPLILDQWQHVELSDG
TAHTITDAYAGKEYIIQVAAKDNEIGTWSDWSVAAHATPWTEEPRHLTTEAQAAETTTST
TSSLAPPPTTKICDPGELGSEQKLISEEDLGGEQKLISEEDLHHHHHH

Sequence of entity 2 (D, H), FASTA

>8D7H_2 Cardiotrophin-like cytokine factor 1 (chains D, H)
LNRTGDPGPGPSIQKTYDLTRYLEHQLRSLAGTYLNYLGPPFNEPDFNPPRLGAETLPRA
TVDLEVWRSLNDKLRLTQNYEAYSHLLCYLRGLNRQAATAELRRSLAHFCTSLQGLLGSI
AGVMAALGYPLPQPLPGTEPTWTPGPAHSDFLQKMDDFWLLKELQTWLWRSAKDFNRLKK
KMQPPAAAVTLHLGAHGFHHHHHH

Sequence of entity 3 (A, E), FASTA

>8D7H_3 Cytokine receptor-like factor 1 (chains A, E)
AHTAVISPQDPTLLIGSSLLATCSVHGDPPGATAEGLYWTLNGRRLPPELSRVLNASTLA
LALANLNGSRQRSGDNLVCHARDGSILAGSCLYVGLPPEKPVNISCWSKNMKDLTCRWTP
GAHGETFLHTNYSLKYKLRWYGQDNTCEEYHTVGPHSCHIPKDLALFTPYEIWVEATNRL
GSARSDVLTLDILDVVTTDPPPDVHVSRVGGLEDQLSVRWVSPPALKDFLFQAKYQIRYR
VEDSVDWKVVDDVSNQTSCRLAGLKPGTVYFVQVRCNPFGIYGSKKAGIWSEWSHPTAAS
TPRSERPGPGGGACEPRGGEPSSGPVRRELKQFLGWLKKHAYCSNLSFRLYDQWRAWMQK
SHKTRNQDEGILPSGRRGTARGPARHHHHHHHHHH

Ligands and cofactors

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

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 P26992 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8D7E 2.93 Å, Cryo-EM structure of human CNTFR alpha in complex with the Fab fragments of two antibodies
8D74 3.03 Å, Cryo-EM structure of human CNTF signaling complex: model containing the interaction core…
8D7R 3.9 Å, Cryo-EM structure of human CLCF1 signaling complex: model containing the interaction…
1UC6 Solution Structure of the Carboxyl Terminal Domain of the Ciliary Neurotrophic Factor…

Browse structure collections

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