9ivr

Cryo-EM structure of the CHIKV nsP3 peptide in complex with the NTF2L domain of G3BP1 (Conformation II)

Method: ELECTRON MICROSCOPY D_max: 127.5 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ras GTPase-activating protein-binding protein 1

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 24 PDB declaration: 24-meric（24） Consistent with protein copy count	Chain A； UniProt 1–138 Chain B； UniProt 1–138 Chain C； UniProt 1–138 Chain D； UniProt 1–138 Chain E； UniProt 1–138 Chain F； UniProt 1–138 Chain G； UniProt 1–138 Chain H； UniProt 1–138 Chain M； UniProt 1–138 Chain N； UniProt 1–138 Chain O； UniProt 1–138 Chain P； UniProt 1–138 Chain Q； UniProt 1–138 Chain R； UniProt 1–138 Chain S； UniProt 1–138 Chain T； UniProt 1–138	Not recorded	Polyprotein P1234 × 8 （A0A0U5KFN5）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.80 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9IVR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3Q90 Crystal structure of the NTF2 domain of Ras GTPase-activating protein-binding protein 1 Deposited 2011-01-07	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–139（139 aa） Fragment：unp residues 1-139 Chain B 1–139（139 aa） Fragment：unp residues 1-139	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；25% w/v PEG3350, 0.2M AMMONIUM ACETATE, 0.1M BIS-TRIS, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 5.5	Resolution 1.70 Å R-free 0.238
4FCJ Crystal structure of the NTF2-like domain of human G3BP1 Deposited 2012-05-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–139（139 aa） Fragment：NTF2-like domain Chain B 1–139（139 aa） Fragment：NTF2-like domain	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；279 K；20% PEG3350, 0.1 M Bis-tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K	Resolution 1.62 Å R-free 0.231
4FCM Crystal structure of the NTF2-like domain of human G3BP1 in complex with a peptide Deposited 2012-05-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–139（139 aa） Fragment：NTF2-like domain Chain B 1–139（139 aa） Fragment：NTF2-like domain	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；279 K；20% PEG3350, 0.1 M Bis-tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 279K	Resolution 2.69 Å R-free 0.282
4IIA Low resolution crystal structure of the NTF2-like domain of human G3BP1 Deposited 2012-12-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 11–139（129 aa） Fragment：NTF2-LIKE DOMAIN	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；1.6 M diammonium phosphate, 0.1 M MOPS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.359
5FW5 Crystal structure of human G3BP1 in complex with Semliki Forest Virus nsP3-25 comprising two FGDF motives Deposited 2016-02-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–139（139 aa） Fragment：NTF2-LIKE, RESIDUES 1-139 Chain B 1–139（139 aa） Fragment：NTF2-LIKE, RESIDUES 1-139	Not recorded	SO4 SULFATE ION × 8 ACT ACETATE ION × 4 GOL GLYCEROL × 8 K POTASSIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions 0.1 M SODIUM ACETATE TRIHYDRATE PH 4.6, 2 M AMMONIUMSULFATE	Resolution 1.92 Å R-free 0.202
6TA7 CRYSTAL STRUCTURE OF HUMAN G3BP1-NTF2 IN COMPLEX WITH HUMAN CAPRIN1-DERIVED SOLOMON MOTIF Deposited 2019-10-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–139（139 aa） Chain E 1–139（139 aa）	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.2M Sodium chloride, 0.1M Tris 8.0, 20% w/v PEG 4000 of the Proplex crystallization screen (Molecular Dimensions)	Resolution 1.93 Å R-free 0.252
6TA7 CRYSTAL STRUCTURE OF HUMAN G3BP1-NTF2 IN COMPLEX WITH HUMAN CAPRIN1-DERIVED SOLOMON MOTIF Deposited 2019-10-29	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–139（139 aa） Chain F 1–139（139 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.2M Sodium chloride, 0.1M Tris 8.0, 20% w/v PEG 4000 of the Proplex crystallization screen (Molecular Dimensions)	Resolution 1.93 Å R-free 0.252
6TA7 CRYSTAL STRUCTURE OF HUMAN G3BP1-NTF2 IN COMPLEX WITH HUMAN CAPRIN1-DERIVED SOLOMON MOTIF Deposited 2019-10-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–139（139 aa） Chain D 1–139（139 aa）	Not recorded	NA SODIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.2M Sodium chloride, 0.1M Tris 8.0, 20% w/v PEG 4000 of the Proplex crystallization screen (Molecular Dimensions)	Resolution 1.93 Å R-free 0.252
7S17 Crystal structure of human G3BP1-NTF2 with three mutations- F15W, F33W, and F124W Deposited 2021-09-01	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–138（138 aa） Chain B 1–138（138 aa）	Mutation：F15W, F33W, F124W Mutation：F15W, F33W, F124W	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；20% PEG 8000, 100 mM HEPES	Resolution 2.36 Å R-free 0.271
7SUO Crystal Structure of the G3BP1 NTF2-like domain bound to the IDR1 of SARS-CoV-2 nucleocapsid protein Deposited 2021-11-17	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 2–139（138 aa） Chain B 2–139（138 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277.15 K；20% propan-2-ol, 0.1 M MES monohydrate (pH 6.0), 20% PEG MME 20,000	Resolution 2.35 Å R-free 0.248
7XHF Crystal structure of the NTF2L domain of human G3BP1 in complex with the USP10 derived peptide Deposited 2022-04-08	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–139（139 aa） Chain B 1–139（139 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.1 M Sodium citrate tribasic dihydrate pH 5.0; 19 % w/v Polyethylene glycol 3,350	Resolution 2.68 Å R-free 0.254
7XHG Crystal structure of the NTF2L domain of human G3BP1 in complex with the Caprin-1 derived peptide Deposited 2022-04-08	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–139（139 aa） Chain D 1–139（139 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.2 M Sodium acetate trihydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 30 % w/v Polyethylene glycol 8,000	Resolution 2.46 Å R-free 0.275
7XHG Crystal structure of the NTF2L domain of human G3BP1 in complex with the Caprin-1 derived peptide Deposited 2022-04-08	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–139（139 aa） Chain C 1–139（139 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.2 M Sodium acetate trihydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 30 % w/v Polyethylene glycol 8,000	Resolution 2.46 Å R-free 0.275
8TH1 Crystal Structure of the G3BP1 NTF2-like domain bound to the IDR1 of SARS-CoV-2 nucleocapsid protein D3L mutant Deposited 2023-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–139（139 aa） Chain B 1–139（139 aa） Chain C 1–139（139 aa） Chain D 1–139（139 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；0.2 M sodium thiocyanate, 20% PEG 3350	Resolution 1.80 Å R-free 0.238
8TH5 Crystal Structure of the G3BP1 NTF2-like domain bound to the IDR1 of SARS-CoV-2 nucleocapsid protein P13L mutant Deposited 2023-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–139（139 aa） Chain F 1–139（139 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277.15 K；0.2 M lithium sulfate, 0.1 M Tris pH 8.5, 25% PEG3350	Resolution 2.62 Å R-free 0.336
8TH5 Crystal Structure of the G3BP1 NTF2-like domain bound to the IDR1 of SARS-CoV-2 nucleocapsid protein P13L mutant Deposited 2023-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–139（139 aa） Chain E 1–139（139 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277.15 K；0.2 M lithium sulfate, 0.1 M Tris pH 8.5, 25% PEG3350	Resolution 2.62 Å R-free 0.336
8TH5 Crystal Structure of the G3BP1 NTF2-like domain bound to the IDR1 of SARS-CoV-2 nucleocapsid protein P13L mutant Deposited 2023-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–139（139 aa） Chain H 1–139（139 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277.15 K；0.2 M lithium sulfate, 0.1 M Tris pH 8.5, 25% PEG3350	Resolution 2.62 Å R-free 0.336
8TH5 Crystal Structure of the G3BP1 NTF2-like domain bound to the IDR1 of SARS-CoV-2 nucleocapsid protein P13L mutant Deposited 2023-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–139（139 aa） Chain G 1–139（139 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277.15 K；0.2 M lithium sulfate, 0.1 M Tris pH 8.5, 25% PEG3350	Resolution 2.62 Å R-free 0.336
8TH5 Crystal Structure of the G3BP1 NTF2-like domain bound to the IDR1 of SARS-CoV-2 nucleocapsid protein P13L mutant Deposited 2023-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 1–139（139 aa） Chain J 1–139（139 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277.15 K；0.2 M lithium sulfate, 0.1 M Tris pH 8.5, 25% PEG3350	Resolution 2.62 Å R-free 0.336
8TH6 Crystal Structure of the G3BP1 NTF2-like domain bound to USP10 peptide Deposited 2023-07-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–139（139 aa） Chain D 1–139（139 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277.15 K；0.1 M HEPES pH 7.5, 25% PEG3350	Resolution 2.34 Å R-free 0.295
8TH6 Crystal Structure of the G3BP1 NTF2-like domain bound to USP10 peptide Deposited 2023-07-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–139（139 aa） Chain C 1–139（139 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277.15 K；0.1 M HEPES pH 7.5, 25% PEG3350	Resolution 2.34 Å R-free 0.295
8TH7 Crystal Structure of the G3BP1 NTF2-like domain bound to the Caprin1 peptide Deposited 2023-07-14	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–139（139 aa） Chain B 1–139（139 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291.15 K；1.8M tri-ammonium citrate pH 7.0	Resolution 2.88 Å R-free 0.277
8V1L Crystal structure of the NTF2L domain of human G3BP1 in complex with small molecule Deposited 2023-11-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–139（139 aa） Chain C 1–139（139 aa）	Not recorded	Y9M N-[(2S)-2-fluoro-4,4-dimethylpentanoyl]-3-hydroxy-L-valyl-(betaS)-beta-methyl-L-phenylalanyl-D-alanyl-N-benzyl-N,O-dimethyl-L-homoserinamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.1 M MES pH 6.5, 15% PEG 550 MME	Resolution 2.68 Å R-free 0.395
8V1L Crystal structure of the NTF2L domain of human G3BP1 in complex with small molecule Deposited 2023-11-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–139（139 aa） Chain D 1–139（139 aa）	Not recorded	Y9M N-[(2S)-2-fluoro-4,4-dimethylpentanoyl]-3-hydroxy-L-valyl-(betaS)-beta-methyl-L-phenylalanyl-D-alanyl-N-benzyl-N,O-dimethyl-L-homoserinamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.1 M MES pH 6.5, 15% PEG 550 MME	Resolution 2.68 Å R-free 0.395
8V1L Crystal structure of the NTF2L domain of human G3BP1 in complex with small molecule Deposited 2023-11-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 1–139（139 aa） Chain F 1–139（139 aa）	Not recorded	Y9M N-[(2S)-2-fluoro-4,4-dimethylpentanoyl]-3-hydroxy-L-valyl-(betaS)-beta-methyl-L-phenylalanyl-D-alanyl-N-benzyl-N,O-dimethyl-L-homoserinamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.1 M MES pH 6.5, 15% PEG 550 MME	Resolution 2.68 Å R-free 0.395
9CC6 De novo design of high-affinity protein binders to RNA binding domain of G3bp1 Deposited 2024-06-20	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 453–465（13 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.05 M Calcium chloride dihydrate, 0.1 M BIS-TRIS pH 6.5, and 30% v/v Polyethylene glycol monomethyl ether 550	Resolution 2.40 Å R-free 0.258
9IVQ Cryo-EM structure of the CHIKV nsP3 peptide in complex with the NTF2L domain of G3BP1 (Conformation I) Deposited 2024-07-24	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric	Chain A 1–138（138 aa） Chain B 1–138（138 aa） Chain C 1–138（138 aa） Chain D 1–138（138 aa） Chain E 1–138（138 aa） Chain F 1–138（138 aa） Chain G 1–138（138 aa） Chain H 1–138（138 aa） Chain M 1–138（138 aa） Chain N 1–138（138 aa） Chain O 1–138（138 aa） Chain P 1–138（138 aa） Chain Q 1–138（138 aa） Chain R 1–138（138 aa） Chain S 1–138（138 aa） Chain T 1–138（138 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.66 Å
9IVS Cryo-EM structure of the CHIKV nsP3 peptide in complex with the NTF2L domain of G3BP1 (Conformation III) Deposited 2024-07-24	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric	Chain A 1–138（138 aa） Chain B 1–138（138 aa） Chain C 1–138（138 aa） Chain D 1–138（138 aa） Chain E 1–138（138 aa） Chain F 1–138（138 aa） Chain G 1–138（138 aa） Chain H 1–138（138 aa） Chain M 1–138（138 aa） Chain N 1–138（138 aa） Chain O 1–138（138 aa） Chain P 1–138（138 aa） Chain Q 1–138（138 aa） Chain R 1–138（138 aa） Chain S 1–138（138 aa） Chain T 1–138（138 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.97 Å
9J5S Crystal structure of human G3BP1 in complex with CHIKV nsP3 peptide Deposited 2024-08-13	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–138（138 aa） Chain B 1–138（138 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；291 K；20%(w/v) PEG 3350, 200mM Sodium citrate tribasic, 100mM Sodium citrate/Citric acid pH 4.0	Resolution 2.84 Å R-free 0.280

19 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	G3BP1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–141； UniProt 1–138 Author chain B； PDBConstruct 4–141； UniProt 1–138 Author chain C； PDBConstruct 4–141； UniProt 1–138 Author chain D； PDBConstruct 4–141； UniProt 1–138 Author chain E； PDBConstruct 4–141； UniProt 1–138 Author chain F； PDBConstruct 4–141； UniProt 1–138 Author chain G； PDBConstruct 4–141； UniProt 1–138 Author chain H； PDBConstruct 4–141； UniProt 1–138 Author chain M； PDBConstruct 4–141； UniProt 1–138 Author chain N； PDBConstruct 4–141； UniProt 1–138 Author chain O； PDBConstruct 4–141； UniProt 1–138 Author chain P； PDBConstruct 4–141； UniProt 1–138 Author chain Q； PDBConstruct 4–141； UniProt 1–138 Author chain R； PDBConstruct 4–141； UniProt 1–138 Author chain S； PDBConstruct 4–141； UniProt 1–138 Author chain T； PDBConstruct 4–141； UniProt 1–138

Polyprotein P1234

Chikungunya virus

UniProt A0A0U5KFN5

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 24 PDB declaration: 24-meric（24） Consistent with protein copy count	Chain I； UniProt 1801–1844 Chain J； UniProt 1801–1844 Chain K； UniProt 1801–1844 Chain L； UniProt 1801–1844 Chain U； UniProt 1801–1844 Chain V； UniProt 1801–1844 Chain W； UniProt 1801–1844 Chain X； UniProt 1801–1844	Not recorded	Ras GTPase-activating protein-binding protein 1 × 16 （Q13283）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.80 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9IVR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9IVQ Cryo-EM structure of the CHIKV nsP3 peptide in complex with the NTF2L domain of G3BP1 (Conformation I) Deposited 2024-07-24	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric	Chain I 1801–1844（44 aa） Chain J 1801–1844（44 aa） Chain K 1801–1844（44 aa） Chain L 1801–1844（44 aa） Chain U 1801–1844（44 aa） Chain V 1801–1844（44 aa） Chain W 1801–1844（44 aa） Chain X 1801–1844（44 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.66 Å
9IVS Cryo-EM structure of the CHIKV nsP3 peptide in complex with the NTF2L domain of G3BP1 (Conformation III) Deposited 2024-07-24	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric	Chain I 1801–1844（44 aa） Chain J 1801–1844（44 aa） Chain K 1801–1844（44 aa） Chain L 1801–1844（44 aa） Chain U 1801–1844（44 aa） Chain V 1801–1844（44 aa） Chain W 1801–1844（44 aa） Chain X 1801–1844（44 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.97 Å
9J5S Crystal structure of human G3BP1 in complex with CHIKV nsP3 peptide Deposited 2024-08-13	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1806–1831（26 aa） Chain D 1806–1831（26 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；291 K；20%(w/v) PEG 3350, 200mM Sodium citrate tribasic, 100mM Sodium citrate/Citric acid pH 4.0	Resolution 2.84 Å R-free 0.280

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A0U5KFN5_CHIKV
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain I； PDBConstruct 5–48； UniProt 1801–1844 Author chain J； PDBConstruct 5–48； UniProt 1801–1844 Author chain K； PDBConstruct 5–48； UniProt 1801–1844 Author chain L； PDBConstruct 5–48； UniProt 1801–1844 Author chain U； PDBConstruct 5–48； UniProt 1801–1844 Author chain V； PDBConstruct 5–48； UniProt 1801–1844 Author chain W； PDBConstruct 5–48； UniProt 1801–1844 Author chain X； PDBConstruct 5–48； UniProt 1801–1844

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9ivr
Deposition date deposition_date	2024-07-24
Structure title title	Cryo-EM structure of the CHIKV nsP3 peptide in complex with the NTF2L domain of G3BP1 (Conformation II)
Keywords keywords	Chikungunya virus, nsP3, G3BP1, protein-protein interaction., VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	42.16 Å
Radius of gyration Rg (electron density) rg_electron	41.42 Å
Forward intensity I(0) i0	1190060000.00
Molecular weight molecular_weight	279880.0 kDa
Excluded volume excluded_volume	347750 Å³
Envelope volume envelope_volume	467820 Å³
Hydration-shell volume shell_volume	89052 Å³
Envelope diameter envelope_diameter	125.4 Å
Shell Rg shell_rg	51.10 Å
Envelope Rg envelope_rg	40.15 Å
Shape Rg shape_rg	41.41 Å
Total Rg total_rg	41.86 Å
Total atoms total_atoms	19752
Residues n_residues	2460
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	127.5 Å
Rg (real space) rg_real	41.84 Å
Rg uncertainty (real space) rg_real_error	0.70 Å
I(0) (real space) i0_real	1.1900e+09
I(0) uncertainty (real space) i0_real_error	1.8570e+07
Rg (reciprocal space) rg_reciprocal	42.16 Å
I(0) (reciprocal space) i0_reciprocal	1190000000.0000
Solution quality estimate total_estimate	0.8946
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	58.6 Å
Skewness Skewness skewness	-0.020
Kurtosis Kurtosis kurtosis	-0.565
Angular range angular_range	— – 0.1850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	296200000.0000
Real-space data points n_real_points	38
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.906; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.954; Smooth: 0.955

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Ras GTPase-activating protein-binding protein 1
Molecular weight formula_weight	16057.2 kDa
EC 编号 ec_number	3.6.4.12,3.6.4.13
Source method src_method	man
Copy count entity_count	16

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,D,B,P,N,M,O,T,R,Q,S,E,G,H,F
Atom count atom_count	19758

GASMVMEKPSPLLVGREFVRQYYTLLNQAPDMLHRFYGKNSSYVHGGLDSNGKPADAVYGQKEIHRKVMSQNFTNCHTKIRHVDAHATLNDGVVVQVMGLLSNNNQALRRFMQTFVLAPEGSVANKFYVHNDIFRYQDEVF

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Polyprotein P1234
Molecular weight formula_weight	6000.3 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,I,V,U,X,W,J,K

GPLGSETFPITFGDFNDGEIESLSSELLTFGDFLPGEVDDLTDSDWSTHHHHHH

来源 Source

来源生物 organism	Chikungunya virus
NCBI Class编号 ncbi_taxonomy_id	37124
宿主生物 host_organism	Escherichia coli

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	2.80 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	296402

fit	/app/data/saxs_computation/iv/9ivr/9ivr.fit
pddf	/app/data/pr_computation/iv/9ivr/9ivr.pr.out
profile	/app/data/saxs_computation/iv/9ivr/9ivr.dat

Cryo-EM structure of the CHIKV nsP3 peptide in complex with the NTF2L domain of G3BP1 (Conformation II)

1. Protein Identity and Related Structures Protein Identity & Related Structures

Ras GTPase-activating protein-binding protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Polyprotein P1234

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)