9CC6: G3bp1 Binder

De novo design of high-affinity protein binders to RNA binding domain of G3bp1. Determined by X-ray diffraction at 2.4 Å resolution. Released 14 May 2025.

Method: X-ray diffraction
Resolution: 2.4 Å
Organisms: synthetic construct, Homo sapiens
Chains: 2
Atoms: 1,197
Mol. weight: 18.63 kDa
Released: 14 May 2025

Explore 9CC6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9CC6 contains 8 α-helices and 4 β-strands across 2 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, 3 β-strands

Element	Residues	Length	Sheet
α-helix	3-23	21
β-strand	26-32	7	1
α-helix	34-36	3
α-helix	37-52	16
α-helix	55-57	3
α-helix	58-72	15
β-strand	76-84	9	1
α-helix	87-89	3
α-helix	90-103	14
α-helix	108-122	15
β-strand	130-138	9	1

Chain B: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	143-149	7	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
G3bp1 Binder	A	protein	150	synthetic construct
Ras GTPase-activating protein-binding protein 1	B	protein	13	Homo sapiens	Q13283 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9CC6_1 G3bp1 Binder (chains A)
MSGMPPRVRRRVEELLRRARELAEELGIRVEVLEVDPEYELELTAVITLAILAVLAPPER
QDEVLELLRETLKTLSEVVESLAVSIWAPPEREEAARRVERLVEEAFNTTPETRERARKL
RDEARRDAEPDEVVVAVHLVPKGSHHHHHH

Sequence of entity 2 (B), FASTA

>9CC6_2 Ras GTPase-activating protein-binding protein 1 (chains B)
KPGFGVGRGLAPR

Primary citation

Diffusing protein binders to intrinsically disordered proteins. Liu, C., Wu, K., Choi, H. et al. Nature (2025) 644:809-817. DOI 10.1038/s41586-025-09248-9 · PubMed

Other PDB entries of the same protein (UniProt Q13283 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4FCJ 1.62 Å, Crystal structure of the NTF2-like domain of human G3BP1
3Q90 1.7 Å, Crystal structure of the NTF2 domain of Ras GTPase-activating protein-binding protein 1
8TH1 1.8 Å, Crystal Structure of the G3BP1 NTF2-like domain bound to the IDR1 of SARS-CoV-2…
5FW5 1.92 Å, Crystal structure of human G3BP1 in complex with Semliki Forest Virus nsP3-25 comprising…
6TA7 1.93 Å, Crystal structure of human G3BP1-NTF2 in complex with human CAPRIN1-derived solomon motif
8TH6 2.34 Å, Crystal Structure of the G3BP1 NTF2-like domain bound to USP10 peptide
7SUO 2.35 Å, Crystal Structure of the G3BP1 NTF2-like domain bound to the IDR1 of SARS-CoV-2…
7S17 2.36 Å, Crystal structure of human G3BP1-NTF2 with three mutations- F15W, F33W, and F124W
7XHG 2.46 Å, Crystal structure of the NTF2L domain of human G3BP1 in complex with the Caprin-1…
8TH5 2.62 Å, Crystal Structure of the G3BP1 NTF2-like domain bound to the IDR1 of SARS-CoV-2…
9IVQ 2.66 Å, Cryo-EM structure of the CHIKV nsP3 peptide in complex with the NTF2L domain of G3BP1…
7XHF 2.68 Å, Crystal structure of the NTF2L domain of human G3BP1 in complex with the USP10 derived…

Browse structure collections

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