7SUO: G3BP1 NTF2-like domain

Crystal Structure of the G3BP1 NTF2-like domain bound to the IDR1 of SARS-CoV-2 nucleocapsid protein. Determined by X-ray diffraction at 2.35 Å resolution. Released 16 Mar 2022.

Method: X-ray diffraction
Resolution: 2.35 Å
Organisms: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Chains: 4
Atoms: 2,448
Mol. weight: 33.77 kDa
Released: 16 Mar 2022

Explore 7SUO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7SUO contains 10 α-helices and 18 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: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3
α-helix	8-25	18
α-helix	27-33	7
β-strand	34-42	9	1
β-strand	45	1	2
β-strand	51	1	2
β-strand	55-56	2	1
α-helix	58-67	10
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

Chain B: 5 helices, 8 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	3
β-strand	45	1	4
β-strand	51	1	4
β-strand	55-56	2	3
α-helix	58-68	11
β-strand	74-85	12	3
β-strand	89-99	11	3
β-strand	106-116	11	3
β-strand	123-133	11	3
α-helix	134-136	3

Chains C and D: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	16-17	2	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ras GTPase-activating protein-binding protein 1	A, B	protein	138	Homo sapiens	Q13283 (AlphaFold model)
Nucleoprotein	C, D	protein	11	Severe acute respiratory syndrome coronavirus 2	P0DTC9 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7SUO_1 Ras GTPase-activating protein-binding protein 1 (chains A, B)
VMEKPSPLLVGREFVRQYYTLLNQAPDMLHRFYGKNSSYVHGGLDSNGKPADAVYGQKEI
HRKVMSQNFTNCHTKIRHVDAHATLNDGVVVQVMGLLSNNNQALRRFMQTFVLAPEGSVA
NKFYVHNDIFRYQDEVFG

Sequence of entity 2 (C, D), FASTA

>7SUO_2 Nucleoprotein (chains C, D)
APRITFGGPSD

Primary citation

SARS-CoV-2 Nucleocapsid Protein Targets a Conserved Surface Groove of the NTF2-like Domain of G3BP1. Biswal, M., Lu, J., Song, J. J Mol Biol (2022) 434:167516-167516. DOI 10.1016/j.jmb.2022.167516 · 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
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…

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