9IVS: CHIKV nsP3 peptide

Cryo-EM structure of the CHIKV nsP3 peptide in complex with the NTF2L domain of G3BP1 (Conformation III). Determined by electron microscopy at 2.97 Å resolution. Released 9 Apr 2025.

Method: Electron microscopy
Resolution: 2.97 Å
Organisms: Homo sapiens, Chikungunya virus
Chains: 24
Atoms: 19,758
Mol. weight: 304.92 kDa
Released: 9 Apr 2025

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

Secondary structure: helices and β-sheets

9IVS contains 111 α-helices and 127 β-strands across 24 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, 6 β-strands

Element	Residues	Length	Sheet
α-helix	8-25	18
α-helix	27-32	6
β-strand	34-40	7	1
α-helix	51-54	4
β-strand	55-56	2	1
α-helix	57-68	12
β-strand	74-85	12	1
β-strand	89-99	11	1
α-helix	100-102	3
β-strand	106-116	11	1
α-helix	117	1
β-strand	123-133	11	1

Chain B: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	8-22	15
α-helix	27-33	7
β-strand	34-42	9	5
β-strand	45	1	6
α-helix	50	1
β-strand	51	1	6
α-helix	52-54	3
β-strand	55-56	2	5
α-helix	58-68	11
β-strand	74-84	11	5
α-helix	86-88	3
β-strand	90-99	10	5
β-strand	106-116	11	5
β-strand	123-133	11	5
α-helix	134-137	4

Chain C: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	8-25	18
α-helix	27-33	7
β-strand	34-41	8	2
β-strand	45	1	3
β-strand	51	1	3
β-strand	55-56	2	2
α-helix	59-67	9
β-strand	74-85	12	2
β-strand	89-99	11	2
β-strand	106-116	11	2
β-strand	123-133	11	2
α-helix	134-137	4

Chain D: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	8-25	18
α-helix	28-33	6
β-strand	39-42	4	4
β-strand	55-56	2	4
α-helix	57-68	12
β-strand	74-84	11	4
β-strand	90-99	10	4
β-strand	106-116	11	4
β-strand	123-133	11	4
α-helix	134-136	3

Chain E: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	8-25	18
α-helix	27-32	6
β-strand	39-40	2	20
β-strand	55-56	2	20
α-helix	57-68	12
β-strand	74-85	12	20
β-strand	89-99	11	20
β-strand	106-116	11	20
β-strand	124-133	10	20

Chain F: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	8-24	17
α-helix	27-33	7
β-strand	34-42	9	23
β-strand	45	1	24
α-helix	50	1
β-strand	51	1	24
α-helix	52-54	3
β-strand	55-56	2	23
α-helix	58-68	11
β-strand	74-84	11	23
α-helix	86-88	3
β-strand	90-99	10	23
β-strand	106-116	11	23
β-strand	123-133	11	23
α-helix	134-137	4

Chains G and R: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	8-25	18
α-helix	27-33	7
β-strand	34-42	9	21
β-strand	45	1	22
β-strand	51	1	22
α-helix	52	1
β-strand	55-56	2	21
α-helix	59-67	9
β-strand	74-84	11	21
α-helix	86-88	3
β-strand	90-99	10	21
β-strand	106-116	11	21
β-strand	123-133	11	21

Chain H: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	8-25	18
α-helix	27-33	7
β-strand	39-42	4	7
β-strand	55-56	2	7
α-helix	58-68	11
β-strand	74-85	12	7
β-strand	89-99	11	7
β-strand	106-116	11	7
β-strand	123-133	11	7

15 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, M, N, O, P, Q, R, S, T	protein	141	Homo sapiens	Q13283 (AlphaFold model)
Polyprotein P1234	I, J, K, L, U, V, W, X	protein	54	Chikungunya virus	A0A0U5KFN5

Sequence of entity 1 (A, B, C, D, E, F, G, H, M, N, O, P, Q, R, S, T), FASTA

>9IVS_1 Ras GTPase-activating protein-binding protein 1 (chains A, B, C, D, E, F, G, H, M, N, O, P, Q, R, S, T)
GASMVMEKPSPLLVGREFVRQYYTLLNQAPDMLHRFYGKNSSYVHGGLDSNGKPADAVYG
QKEIHRKVMSQNFTNCHTKIRHVDAHATLNDGVVVQVMGLLSNNNQALRRFMQTFVLAPE
GSVANKFYVHNDIFRYQDEVF

Sequence of entity 2 (I, J, K, L, U, V, W, X), FASTA

>9IVS_2 Polyprotein P1234 (chains I, J, K, L, U, V, W, X)
GPLGSETFPITFGDFNDGEIESLSSELLTFGDFLPGEVDDLTDSDWSTHHHHHH

Primary citation

Cryo-EM reveals a double oligomeric ring scaffold of the CHIKV nsP3 peptide in complex with the NTF2L domain of host G3BP1. Liu, Y., Wang, J., Han, Y. et al. mBio (2025) 16:e0396724-e0396724. DOI 10.1128/mbio.03967-24 · 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…

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