8TH5: G3BP1 NTF2-like domain

Crystal Structure of the G3BP1 NTF2-like domain bound to the IDR1 of SARS-CoV-2 nucleocapsid protein P13L mutant. Determined by X-ray diffraction at 2.62 Å resolution. Released 20 Mar 2024.

Method: X-ray diffraction
Resolution: 2.62 Å
Organisms: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Chains: 17
Atoms: 10,350
Mol. weight: 177.35 kDa
Released: 20 Mar 2024

Explore 8TH5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8TH5 contains 44 α-helices and 77 β-strands across 17 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: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	8-25	18
α-helix	27-33	7
β-strand	34	1	1
β-strand	39-40	2	2
β-strand	41	1	1
α-helix	52-54	3
β-strand	55-56	2	2
α-helix	57-67	11
β-strand	75-85	11	1
β-strand	89-98	10	1
β-strand	106-116	11	1
β-strand	123-133	11	1

Chain B: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	8-25	18
α-helix	27-33	7
β-strand	34-40	7	3
β-strand	55-56	2	3
α-helix	58-67	10
β-strand	74-85	12	3
β-strand	89-99	11	3
β-strand	106-116	11	3
β-strand	123-133	11	3

Chain C: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	8-25	18
α-helix	27-29	3
α-helix	31-33	3
β-strand	34-41	8	4
β-strand	55-56	2	4
α-helix	57-67	11
β-strand	74-84	11	4
α-helix	86-88	3
β-strand	90-99	10	4
β-strand	106-116	11	4
β-strand	124-133	10	4
α-helix	134-137	4

Chain D: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	4-7	4
α-helix	8-25	18
α-helix	28-33	6
β-strand	34-41	8	5
β-strand	55-56	2	5
α-helix	57-66	10
β-strand	74-85	12	5
α-helix	86-88	3
β-strand	89-99	11	5
β-strand	106-116	11	5
β-strand	124-133	10	5

Chain E: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3
α-helix	8-25	18
α-helix	31-33	3
β-strand	34-41	8	6
α-helix	52-54	3
β-strand	55-56	2	6
α-helix	58-67	10
β-strand	74-85	12	6
β-strand	89-99	11	6
β-strand	106-116	11	6
β-strand	123-133	11	6

Chain F: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	8-25	18
α-helix	27-33	7
β-strand	34	1	7
β-strand	39-41	3	7
β-strand	55-56	2	7
α-helix	58-66	9
β-strand	74-84	11	7
α-helix	86-88	3
β-strand	90-99	10	7
β-strand	106-116	11	7
β-strand	123	1	8
β-strand	124-130	7	7
β-strand	133	1	7

Chain G: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3
α-helix	8-25	18
α-helix	31-33	3
β-strand	39-42	4	9
β-strand	45	1	10
β-strand	51	1	10
α-helix	52-54	3
β-strand	55-56	2	9
α-helix	58-67	10
β-strand	74-84	11	9
β-strand	90-99	10	9
β-strand	106-115	10	9
β-strand	125-133	9	9
α-helix	134-136	3

Chain H: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	8-25	18
β-strand	34-40	7	11
β-strand	43	1	11
β-strand	45	1	12
α-helix	50	1
β-strand	51	1	12
α-helix	52-54	3
β-strand	55-56	2	11
α-helix	58-68	11
β-strand	76-85	10	11
β-strand	89-98	10	11
β-strand	106-116	11	11
β-strand	124-133	10	11

6 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ras GTPase-activating protein-binding protein 1	A, B, C, D, E, F, G, H, I, J	protein	139	Homo sapiens	Q13283 (AlphaFold model)
Nucleoprotein	K, L, M, N, O, P, Q	protein	25	Severe acute respiratory syndrome coronavirus 2	P0DTC9 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H, I, J), FASTA

>8TH5_1 Ras GTPase-activating protein-binding protein 1 (chains A, B, C, D, E, F, G, H, I, J)
MVMEKPSPLLVGREFVRQYYTLLNQAPDMLHRFYGKNSSYVHGGLDSNGKPADAVYGQKE
IHRKVMSQNFTNCHTKIRHVDAHATLNDGVVVQVMGLLSNNNQALRRFMQTFVLAPEGSV
ANKFYVHNDIFRYQDEVFG

Sequence of entity 2 (K, L, M, N, O, P, Q), FASTA

>8TH5_2 Nucleoprotein (chains K, L, M, N, O, P, Q)
MSDNGPQNQRNALRITFGGPSDSTG

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
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
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…
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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