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- PDB-4iia: Low resolution crystal structure of the NTF2-like domain of human... -

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Basic information

Entry
Database: PDB / ID: 4iia
TitleLow resolution crystal structure of the NTF2-like domain of human G3BP1
ComponentsRas GTPase-activating protein-binding protein 1
KeywordsHYDROLASE / NTF2-LIKE DOMAIN
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 / stress granule assembly / DNA helicase activity / molecular condensate scaffold activity / negative regulation of canonical Wnt signaling pathway / cytoplasmic stress granule / perikaryon ...DNA/RNA helicase activity / positive regulation of stress granule assembly / 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 / DNA helicase / Ras protein signal transduction / RNA helicase activity / RNA helicase / ribonucleoprotein complex / focal adhesion / innate immune response / 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 domain / Nuclear transport factor 2 (NTF2) 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 domain / Nuclear transport factor 2 (NTF2) 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
PHOSPHATE ION / Ras GTPase-activating protein-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS, molecular replacement / Resolution: 3.3 Å
AuthorsVognsen, T. / Moeller, I.R. / Kristensen, O.
Citation
Journal: Plos One / Year: 2013
Title: Crystal Structures of the Human G3BP1 NTF2-Like Domain Visualize FxFG Nup Repeat Specificity.
Authors: Vognsen, T. / Moller, I.R. / Kristensen, O.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Purification, crystallization and preliminary X-ray diffraction of the G3BP1 NTF2-like domain.
Authors: Vognsen, T. / Moller, I.R. / Kristensen, O.
#2: Journal: Biochem.Biophys.Res.Commun. / Year: 2012
Title: Crystal structure of the Rasputin NTF2-like domain from Drosophila melanogaster.
Authors: Vognsen, T. / Kristensen, O.
History
DepositionDec 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Data collection / Database references / Category: citation_author / diffrn_source
Item: _citation_author.name / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2802
Polymers15,1851
Non-polymers951
Water0
1
A: Ras GTPase-activating protein-binding protein 1
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)30,5604
Polymers30,3702
Non-polymers1902
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/21
Buried area2690 Å2
ΔGint-19 kcal/mol
Surface area13150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.397, 89.397, 70.136
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-109-

MET

21A-201-

PO4

31A-201-

PO4

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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: 15185.106 Da / Num. of mol.: 1 / Fragment: NTF2-LIKE DOMAIN
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-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4

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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: 2.66 Å3/Da / Density % sol: 53.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.6 M diammonium phosphate, 0.1 M MOPS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 27, 2010
RadiationMonochromator: BENT SI (111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 3.3→29.35 Å / Num. obs: 2719 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Biso Wilson estimate: 121.6 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 15.7
Reflection shellResolution: 3.3→3.39 Å / Redundancy: 10.1 % / Mean I/σ(I) obs: 1.5 / % possible all: 99.1

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Processing

Software
NameVersionClassification
MAR345data collection
AutoSolphasing
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
xia2data reduction
XDSdata scaling
xia2data scaling
RefinementMethod to determine structure: SIRAS, molecular replacement / Resolution: 3.3→27.006 Å / SU ML: 0.3 / σ(F): 1.35 / Phase error: 48 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.3595 408 15.01 %
Rwork0.3016 --
obs0.3111 2719 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→27.006 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1060 0 5 0 1065
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061091
X-RAY DIFFRACTIONf_angle_d0.5511468
X-RAY DIFFRACTIONf_dihedral_angle_d10.117392
X-RAY DIFFRACTIONf_chiral_restr0.044153
X-RAY DIFFRACTIONf_plane_restr0.001194
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.77640.56871300.4326748X-RAY DIFFRACTION99
3.7764-4.75370.37471350.3328742X-RAY DIFFRACTION98
4.7537-27.00670.31941430.2665821X-RAY DIFFRACTION100

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