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- PDB-7s17: Crystal structure of human G3BP1-NTF2 with three mutations- F15W,... -

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Basic information

Entry
Database: PDB / ID: 7s17
TitleCrystal structure of human G3BP1-NTF2 with three mutations- F15W, F33W, and F124W
ComponentsRas GTPase-activating protein-binding protein 1
KeywordsRNA BINDING PROTEIN / NTF2-like domain / binding mutant
Function / homology
Function and homology information


DNA/RNA helicase activity / positive regulation of stress granule assembly / ribosomal small subunit binding / positive regulation of type I interferon production / DNA helicase activity / stress granule assembly / negative regulation of canonical Wnt signaling pathway / molecular condensate scaffold activity / cytoplasmic stress granule / endonuclease activity ...DNA/RNA helicase activity / positive regulation of stress granule assembly / ribosomal small subunit binding / positive regulation of type I interferon production / DNA helicase activity / stress granule assembly / negative regulation of canonical Wnt signaling pathway / molecular condensate scaffold activity / cytoplasmic stress granule / endonuclease activity / defense response to virus / DNA helicase / perikaryon / Ras protein signal transduction / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / 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 / 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 (NTF2) domain / Nuclear transport factor 2 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 (NTF2) domain / Nuclear transport factor 2 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: 2.36 Å
AuthorsSheehan, C.T. / Madden, D.R.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI091699 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20-GM113132 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)T32-HL134598 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)P30-DK117469 United States
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Tryptophan mutations in G3BP1 tune the stability of a cellular signaling hub by weakening transient interactions with Caprin1 and USP10.
Authors: Sheehan, C.T. / Hampton, T.H. / Madden, D.R.
History
DepositionSep 1, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 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

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


Theoretical massNumber of molelcules
Total (without water)32,0922
Polymers32,0922
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-19 kcal/mol
Surface area14040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.652, 71.669, 87.731
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 38 or resid 40...
d_2ens_1(chain "B" and (resid 1 through 38 or resid 40 through 138))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1METSERA2 - 39
d_12ens_1TYRSERA41 - 48
d_13ens_1PROPROA52 - 117
d_14ens_1TRPPHEA125 - 139
d_21ens_1METSERB1 - 38
d_22ens_1TYRPHEB40 - 128

NCS oper: (Code: givenMatrix: (0.654412504888, -0.0678064577429, -0.753091334258), (-0.0700467309402, -0.997124693616, 0.0289102207897), (-0.752886265602, 0.0338323760604, -0.657280489136)Vector: 15. ...NCS oper: (Code: given
Matrix: (0.654412504888, -0.0678064577429, -0.753091334258), (-0.0700467309402, -0.997124693616, 0.0289102207897), (-0.752886265602, 0.0338323760604, -0.657280489136)
Vector: 15.6911646211, -24.9061351514, 36.8164375127)

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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: 16046.211 Da / Num. of mol.: 2 / Mutation: F15W, F33W, F124W
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.08 Å3/Da / Density % sol: 41.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% PEG 8000, 100 mM HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92011 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92011 Å / Relative weight: 1
ReflectionResolution: 2.36→19.91 Å / Num. obs: 11543 / % possible obs: 99.7 % / Redundancy: 6.4 % / Biso Wilson estimate: 43.95 Å2 / CC1/2: 0.991 / Net I/σ(I): 7.02
Reflection shellResolution: 2.36→2.5 Å / Num. unique obs: 1793 / CC1/2: 0.349

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FCJ

4fcj


Resolution: 2.36→19.91 Å / SU ML: 0.362 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.0615
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2714 579 5.02 %
Rwork0.2223 10958 -
obs0.2249 11537 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.7 Å2
Refinement stepCycle: LAST / Resolution: 2.36→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2181 0 0 17 2198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00742244
X-RAY DIFFRACTIONf_angle_d1.06983039
X-RAY DIFFRACTIONf_chiral_restr0.0663319
X-RAY DIFFRACTIONf_plane_restr0.0057393
X-RAY DIFFRACTIONf_dihedral_angle_d20.3009816
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.30244163212 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.36-2.60.34241450.29422671X-RAY DIFFRACTION99.89
2.6-2.970.3061440.28212700X-RAY DIFFRACTION99.86
2.97-3.740.28721450.22222724X-RAY DIFFRACTION99.93
3.74-19.910.2361450.19122863X-RAY DIFFRACTION99.77

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