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- PDB-7xhf: Crystal structure of the NTF2L domain of human G3BP1 in complex w... -

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Basic information

Entry
Database: PDB / ID: 7xhf
TitleCrystal structure of the NTF2L domain of human G3BP1 in complex with the USP10 derived peptide
Components
  • Ras GTPase-activating protein-binding protein 1
  • USP10/6-21
KeywordsRNA BINDING PROTEIN / Complex / Stress granules / Lipid-lipid phase separation
Function / homology
Function and homology information


DNA/RNA helicase activity / ribosomal small subunit binding / positive regulation of type I interferon production / stress granule assembly / DNA helicase activity / molecular condensate scaffold activity / negative regulation of canonical Wnt signaling pathway / cytoplasmic stress granule / endonuclease activity / perikaryon ...DNA/RNA helicase activity / ribosomal small subunit binding / positive regulation of type I interferon production / stress granule assembly / DNA helicase activity / molecular condensate scaffold activity / negative regulation of canonical Wnt signaling pathway / cytoplasmic stress granule / endonuclease activity / perikaryon / defense response to virus / DNA helicase / Ras protein signal transduction / RNA helicase activity / RNA helicase / innate immune response / focal adhesion / mRNA binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / DNA binding / RNA binding / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
G3BP1, RNA recognition motif / Ras GTPase-activating protein-binding protein / Nuclear transport factor 2, eukaryote / Nuclear transport factor 2 domain profile. / Nuclear transport factor 2 (NTF2) domain / Nuclear transport factor 2 domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / RNA recognition motif ...G3BP1, RNA recognition motif / Ras GTPase-activating protein-binding protein / Nuclear transport factor 2, eukaryote / Nuclear transport factor 2 domain profile. / Nuclear transport factor 2 (NTF2) domain / Nuclear transport factor 2 domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Ras GTPase-activating protein-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsDan, S. / Weimin, G.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Yin and yang regulation of stress granules by Caprin-1.
Authors: Song, D. / Kuang, L. / Yang, L. / Wang, L. / Li, H. / Li, X. / Zhu, Z. / Shi, C. / Zhu, H. / Gong, W.
History
DepositionApr 8, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ras GTPase-activating protein-binding protein 1
B: Ras GTPase-activating protein-binding protein 1
C: USP10/6-21
D: USP10/6-21


Theoretical massNumber of molelcules
Total (without water)35,7004
Polymers35,7004
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-32 kcal/mol
Surface area12870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.874, 81.874, 94.247
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Ras GTPase-activating protein-binding protein 1 / G3BP-1 / ATP-dependent DNA helicase VIII / hDH VIII / GAP SH3 domain-binding protein 1


Mass: 15899.076 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: G3BP1, G3BP / Production host: Escherichia coli (E. coli) / References: UniProt: Q13283, DNA helicase, RNA helicase
#2: Protein/peptide USP10/6-21


Mass: 1951.051 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.85 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium citrate tribasic dihydrate pH 5.0; 19 % w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.68→70.9 Å / Num. obs: 9910 / % possible obs: 92.7 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.034 / Rrim(I) all: 0.099 / Net I/σ(I): 57.1
Reflection shellResolution: 2.68→2.73 Å / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 5.1 / Num. unique obs: 528 / CC1/2: 0.934 / Rpim(I) all: 0.187 / Rrim(I) all: 0.561

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4fcj

4fcj


Resolution: 2.68→70.9 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.922 / SU B: 12.211 / SU ML: 0.256 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 3.549 / ESU R Free: 0.354 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2543 482 4.9 %RANDOM
Rwork0.2103 ---
obs0.2127 9408 92.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 129.3 Å2 / Biso mean: 54.434 Å2 / Biso min: 27.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å2-0.37 Å2-0 Å2
2---0.74 Å20 Å2
3---2.39 Å2
Refinement stepCycle: final / Resolution: 2.68→70.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2258 0 0 0 2258
Num. residues----280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192402
X-RAY DIFFRACTIONr_bond_other_d0.0020.022209
X-RAY DIFFRACTIONr_angle_refined_deg1.7281.9143259
X-RAY DIFFRACTIONr_angle_other_deg1.02835038
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3265293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.04923.657134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.54615379
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8531516
X-RAY DIFFRACTIONr_chiral_restr0.0970.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022846
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02662
LS refinement shellResolution: 2.68→2.745 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.336 27 -
Rwork0.251 721 -
obs--95.77 %

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