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- PDB-8th6: Crystal Structure of the G3BP1 NTF2-like domain bound to USP10 peptide -

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Basic information

Entry
Database: PDB / ID: 8th6
TitleCrystal Structure of the G3BP1 NTF2-like domain bound to USP10 peptide
Components
  • Ras GTPase-activating protein-binding protein 1
  • Ubiquitin carboxyl-terminal hydrolase 10
KeywordsHYDROLASE / NTF2L USP10
Function / homology
Function and homology information


negative regulation of stress granule assembly / positive regulation of stress granule assembly / DNA/RNA helicase activity / monoubiquitinated protein deubiquitination / intermediate filament cytoskeleton / molecular function inhibitor activity / protein deubiquitination / ribosomal small subunit binding / DNA damage response, signal transduction by p53 class mediator / positive regulation of type I interferon production ...negative regulation of stress granule assembly / positive regulation of stress granule assembly / DNA/RNA helicase activity / monoubiquitinated protein deubiquitination / intermediate filament cytoskeleton / molecular function inhibitor activity / protein deubiquitination / ribosomal small subunit binding / DNA damage response, signal transduction by p53 class mediator / positive regulation of type I interferon production / translesion synthesis / cellular response to interleukin-1 / rescue of stalled ribosome / stress granule assembly / negative regulation of canonical NF-kappaB signal transduction / DNA helicase activity / molecular condensate scaffold activity / cytosolic ribosome / regulation of autophagy / Termination of translesion DNA synthesis / negative regulation of canonical Wnt signaling pathway / autophagy / cytoplasmic stress granule / p53 binding / perikaryon / endonuclease activity / defense response to virus / Ras protein signal transduction / DNA helicase / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / transmembrane transporter binding / RNA helicase activity / early endosome / Ub-specific processing proteases / RNA helicase / ribonucleoprotein complex / cysteine-type endopeptidase activity / focal adhesion / mRNA binding / innate immune response / DNA damage response / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / protein-containing complex / proteolysis / DNA binding / RNA binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ataxin-2, C-terminal / Ataxin-2 C-terminal region / 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 / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. ...Ataxin-2, C-terminal / Ataxin-2 C-terminal region / 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 / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / NTF2-like domain superfamily / Papain-like cysteine peptidase 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 / Ubiquitin carboxyl-terminal hydrolase 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsHughes, M.P. / Taylor, J.P. / Yang, Z.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)R35NS097974 United States
CitationJournal: Cell Rep / Year: 2024
Title: Interaction between host G3BP and viral nucleocapsid protein regulates SARS-CoV-2 replication and pathogenicity.
Authors: Yang, Z. / Johnson, B.A. / Meliopoulos, V.A. / Ju, X. / Zhang, P. / Hughes, M.P. / Wu, J. / Koreski, K.P. / Clary, J.E. / Chang, T.C. / Wu, G. / Hixon, J. / Duffner, J. / Wong, K. / Lemieux, ...Authors: Yang, Z. / Johnson, B.A. / Meliopoulos, V.A. / Ju, X. / Zhang, P. / Hughes, M.P. / Wu, J. / Koreski, K.P. / Clary, J.E. / Chang, T.C. / Wu, G. / Hixon, J. / Duffner, J. / Wong, K. / Lemieux, R. / Lokugamage, K.G. / Alvarado, R.E. / Crocquet-Valdes, P.A. / Walker, D.H. / Plante, K.S. / Plante, J.A. / Weaver, S.C. / Kim, H.J. / Meyers, R. / Schultz-Cherry, S. / Ding, Q. / Menachery, V.D. / Taylor, J.P.
History
DepositionJul 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _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 1.2May 8, 2024Group: Structure summary / Category: audit_author

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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: Ras GTPase-activating protein-binding protein 1
D: Ras GTPase-activating protein-binding protein 1
E: Ubiquitin carboxyl-terminal hydrolase 10
F: Ubiquitin carboxyl-terminal hydrolase 10
G: Ubiquitin carboxyl-terminal hydrolase 10
H: Ubiquitin carboxyl-terminal hydrolase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,58723
Polymers74,6568
Non-polymers93115
Water1,22568
1
A: Ras GTPase-activating protein-binding protein 1
D: Ras GTPase-activating protein-binding protein 1
E: Ubiquitin carboxyl-terminal hydrolase 10
H: Ubiquitin carboxyl-terminal hydrolase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,01115
Polymers37,3284
Non-polymers68311
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
ΔGint-23 kcal/mol
Surface area14840 Å2
MethodPISA
2
B: Ras GTPase-activating protein-binding protein 1
C: Ras GTPase-activating protein-binding protein 1
F: Ubiquitin carboxyl-terminal hydrolase 10
G: Ubiquitin carboxyl-terminal hydrolase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5768
Polymers37,3284
Non-polymers2484
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6480 Å2
ΔGint-34 kcal/mol
Surface area15210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.390, 78.380, 73.410
Angle α, β, γ (deg.)90.00, 108.63, 90.00
Int Tables number4
Space group name H-MP1211

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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: 15899.076 Da / Num. of mol.: 4
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
Ubiquitin carboxyl-terminal hydrolase 10 / Deubiquitinating enzyme 10 / Ubiquitin thioesterase 10 / Ubiquitin-specific-processing protease 10


Mass: 2764.971 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP10, KIAA0190 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14694, ubiquitinyl hydrolase 1
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.13 Å3/Da / Density % sol: 42.31 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.34→45.21 Å / Num. obs: 15966 / % possible obs: 63.1 % / Redundancy: 3.3 % / CC1/2: 0.918 / Net I/σ(I): 9.2
Reflection shellResolution: 2.34→2.42 Å / Num. unique obs: 177 / CC1/2: 0.848

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Processing

Software
NameVersionClassification
REFMAC5.8.0349refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.34→45.2 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.839 / SU B: 11.879 / SU ML: 0.281 / Cross valid method: THROUGHOUT / ESU R Free: 0.458 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29535 817 4.9 %RANDOM
Rwork0.21277 ---
obs0.21698 15966 63.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.777 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0.05 Å2
2--0.05 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.34→45.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4862 0 60 68 4990
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0125041
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164358
X-RAY DIFFRACTIONr_angle_refined_deg1.2151.6446785
X-RAY DIFFRACTIONr_angle_other_deg0.4231.5510115
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3265594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.9311030
X-RAY DIFFRACTIONr_dihedral_angle_3_deg1710774
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0550.2704
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025786
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021106
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9152.872403
X-RAY DIFFRACTIONr_mcbond_other1.9152.872403
X-RAY DIFFRACTIONr_mcangle_it3.2534.2882988
X-RAY DIFFRACTIONr_mcangle_other3.2524.2892989
X-RAY DIFFRACTIONr_scbond_it1.592.9292638
X-RAY DIFFRACTIONr_scbond_other1.592.9292639
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6544.3453798
X-RAY DIFFRACTIONr_long_range_B_refined5.41639.3225287
X-RAY DIFFRACTIONr_long_range_B_other5.439.3315286
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.34→2.401 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.179 2 -
Rwork0.31 97 -
obs--5.18 %

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