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- PDB-4fcm: Crystal structure of the NTF2-like domain of human G3BP1 in compl... -

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Basic information

Entry
Database: PDB / ID: 4fcm
TitleCrystal structure of the NTF2-like domain of human G3BP1 in complex with a peptide
Components
  • Nucleoporin repeat peptide
  • Ras GTPase-activating protein-binding protein 1
KeywordsHYDROLASE / NTF2-like domain
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 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsVognsen, T. / Kristensen, O.
CitationJournal: 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.
History
DepositionMay 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Aug 9, 2017Group: Data collection / Database references / Category: citation_author / diffrn_source
Item: _citation_author.name / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_sheet / 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_sheet.number_strands / _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

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: Nucleoporin repeat peptide
D: Nucleoporin repeat peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3225
Polymers34,2274
Non-polymers951
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-37 kcal/mol
Surface area13280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.780, 71.490, 89.500
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: 16181.351 Da / Num. of mol.: 2 / 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: Protein/peptide Nucleoporin repeat peptide


Mass: 931.967 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / 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 Å3/Da / Density % sol: 38.48 %
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20% PEG3350, 0.1 M Bis-tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 279K

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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: Aug 9, 2011
RadiationMonochromator: Bent Si (111) crystal, horizontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 2.69→28.38 Å / Num. all: 7987 / Num. obs: 7987 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 63.7 Å2 / Rmerge(I) obs: 0.129 / Rsym value: 0.15 / Net I/σ(I): 10
Reflection shellResolution: 2.69→2.76 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.943 / Mean I/σ(I) obs: 1.8 / Num. unique all: 566 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MAR345data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4fcj

4fcj


Resolution: 2.69→28.38 Å / SU ML: 0.55 / σ(F): 1.34 / Phase error: 28.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2822 366 4.6 %random
Rwork0.2252 ---
obs0.2277 7954 99.16 %-
all-7987 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.93 Å2 / ksol: 0.357 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--10.2063 Å20 Å20 Å2
2--0.6092 Å20 Å2
3---9.5972 Å2
Refinement stepCycle: LAST / Resolution: 2.69→28.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2236 0 5 62 2303
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032292
X-RAY DIFFRACTIONf_angle_d0.5893090
X-RAY DIFFRACTIONf_dihedral_angle_d12.358830
X-RAY DIFFRACTIONf_chiral_restr0.044325
X-RAY DIFFRACTIONf_plane_restr0.002405
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-3.08310.42181310.30952470X-RAY DIFFRACTION100
3.0831-3.88280.27551220.2292493X-RAY DIFFRACTION99
3.8828-28.38330.23431130.19422625X-RAY DIFFRACTION99
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)
13.5711-1.50171.68312.9276-0.54067.8695-0.1155-0.2307-0.1246-0.19270.1533-0.51920.1366-0.59950.03810.1736-0.02230.04920.26830.02820.2691-5.431214.7132-8.7681
23.90840.24791.34021.9767-1.23433.94440.02620.0351-0.3727-0.09090.0252-0.11890.38780.1655-0.05830.21970.02950.0430.1563-0.02270.24851.95339.828-10.5288
32.0407-4.2761-0.2222.69840.54950.8515-0.20280.34630.12170.08050.16420.0144-0.0168-0.04210.03220.1894-0.0580.02530.34140.08190.3621-2.638111.0248-14.6801
44.0296-0.708-0.69935.0433-1.57742.18570.20470.29140.0172-0.0901-0.0927-0.0140.14920.3168-0.09590.42790.0238-0.04430.3324-0.02290.16065.75112.7152-34.8087
56.04661.3151-0.0364.5332-0.38032.9159-0.09890.454-0.049-0.22490.0657-0.11590.23770.19150.03610.30580.0569-0.01540.30970.01160.11478.445211.3299-27.9016
62.1487-1.05490.89511.6751.53363.73960.1831-0.18670.13360.2129-0.07810.5340.1621-0.3546-0.037-0.11560.2480.08620.85370.08610.73-13.080715.9645-11.0542
71.67163.1053-2.49381.9996-4.80283.7247-0.01260.25090.1105-0.2225-0.03810.1647-0.0679-0.20550.0841.1735-0.1879-0.36171.1822-0.47140.55140.06647.4341-39.6791
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 7:42)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 43:116)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 117:138)
4X-RAY DIFFRACTION4CHAIN B AND (RESSEQ 1:66)
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 67:138)
6X-RAY DIFFRACTION6CHAIN C AND (RESSEQ 2:4)
7X-RAY DIFFRACTION7CHAIN D AND (RESSEQ 2:4)

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