8V1L: NTF2L domain of human G3BP1

Crystal structure of the NTF2L domain of human G3BP1 in complex with small molecule. Determined by X-ray diffraction at 2.68 Å resolution. Released 14 Feb 2024.

Method: X-ray diffraction
Resolution: 2.68 Å
Organism: Homo sapiens
Chains: 6
Atoms: 6,490
Mol. weight: 99.68 kDa
Ligands: Y9M
Released: 14 Feb 2024

Explore 8V1L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8V1L contains 31 α-helices and 44 β-strands across 6 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	8-24	17
α-helix	27-33	7
β-strand	34-41	8	1
β-strand	55-56	2	1
α-helix	57-67	11
β-strand	74	1	2
β-strand	77-85	9	1
α-helix	86-88	3
β-strand	89-97	9	1
β-strand	99	1	2
β-strand	107-116	10	1
β-strand	124-133	10	1
α-helix	134-136	3

Chain B: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	8-22	15
α-helix	27-33	7
β-strand	34	1	3
β-strand	39-40	2	4
β-strand	41	1	3
β-strand	45	1	5
β-strand	51	1	5
α-helix	52-54	3
β-strand	55-56	2	4
α-helix	57-66	10
β-strand	74-85	12	3
α-helix	86-88	3
β-strand	89-99	11	3
β-strand	106-116	11	3
β-strand	124-133	10	3

Chain C: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	8-25	18
α-helix	30-33	4
β-strand	34	1	6
β-strand	39-40	2	6
α-helix	52-54	3
β-strand	55-56	2	6
α-helix	58-67	10
β-strand	75-85	11	6
β-strand	89-98	10	6
β-strand	106-116	11	6
β-strand	124-133	10	6
α-helix	134-137	4

Chain D: 4 helices, 7 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
α-helix	53-54	2
β-strand	55-56	2	7
α-helix	57-67	11
β-strand	74-85	12	7
β-strand	89-99	11	7
β-strand	106-116	11	7
β-strand	124-133	10	7

Chain E: 7 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	39-42	4	8
α-helix	51-53	3
β-strand	55-56	2	8
α-helix	57-66	10
β-strand	74-84	11	8
α-helix	86-88	3
β-strand	90-99	10	8
α-helix	104-105	2
β-strand	106-116	11	8
β-strand	124-133	10	8

Chain F: 5 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	39-41	3	9
α-helix	53-54	2
β-strand	55-56	2	9
α-helix	58-66	9
β-strand	74-85	12	9
β-strand	89-99	11	9
β-strand	106-116	11	9
β-strand	124-133	10	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ras GTPase-activating protein-binding protein 1	A, B, C, D, E, F	protein	139	Homo sapiens	Q13283 (AlphaFold model)

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

>8V1L_1 Ras GTPase-activating protein-binding protein 1 (chains A, B, C, D, E, F)
MVMEKPSPLLVGREFVRQYYTLLNQAPDMLHRFYGKNSSYVHGGLDSNGKPADAVYGQKE
IHRKVMSQNFTNCHTKIRHVDAHATLNDGVVVQVMGLLSNNNQALRRFMQTFVLAPEGSV
ANKFYVHNDIFRYQDEVFG

Ligands and cofactors

ID	Name	Formula	Copies
Y9M	N-[(2S)-2-fluoro-4,4-dimethylpentanoyl]-3-hydroxy-L-valyl-(betaS)-beta-methyl-L…	C38 H56 F N5 O7	6

Primary citation

Identification of small molecule inhibitors of G3BP-driven stress granule formation. Freibaum, B.D., Messing, J., Nakamura, H. et al. J Cell Biol (2024) 223. DOI 10.1083/jcb.202308083 · 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…
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…

Browse structure collections

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