8TH1: G3BP1 NTF2-like domain

Crystal Structure of the G3BP1 NTF2-like domain bound to the IDR1 of SARS-CoV-2 nucleocapsid protein D3L mutant. Determined by X-ray diffraction at 1.8 Å resolution. Released 27 Dec 2023.

Method: X-ray diffraction
Resolution: 1.8 Å
Organisms: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Chains: 8
Atoms: 4,870
Mol. weight: 84.48 kDa
Released: 27 Dec 2023

Explore 8TH1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8TH1 contains 29 α-helices and 35 β-strands across 8 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: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	1
α-helix	8-25	18
α-helix	27-33	7
β-strand	34-42	9	2
β-strand	45	1	3
β-strand	51	1	3
α-helix	52-54	3
β-strand	55-56	2	2
α-helix	58-67	10
β-strand	74-84	11	2
α-helix	86-88	3
β-strand	90-99	10	2
β-strand	106-116	11	2
β-strand	123-133	11	2
α-helix	135-138	4

Chain B: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	8-25	18
α-helix	27-33	7
β-strand	34-42	9	1
β-strand	45	1	4
β-strand	51	1	4
α-helix	52-54	3
β-strand	55-56	2	1
α-helix	57-67	11
β-strand	74-84	11	1
α-helix	86-88	3
β-strand	90-99	10	1
β-strand	106-116	11	1
β-strand	123-133	11	1
α-helix	135-138	4

Chain C: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	4-7	4
α-helix	8-25	18
α-helix	27-33	7
β-strand	34-42	9	5
α-helix	52-54	3
β-strand	55-56	2	5
α-helix	57-67	11
β-strand	74-84	11	5
α-helix	86-88	3
β-strand	90-99	10	5
α-helix	103-105	3
β-strand	106-116	11	5
β-strand	123-133	11	5
α-helix	135-138	4

Chain D: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	8-25	18
α-helix	27-33	7
β-strand	34-42	9	6
β-strand	45	1	7
α-helix	50	1
β-strand	51	1	7
α-helix	52-54	3
β-strand	55-56	2	6
α-helix	57-67	11
β-strand	74-84	11	6
α-helix	86-88	3
β-strand	90-99	10	6
α-helix	103-105	3
β-strand	106-116	11	6
β-strand	123-133	11	6

Chains E, F and G: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	16-17	2	2

Chain H: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	13-15	3
β-strand	16-17	2	6
α-helix	19-21	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ras GTPase-activating protein-binding protein 1	A, B, C, D	protein	164	Homo sapiens	Q13283 (AlphaFold model)
Nucleoprotein	E, F, G, H	protein	25	Severe acute respiratory syndrome coronavirus 2	P0DTC9 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>8TH1_1 Ras GTPase-activating protein-binding protein 1 (chains A, B, C, D)
MSLNGPQNQRNAPRITFGGPSDSTSMVMEKPSPLLVGREFVRQYYTLLNQAPDMLHRFYG
KNSSYVHGGLDSNGKPADAVYGQKEIHRKVMSQNFTNCHTKIRHVDAHATLNDGVVVQVM
GLLSNNNQALRRFMQTFVLAPEGSVANKFYVHNDIFRYQDEVFG

Sequence of entity 2 (E, F, G, H), FASTA

>8TH1_2 Nucleoprotein (chains E, F, G, H)
MSLNGPQNQRNAPRITFGGPSDSTG

Primary citation

Interaction between host G3BP and viral nucleocapsid protein regulates SARS-CoV-2 replication and pathogenicity. Yang, Z., Johnson, B.A., Meliopoulos, V.A. et al. Cell Rep (2024) 43:113965-113965. DOI 10.1016/j.celrep.2024.113965 · 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
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
9CC6 2.4 Å, De novo design of high-affinity protein binders to RNA binding domain of G3bp1
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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