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- PDB-8v1l: Crystal structure of the NTF2L domain of human G3BP1 in complex w... -

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Basic information

Entry
Database: PDB / ID: 8v1l
TitleCrystal structure of the NTF2L domain of human G3BP1 in complex with small molecule
ComponentsRas GTPase-activating protein-binding protein 1
KeywordsRNA BINDING PROTEIN / Small Molecule / complex / NTF2L / G3BP1 FAZ compound
Function / homology
Function and homology information


positive regulation of stress granule assembly / 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 / perikaryon ...positive regulation of stress granule assembly / 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 / perikaryon / endonuclease activity / defense response to virus / Ras protein signal transduction / DNA helicase / RNA helicase activity / RNA helicase / ribonucleoprotein complex / focal adhesion / mRNA binding / innate immune response / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / DNA binding / RNA binding / ATP binding / nucleus / cytosol / cytoplasm
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 domain / Nuclear transport factor 2 (NTF2) domain / NTF2-like domain superfamily / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. ...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 domain / Nuclear transport factor 2 (NTF2) domain / NTF2-like domain superfamily / 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
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
AuthorsHughes, M.P. / Taylor, J.P.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)R35NS097974 United States
CitationJournal: J.Cell Biol. / Year: 2024
Title: Identification of small molecule inhibitors of G3BP-driven stress granule formation.
Authors: Freibaum, B.D. / Messing, J. / Nakamura, H. / Yurtsever, U. / Wu, J. / Kim, H.J. / Hixon, J. / Lemieux, R.M. / Duffner, J. / Huynh, W. / Wong, K. / White, M. / Lee, C. / Meyers, R.E. / Parker, R. / Taylor, J.P.
History
DepositionNov 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
E: Ras GTPase-activating protein-binding protein 1
F: Ras GTPase-activating protein-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,67812
Polymers95,3946
Non-polymers4,2836
Water1,65792
1
A: Ras GTPase-activating protein-binding protein 1
C: Ras GTPase-activating protein-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2264
Polymers31,7982
Non-polymers1,4282
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-20 kcal/mol
Surface area12090 Å2
MethodPISA
2
B: Ras GTPase-activating protein-binding protein 1
D: Ras GTPase-activating protein-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2264
Polymers31,7982
Non-polymers1,4282
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-23 kcal/mol
Surface area12400 Å2
MethodPISA
3
E: Ras GTPase-activating protein-binding protein 1
hetero molecules

F: Ras GTPase-activating protein-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2264
Polymers31,7982
Non-polymers1,4282
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_446-x-1,y-1/2,-z+11
Buried area2910 Å2
ΔGint-17 kcal/mol
Surface area12480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.170, 84.690, 102.150
Angle α, β, γ (deg.)90.00, 91.26, 90.00
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.: 6
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: Chemical
ChemComp-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


Mass: 713.879 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C38H56FN5O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.37 Å3/Da / Density % sol: 47.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES pH 6.5, 15% PEG 550 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9655 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 2.68→46.87 Å / Num. obs: 23085 / % possible obs: 96.51 % / Redundancy: 1.05 % / CC1/2: 0.875 / CC star: 0.72 / Net I/σ(I): 0.281
Reflection shellResolution: 2.68→2.749 Å / Rmerge(I) obs: 0.337 / Num. unique obs: 1685 / % possible all: 95.91

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
DIALSdata scaling
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.68→46.87 Å / Cor.coef. Fo:Fc: 0.875 / Cor.coef. Fo:Fc free: 0.72 / SU B: 26.271 / SU ML: 0.548 / Cross valid method: THROUGHOUT / ESU R Free: 0.577 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.39465 1165 4.8 %RANDOM
Rwork0.27558 ---
obs0.28101 23085 96.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.201 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0 Å20 Å2
2--0.05 Å20 Å2
3----0.09 Å2
Refinement stepCycle: 1 / Resolution: 2.68→46.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6069 0 291 92 6452
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0126556
X-RAY DIFFRACTIONr_bond_other_d0.0020.0165692
X-RAY DIFFRACTIONr_angle_refined_deg1.1791.6838919
X-RAY DIFFRACTIONr_angle_other_deg0.4211.58413115
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2425779
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.012560
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.13910932
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0520.2973
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027602
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021430
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1793.763110
X-RAY DIFFRACTIONr_mcbond_other2.1783.763110
X-RAY DIFFRACTIONr_mcangle_it3.6095.6293870
X-RAY DIFFRACTIONr_mcangle_other3.6085.6293871
X-RAY DIFFRACTIONr_scbond_it1.9153.8693446
X-RAY DIFFRACTIONr_scbond_other1.9153.8693447
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1255.7545043
X-RAY DIFFRACTIONr_long_range_B_refined6.41453.3187469
X-RAY DIFFRACTIONr_long_range_B_other6.41353.3157470
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.68→2.749 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.445 98 -
Rwork0.337 1685 -
obs--95.91 %

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