8th6

Crystal Structure of the G3BP1 NTF2-like domain bound to USP10 peptide

Method: X-RAY DIFFRACTION D_max: 92.4 Å Quality: EXCELLENT

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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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–139 Chain D； UniProt 1–139	Not recorded	Ubiquitin carboxyl-terminal hydrolase 10 × 2 （Q14694） 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
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 1–139 Chain C； UniProt 1–139	Not recorded	Ubiquitin carboxyl-terminal hydrolase 10 × 2 （Q14694） 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

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 8TH6	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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 ligand/ion 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 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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
8TH7 Crystal Structure of the G3BP1 NTF2-like domain bound to the Caprin1 peptide Deposited 2023-07-14	Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 ligand/ion 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 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 × 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
9IVR Cryo-EM structure of the CHIKV nsP3 peptide in complex with the NTF2L domain of G3BP1 (Conformation II) Deposited 2024-07-24	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 × 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 2.80 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 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 × 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 ligand/ion 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 28 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 1–139； UniProt 1–139 Author chain B； PDBConstruct 1–139； UniProt 1–139 Author chain C； PDBConstruct 1–139； UniProt 1–139 Author chain D； PDBConstruct 1–139； UniProt 1–139

Ubiquitin carboxyl-terminal hydrolase 10

Homo sapiens

UniProt Q14694

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain E； UniProt 2–24 Chain H； UniProt 2–24	Not recorded	Ras GTPase-activating protein-binding protein 1 × 2 （Q13283） 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
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain F； UniProt 2–24 Chain G； UniProt 2–24	Not recorded	Ras GTPase-activating protein-binding protein 1 × 2 （Q13283） 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

Other States of the Same Protein in the Database

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	UBP10_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 2–24； UniProt 2–24 Author chain F； PDBConstruct 2–24； UniProt 2–24 Author chain G； PDBConstruct 2–24； UniProt 2–24 Author chain H； PDBConstruct 2–24； UniProt 2–24

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	8th6
Deposition date deposition_date	2023-07-14
Structure title title	Crystal Structure of the G3BP1 NTF2-like domain bound to USP10 peptide
Keywords keywords	NTF2L USP10, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	29.57 Å
Radius of gyration Rg (electron density) rg_electron	28.55 Å
Forward intensity I(0) i0	79891100.00
Molecular weight molecular_weight	69697.0 kDa
Excluded volume excluded_volume	86910 Å³
Envelope volume envelope_volume	112710 Å³
Hydration-shell volume shell_volume	32617 Å³
Envelope diameter envelope_diameter	101.0 Å
Shell Rg shell_rg	36.34 Å
Envelope Rg envelope_rg	28.30 Å
Shape Rg shape_rg	28.51 Å
Total Rg total_rg	29.48 Å
Total atoms total_atoms	4922
Residues n_residues	602
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	92.4 Å
Rg (real space) rg_real	29.50 Å
Rg uncertainty (real space) rg_real_error	0.62 Å
I(0) (real space) i0_real	7.9890e+07
I(0) uncertainty (real space) i0_real_error	1.2180e+06
Rg (reciprocal space) rg_reciprocal	29.54 Å
I(0) (reciprocal space) i0_reciprocal	79890000.0000
Solution quality estimate total_estimate	0.9118
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	90.7 Å
Skewness Skewness skewness	0.178
Kurtosis Kurtosis kurtosis	-0.686
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	30530000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.952; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.994

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Ras GTPase-activating protein-binding protein 1
Molecular weight formula_weight	15899.1 kDa
EC 编号 ec_number	3.6.4.12,3.6.4.13
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	4996

MVMEKPSPLLVGREFVRQYYTLLNQAPDMLHRFYGKNSSYVHGGLDSNGKPADAVYGQKEIHRKVMSQNFTNCHTKIRHVDAHATLNDGVVVQVMGLLSNNNQALRRFMQTFVLAPEGSVANKFYVHNDIFRYQDEVFG

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	Ubiquitin carboxyl-terminal hydrolase 10
Molecular weight formula_weight	2765.0 kDa
EC 编号 ec_number	3.4.19.12
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,G,H

GALHSPQYIFGDFSPDEFNQFFVT

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 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	15

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	68

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8. Citations (1)

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Unit-cell length a length_a	58.390 Å
Unit-cell length b length_b	78.380 Å
Unit-cell length c length_c	73.410 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	108.63 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.340 Å
Low-resolution limit resolution_low	45.200 Å
R factor r_factor	0.2170
R_work r_work	0.2128
R_free r_free	0.2954

fit	/app/data/saxs_computation/th/8th6/8th6.fit
pddf	/app/data/pr_computation/th/8th6/8th6.pr.out
profile	/app/data/saxs_computation/th/8th6/8th6.dat

Crystal Structure of the G3BP1 NTF2-like domain bound to USP10 peptide

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

Ubiquitin carboxyl-terminal hydrolase 10

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

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)