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- PDB-8th5: Crystal Structure of the G3BP1 NTF2-like domain bound to the IDR1... -

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Basic information

Entry
Database: PDB / ID: 8th5
TitleCrystal Structure of the G3BP1 NTF2-like domain bound to the IDR1 of SARS-CoV-2 nucleocapsid protein P13L mutant
Components
  • Nucleoprotein
  • Ras GTPase-activating protein-binding protein 1
KeywordsHydrolase/Viral Protein / NTF2L USP10 / PEPTIDE BINDING PROTEIN / Hydrolase-Viral Protein complex
Function / homology
Function and homology information


DNA/RNA helicase activity / : / response to host immune response / viral RNA genome packaging / negative regulation of interferon-beta production / Maturation of nucleoprotein / poly(U) RNA binding / intracellular membraneless organelle / positive regulation of NLRP3 inflammasome complex assembly / MHC class I protein binding ...DNA/RNA helicase activity / : / response to host immune response / viral RNA genome packaging / negative regulation of interferon-beta production / Maturation of nucleoprotein / poly(U) RNA binding / intracellular membraneless organelle / positive regulation of NLRP3 inflammasome complex assembly / MHC class I protein binding / ribosomal small subunit binding / CD28 dependent PI3K/Akt signaling / positive regulation of type I interferon production / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / stress granule assembly / DNA helicase activity / protein sequestering activity / VEGFR2 mediated vascular permeability / molecular condensate scaffold activity / negative regulation of canonical Wnt signaling pathway / NOD1/2 Signaling Pathway / TAK1-dependent IKK and NF-kappa-B activation / DDX58/IFIH1-mediated induction of interferon-alpha/beta / MHC class I protein complex / RNA stem-loop binding / Interleukin-1 signaling / cytoplasmic stress granule / Interferon alpha/beta signaling / viral capsid / PIP3 activates AKT signaling / viral nucleocapsid / Transcription of SARS-CoV-2 sgRNAs / host cell endoplasmic reticulum-Golgi intermediate compartment / endonuclease activity / perikaryon / defense response to virus / Translation of Structural Proteins / Virion Assembly and Release / host extracellular space / host cell Golgi apparatus / DNA helicase / Induction of Cell-Cell Fusion / Ras protein signal transduction / Attachment and Entry / RNA helicase activity / host cell perinuclear region of cytoplasm / RNA helicase / ribonucleoprotein complex / innate immune response / focal adhesion / mRNA binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / ATP hydrolysis activity / DNA binding / RNA binding / extracellular region / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol
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 (NTF2) domain / Nucleocapsid protein, betacoronavirus / Nuclear transport factor 2 domain / Nucleocapsid protein, coronavirus / Nucleocapsid protein, C-terminal / Nucleocapsid protein, N-terminal ...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 (NTF2) domain / Nucleocapsid protein, betacoronavirus / Nuclear transport factor 2 domain / Nucleocapsid protein, coronavirus / Nucleocapsid protein, C-terminal / Nucleocapsid protein, N-terminal / Nucleocapsid (N) protein, C-terminal domain, coronavirus / Nucleocapsid (N) protein, N-terminal domain, coronavirus / Coronavirus nucleocapsid / Coronavirus nucleocapsid (CoV N) protein N-terminal (NTD) domain profile. / Coronavirus nucleocapsid (CoV N) protein C-terminal (CTD) domain profile. / NTF2-like domain 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
Nucleoprotein / Ras GTPase-activating protein-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 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 13, 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: Ras GTPase-activating protein-binding protein 1
F: Ras GTPase-activating protein-binding protein 1
G: Ras GTPase-activating protein-binding protein 1
H: Ras GTPase-activating protein-binding protein 1
I: Ras GTPase-activating protein-binding protein 1
J: Ras GTPase-activating protein-binding protein 1
K: Nucleoprotein
P: Nucleoprotein
L: Nucleoprotein
M: Nucleoprotein
O: Nucleoprotein
Q: Nucleoprotein
N: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)177,35017
Polymers177,35017
Non-polymers00
Water1,15364
1
A: Ras GTPase-activating protein-binding protein 1
K: Nucleoprotein
P: Nucleoprotein

F: Ras GTPase-activating protein-binding protein 1


Theoretical massNumber of molelcules
Total (without water)37,0444
Polymers37,0444
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
2
B: Ras GTPase-activating protein-binding protein 1
L: Nucleoprotein

E: Ras GTPase-activating protein-binding protein 1
O: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)37,0444
Polymers37,0444
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area4970 Å2
ΔGint-31 kcal/mol
Surface area12850 Å2
MethodPISA
3
C: Ras GTPase-activating protein-binding protein 1
M: Nucleoprotein

H: Ras GTPase-activating protein-binding protein 1


Theoretical massNumber of molelcules
Total (without water)34,4213
Polymers34,4213
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area4000 Å2
ΔGint-28 kcal/mol
Surface area12460 Å2
MethodPISA
4
D: Ras GTPase-activating protein-binding protein 1
G: Ras GTPase-activating protein-binding protein 1
N: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)34,4213
Polymers34,4213
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-28 kcal/mol
Surface area12780 Å2
MethodPISA
5
I: Ras GTPase-activating protein-binding protein 1
Q: Nucleoprotein

J: Ras GTPase-activating protein-binding protein 1


Theoretical massNumber of molelcules
Total (without water)34,4213
Polymers34,4213
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area3920 Å2
ΔGint-26 kcal/mol
Surface area12900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.600, 69.450, 101.040
Angle α, β, γ (deg.)70.66, 76.86, 88.31
Int Tables number1
Space group name H-MP1

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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.: 10
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
Nucleoprotein / N / Nucleocapsid protein / NC / Protein N


Mass: 2622.785 Da / Num. of mol.: 7 / Mutation: P13L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Escherichia coli (E. coli) / References: UniProt: P0DTC9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.24 Å3/Da / Density % sol: 45.01 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M lithium sulfate, 0.1 M Tris pH 8.5, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.62→92.77 Å / Num. obs: 31252 / % possible obs: 71.4 % / Redundancy: 3.5 % / CC1/2: 0.898 / Net I/σ(I): 10.3
Reflection shellResolution: 2.62→2.74 Å / Rmerge(I) obs: 0.37 / Num. unique obs: 440 / % possible all: 7.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.62→46.7 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.767 / SU B: 16.507 / SU ML: 0.36 / Cross valid method: THROUGHOUT / ESU R Free: 0.578 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33622 1633 5 %RANDOM
Rwork0.22566 ---
obs0.23099 31252 71.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.173 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0.03 Å20.03 Å2
2---0.02 Å20.01 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.62→46.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10235 0 0 64 10299
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01110514
X-RAY DIFFRACTIONr_bond_other_d0.0010.0169755
X-RAY DIFFRACTIONr_angle_refined_deg1.2171.6714207
X-RAY DIFFRACTIONr_angle_other_deg0.4381.58622199
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.90551263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.702574
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.169101640
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0560.21547
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212516
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022712
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_it2.2883.615154
X-RAY DIFFRACTIONr_mcbond_other2.2873.615154
X-RAY DIFFRACTIONr_mcangle_it3.8846.4766374
X-RAY DIFFRACTIONr_mcangle_other3.8836.4766375
X-RAY DIFFRACTIONr_scbond_it1.7773.635360
X-RAY DIFFRACTIONr_scbond_other1.7773.6315361
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.066.6387831
X-RAY DIFFRACTIONr_long_range_B_refined5.80341.111529
X-RAY DIFFRACTIONr_long_range_B_other5.80341.111530
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.62→2.691 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.583 12 -
Rwork0.309 148 -
obs--4.63 %

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