8UPA: Gp130

Name: PDB 8UPA: Structure of gp130 in complex with a de novo designed IL-6 mimetic
Published: 2024-08-28
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: cytokine

Structure of gp130 in complex with a de novo designed IL-6 mimetic. Determined by X-ray diffraction at 3.3 Å resolution. Released 28 Aug 2024.

Method: X-ray diffraction
Resolution: 3.3 Å
Organisms: synthetic construct, Homo sapiens
Chains: 4
Atoms: 4,133
Mol. weight: 60.54 kDa
Ligands: PO4, NAG
Released: 28 Aug 2024

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

Secondary structure: helices and β-sheets

8UPA contains 22 α-helices and 35 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: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	2-19	18
α-helix	22-39	18
α-helix	42-55	14

Chain B: 8 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	125-129	5
β-strand	130-135	6	1
β-strand	136-137	2	2
β-strand	143-147	5	1
β-strand	157-164	8	3
β-strand	167-168	2	3
α-helix	169-171	3
β-strand	172-173	2	3
α-helix	174-175	2
β-strand	181-183	3	1
α-helix	187-188	2
β-strand	194-202	9	3
β-strand	205-208	4	3
β-strand	212-214	3	3
α-helix	216-218	3
β-strand	220-221	2	2
α-helix	222-225	4
β-strand	226-230	5	4
β-strand	240-245	6	4
α-helix	248-251	4
β-strand	255-263	9	5
β-strand	270-271	2	5
β-strand	283-286	4	4
β-strand	294-303	10	5
α-helix	313-316	4
β-strand	317-320	4	5

Chain C: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	2-19	18
α-helix	22-38	17
α-helix	42-55	14

Chain D: 8 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	125-129	5
β-strand	130-137	8	6
β-strand	142-147	6	6
β-strand	157-164	8	7
β-strand	167-168	2	7
α-helix	169-171	3
β-strand	172-173	2	7
α-helix	174-175	2
β-strand	181-183	3	6
α-helix	187-188	2
β-strand	194-202	9	7
β-strand	205-208	4	7
β-strand	212-214	3	7
α-helix	216-218	3
β-strand	220-221	2	6
α-helix	222-225	4
β-strand	226-229	4	8
β-strand	240-245	6	8
α-helix	248-251	4
β-strand	255-261	7	9
β-strand	270-271	2	9
β-strand	283-286	4	8
β-strand	297-303	7	9
α-helix	313-316	4
β-strand	317	1	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
De novo designed IL-6 mimetic	A, C	protein	56	synthetic construct
Interleukin-6 receptor subunit beta	B, D	protein	203	Homo sapiens	P40189 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>8UPA_1 De novo designed IL-6 mimetic (chains A, C)
DISERFRRLMRRADELARRGNPEEARKVLEEAEELMERYGSPELLESVRMLLEVLG

Sequence of entity 2 (B, D), FASTA

>8UPA_2 Interleukin-6 receptor subunit beta (chains B, D)
DGSLPPEKPKNLSCIVNEGKKMRCEWDGGRETHLETNFTLKSEWATHKFADCKAKRDTPT
SCTVDYSTVYFVNIEVWVEAENALGKVTSDHINFDPVYKVKPNPPHNLSVINSEELSSIL
KLTWTNPSIKSVIILKYNIQYRTKDASTWSQIPPEDTASTRSSFTVQDLKPFTEYVFRIR
CMKEDGKGYWSDWSEEASGITAA

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

Primary citation

De novo design of miniprotein antagonists of cytokine storm inducers. Huang, B., Coventry, B., Borowska, M.T. et al. Nat Commun (2024) 15:7064-7064. DOI 10.1038/s41467-024-50919-4 · 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…
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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