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- PDB-3q90: Crystal structure of the NTF2 domain of Ras GTPase-activating pro... -

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Basic information

Entry
Database: PDB / ID: 3q90
TitleCrystal structure of the NTF2 domain of Ras GTPase-activating protein-binding protein 1
ComponentsRas GTPase-activating protein-binding protein 1
KeywordsHYDROLASE / Structural Genomics / Structural Genomics Consortium / SGC / NTF2-like (a+b proteins) / Protein Binding and Helicase / Protein (Ras GTPase-activating protein) / DNA and RNA binding / plasma membrane / nucleus
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
Ras GTPase-activating protein-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsWelin, M. / Tresaugues, L. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Ekblad, T. / Flodin, S. / Flores, A. ...Welin, M. / Tresaugues, L. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Ekblad, T. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Karlberg, T. / Kol, S. / Kotenyova, T. / Kouznetsova, E. / Moche, M. / Nyman, T. / Persson, C. / Schuler, H. / Schutz, P. / Siponen, M.I. / Thorsell, A.G. / Van Der Berg, S. / Wahlberg, E. / Weigelt, J. / Nordlund, P. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the NTF2 domain of Ras GTPase-activating protein-binding protein 1
Authors: Welin, M. / Tresaugues, L. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Ekblad, T. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, ...Authors: Welin, M. / Tresaugues, L. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Ekblad, T. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Karlberg, T. / Kol, S. / Kotenyova, T. / Kouznetsova, E. / Moche, M. / Nyman, T. / Persson, C. / Schuler, H. / Schutz, P. / Siponen, M.I. / Thorsell, A.G. / Van Der Berg, S. / Wahlberg, E. / Weigelt, J. / Nordlund, P.
History
DepositionJan 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)31,9722
Polymers31,9722
Non-polymers00
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-19 kcal/mol
Surface area13090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.850, 71.410, 88.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 15986.153 Da / Num. of mol.: 2 / Fragment: unp residues 1-139
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: G3BP, G3BP1 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) R3 pRARE / References: UniProt: Q13283, DNA helicase, RNA helicase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.12 Å3/Da / Density % sol: 41.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% w/v PEG3350, 0.2M AMMONIUM ACETATE, 0.1M BIS-TRIS, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 20, 2010 / Details: MIRRORS
RadiationMonochromator: horizontally side diffracting Silicon 111 crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 30636 / Num. obs: 30582 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.17 % / Biso Wilson estimate: 22.39 Å2 / Rsym value: 0.063 / Net I/σ(I): 17.17
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 3.67 % / Mean I/σ(I) obs: 3.48 / Num. unique all: 4585 / Rsym value: 0.434 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHASERphasing
BUSTER2.9.2refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Z02

1z02


Resolution: 1.7→44.29 Å / Cor.coef. Fo:Fc: 0.9302 / Cor.coef. Fo:Fc free: 0.9175 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2376 1530 5 %RANDOM
Rwork0.2138 ---
obs0.215 30581 --
Displacement parametersBiso mean: 29.55 Å2
Baniso -1Baniso -2Baniso -3
1-2.5001 Å20 Å20 Å2
2--2.0279 Å20 Å2
3----4.528 Å2
Refine analyzeLuzzati coordinate error obs: 0.239 Å
Refinement stepCycle: LAST / Resolution: 1.7→44.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2015 0 0 119 2134
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0120982
X-RAY DIFFRACTIONt_angle_deg0.9828402
X-RAY DIFFRACTIONt_dihedral_angle_d9632
X-RAY DIFFRACTIONt_trig_c_planes552
X-RAY DIFFRACTIONt_gen_planes3115
X-RAY DIFFRACTIONt_it209820
X-RAY DIFFRACTIONt_omega_torsion3.84
X-RAY DIFFRACTIONt_other_torsion2.72
X-RAY DIFFRACTIONt_chiral_improper_torsion2575
X-RAY DIFFRACTIONt_ideal_dist_contact23994
LS refinement shellResolution: 1.7→1.76 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2585 147 5.02 %
Rwork0.2029 2780 -
all0.2056 2927 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.59470.38130.24190.5268-0.21532.29270.00340.023-0.00340.0368-0.03120.12840.0214-0.11530.0278-0.05870.0082-0.0136-0.0442-0.0219-0.004319.370948.17778.1036
22.51241.19421.50260.91010.23153.7204-0.13570.42850.066-0.2425-0.0362-0.06150.19640.4150.1719-0.09240.020.0176-0.020.0226-0.097729.31747.919958.2965
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|7 - A|41 A|52 - A|137 }A7 - 41
2X-RAY DIFFRACTION1{ A|7 - A|41 A|52 - A|137 }A52 - 137
3X-RAY DIFFRACTION2{ B|0 - B|46 B|51 - B|117 B|124 - B|139 }B0 - 46
4X-RAY DIFFRACTION2{ B|0 - B|46 B|51 - B|117 B|124 - B|139 }B51 - 117
5X-RAY DIFFRACTION2{ B|0 - B|46 B|51 - B|117 B|124 - B|139 }B124 - 139

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