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- PDB-5drv: Crystal structure of the G3BP2 NTF2-like domain in complex with a... -

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Basic information

Entry
Database: PDB / ID: 5drv
TitleCrystal structure of the G3BP2 NTF2-like domain in complex with a peptide
Components
  • Non-structural protein 3
  • Ras GTPase-activating protein-binding protein 2
KeywordsPROTEIN BINDING / NTF2-like / G3BP / peptide complex
Function / homology
Function and homology information


: / positive regulation of stress granule assembly / ADP-ribose 1''-phosphate phosphatase / host cell filopodium / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity ...: / positive regulation of stress granule assembly / ADP-ribose 1''-phosphate phosphatase / host cell filopodium / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / mRNA modification / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / mRNA transport / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / stress granule assembly / cysteine-type peptidase activity / Transferases; Transferring one-carbon groups; Methyltransferases / molecular condensate scaffold activity / protein homooligomerization / host cell cytoplasmic vesicle membrane / cytoplasmic stress granule / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / signaling receptor complex adaptor activity / nucleoside-triphosphate phosphatase / methylation / Ras protein signal transduction / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / RNA helicase / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / innate immune response / RNA-directed RNA polymerase / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / mRNA binding / GTP binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
G3BP2, 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 / : / Alphavirus nsp2 protease (nsp2pro) domain / Alphavirus nsP2 protease domain superfamily / : ...G3BP2, 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 / : / Alphavirus nsp2 protease (nsp2pro) domain / Alphavirus nsP2 protease domain superfamily / : / Peptidase family C9 / Tomato mosaic virus helicase, N-terminal domain / Alphavirus nsp2 protease (nsp2pro) domain profile. / : / Non-structural protein 3, zinc-binding domain / Viral methyltransferase / Alphavirus-like methyltransferase (MT) domain / Alphavirus-like methyltransferase (MT) domain profile. / Tymovirus, RNA-dependent RNA polymerase / RNA dependent RNA polymerase / Nuclear Transport Factor 2; Chain: A, - #50 / Viral (Superfamily 1) RNA helicase / 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 / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Non-structural protein 3, X-domain-like / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like / Nucleotide-binding alpha-beta plait domain superfamily / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Roll / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase / Alpha Beta
Similarity search - Domain/homology
Polyprotein P1234 / Ras GTPase-activating protein-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Semliki forest virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsKristensen, O.
Funding support Denmark, 3items
OrganizationGrant numberCountry
Alfred Benzon Foundation Denmark
Brdr. Hartmann Foundation Denmark
the Danish Natural Science Council (DANSCATT) Denmark
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2015
Title: Crystal structure of the G3BP2 NTF2-like domain in complex with a canonical FGDF motif peptide.
Authors: Kristensen, O.
History
DepositionSep 16, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ras GTPase-activating protein-binding protein 2
B: Non-structural protein 3


Theoretical massNumber of molelcules
Total (without water)17,0812
Polymers17,0812
Non-polymers00
Water00
1
A: Ras GTPase-activating protein-binding protein 2
B: Non-structural protein 3

A: Ras GTPase-activating protein-binding protein 2
B: Non-structural protein 3


Theoretical massNumber of molelcules
Total (without water)34,1624
Polymers34,1624
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area4880 Å2
ΔGint-39 kcal/mol
Surface area14240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.850, 94.850, 114.030
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-109-

MET

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Components

#1: Protein Ras GTPase-activating protein-binding protein 2 / G3BP-2 / GAP SH3 domain-binding protein 2


Mass: 16138.208 Da / Num. of mol.: 1 / Fragment: NTF2-like domain, UNP residues 1-139
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: G3BP2, KIAA0660 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UN86
#2: Protein/peptide Non-structural protein 3 / nsP3


Mass: 942.966 Da / Num. of mol.: 1 / Fragment: UNP residues 1785-1792 / Source method: obtained synthetically / Source: (synth.) Semliki forest virus / References: UniProt: P08411

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 60 % / Description: long trigonal needle
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 0.9 M tri-sodium citrate, 20 % glycerol, 0.1 M sodium cacodylate (pH 6.4)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.75→46.8 Å / Num. all: 5273 / Num. obs: 5273 / % possible obs: 99.6 % / Redundancy: 19 % / Biso Wilson estimate: 70.5 Å2 / Rmerge(I) obs: 0.146 / Net I/σ(I): 21.9
Reflection shellResolution: 2.75→2.82 Å / Redundancy: 20.6 % / Rmerge(I) obs: 2.12 / Mean I/σ(I) obs: 2 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FCM

4fcm


Resolution: 2.75→38.641 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2991 526 9.98 %
Rwork0.2446 --
obs0.2503 5273 99.42 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85 Å2
Refinement stepCycle: LAST / Resolution: 2.75→38.641 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1130 0 0 0 1130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021162
X-RAY DIFFRACTIONf_angle_d0.5771563
X-RAY DIFFRACTIONf_dihedral_angle_d9.402418
X-RAY DIFFRACTIONf_chiral_restr0.019162
X-RAY DIFFRACTIONf_plane_restr0.005205
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7502-3.02680.39231330.36761162X-RAY DIFFRACTION99
3.0268-3.46460.35831250.31051164X-RAY DIFFRACTION99
3.4646-4.36410.3271310.25891186X-RAY DIFFRACTION100
4.3641-38.6450.24541370.19221235X-RAY DIFFRACTION100
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)
18.4191.94051.28454.56281.08053.19980.0025-0.45820.6733-0.49430.09690.2524-0.49380.0404-0.12320.8184-0.1014-0.1620.6315-0.10620.54178.301632.833311.1276
23.751-1.3598-4.67573.57193.03997.24470.72431.43680.0277-0.6991-0.82390.1193-1.78730.10220.23560.9522-0.0364-0.37070.93310.20830.8137-0.901933.6439-3.6077
35.05353.1653-0.95567.64151.85540.94990.0073-0.3097-0.093-0.0775-0.17310.1225-0.429-0.0140.19070.7395-0.1732-0.16920.63810.04420.37036.357525.24194.4714
42.0381-7.61236.69011.9949-8.26736.7665-0.8136-3.31471.5067-0.4181.3646-0.4009-1.9079-2.60170.04081.5166-0.1135-0.18341.0648-0.31970.66315.845439.255614.1652
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 38 )
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 68 )
3X-RAY DIFFRACTION3chain 'A' and (resid 69 through 139 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 8 )

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