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

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Basic information

Entry
Database: PDB / ID: 7xhg
TitleCrystal structure of the NTF2L domain of human G3BP1 in complex with the Caprin-1 derived peptide
Components
  • Caprin-1(369-378)
  • Ras GTPase-activating protein-binding protein 1
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: 2.46 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: Ras GTPase-activating protein-binding protein 1
D: Ras GTPase-activating protein-binding protein 1
F: Caprin-1(369-378)
G: Caprin-1(369-378)
E: Caprin-1(369-378)


Theoretical massNumber of molelcules
Total (without water)67,2787
Polymers67,2787
Non-polymers00
Water73941
1
A: Ras GTPase-activating protein-binding protein 1
D: Ras GTPase-activating protein-binding protein 1
E: Caprin-1(369-378)


Theoretical massNumber of molelcules
Total (without water)33,0263
Polymers33,0263
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-26 kcal/mol
Surface area12820 Å2
MethodPISA
2
B: Ras GTPase-activating protein-binding protein 1
C: Ras GTPase-activating protein-binding protein 1
F: Caprin-1(369-378)
G: Caprin-1(369-378)


Theoretical massNumber of molelcules
Total (without water)34,2534
Polymers34,2534
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-35 kcal/mol
Surface area12760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.669, 171.761, 42.968
Angle α, β, γ (deg.)90.000, 99.820, 90.000
Int Tables number4
Space group name H-MP1211

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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.: 4
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 Caprin-1(369-378)


Mass: 1227.386 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

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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: 2.34 Å3/Da / Density % sol: 47.36 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium acetate trihydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 30 % w/v Polyethylene glycol 8,000

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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 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.45→85.88 Å / Num. obs: 21506 / % possible obs: 99.6 % / Redundancy: 3.4 % / CC1/2: 0.971 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.068 / Rrim(I) all: 0.126 / Net I/σ(I): 28.2
Reflection shellResolution: 2.45→2.49 Å / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 1065 / CC1/2: 0.818 / Rpim(I) all: 0.333 / Rrim(I) all: 0.629

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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: 2.46→85.88 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.882 / SU B: 12.939 / SU ML: 0.284 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.706 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2746 1073 5 %RANDOM
Rwork0.206 ---
obs0.2095 20403 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90.24 Å2 / Biso mean: 39.622 Å2 / Biso min: 16.93 Å2
Baniso -1Baniso -2Baniso -3
1-3.45 Å2-0 Å21.11 Å2
2---2.01 Å2-0 Å2
3----1.73 Å2
Refinement stepCycle: final / Resolution: 2.46→85.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4430 0 0 41 4471
Biso mean---32.69 -
Num. residues----553
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194567
X-RAY DIFFRACTIONr_bond_other_d0.0020.024237
X-RAY DIFFRACTIONr_angle_refined_deg1.5721.9186187
X-RAY DIFFRACTIONr_angle_other_deg0.97439641
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.055558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.45523.78246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.24515723
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8241531
X-RAY DIFFRACTIONr_chiral_restr0.0850.2661
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025367
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021220
LS refinement shellResolution: 2.46→2.519 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.356 58 -
Rwork0.298 1409 -
obs--92.97 %

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