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- PDB-8th7: Crystal Structure of the G3BP1 NTF2-like domain bound to the Capr... -

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Basic information

Entry
Database: PDB / ID: 8th7
TitleCrystal Structure of the G3BP1 NTF2-like domain bound to the Caprin1 peptide
Components
  • Caprin-1
  • Ras GTPase-activating protein-binding protein 1
KeywordsPEPTIDE BINDING PROTEIN / NTF2L Caprin1
Function / homology
Function and homology information


regulation of deadenylation-dependent decapping of nuclear-transcribed mRNA / DNA/RNA helicase activity / positive regulation of stress granule assembly / intracellular mRNA localization / positive regulation of dendritic spine morphogenesis / positive regulation of dendrite morphogenesis / membraneless organelle assembly / intracellular membraneless organelle / generation of neurons / cell leading edge ...regulation of deadenylation-dependent decapping of nuclear-transcribed mRNA / DNA/RNA helicase activity / positive regulation of stress granule assembly / intracellular mRNA localization / positive regulation of dendritic spine morphogenesis / positive regulation of dendrite morphogenesis / membraneless organelle assembly / intracellular membraneless organelle / generation of neurons / cell leading edge / ribosomal small subunit binding / positive regulation of type I interferon production / synapse assembly / signaling adaptor activity / stress granule assembly / DNA helicase activity / molecular function activator activity / P-body / molecular condensate scaffold activity / negative regulation of canonical Wnt signaling pathway / cytoplasmic stress granule / lamellipodium / endonuclease activity / perikaryon / defense response to virus / DNA helicase / Ras protein signal transduction / RNA helicase activity / negative regulation of translation / RNA helicase / innate immune response / focal adhesion / mRNA binding / dendrite / synapse / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / DNA binding / RNA binding / ATP binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Cytoplasmic activation/proliferation-associated protein-1 C term / Cytoplasmic activation/proliferation-associated protein-1 C term / Caprin / Caprin-1 dimerization domain / Caprin-1 dimerization domain / 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 ...Cytoplasmic activation/proliferation-associated protein-1 C term / Cytoplasmic activation/proliferation-associated protein-1 C term / Caprin / Caprin-1 dimerization domain / Caprin-1 dimerization domain / 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 / Nuclear transport factor 2 domain / 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
Ras GTPase-activating protein-binding protein 1 / Caprin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 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

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Assembly

Deposited unit
A: Ras GTPase-activating protein-binding protein 1
B: Ras GTPase-activating protein-binding protein 1
C: Caprin-1
D: Caprin-1


Theoretical massNumber of molelcules
Total (without water)37,2164
Polymers37,2164
Non-polymers00
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6820 Å2
ΔGint-43 kcal/mol
Surface area14170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.650, 71.440, 51.950
Angle α, β, γ (deg.)90.00, 111.26, 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: 15986.153 Da / Num. of mol.: 2
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 Caprin-1 / Cell cycle-associated protein 1 / Cytoplasmic activation- and proliferation-associated protein 1 / ...Cell cycle-associated protein 1 / Cytoplasmic activation- and proliferation-associated protein 1 / GPI-anchored membrane protein 1 / GPI-anchored protein p137 / GPI-p137 / p137GPI / Membrane component chromosome 11 surface marker 1 / RNA granule protein 105


Mass: 2621.915 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAPRIN1, GPIAP1, GPIP137, M11S1, RNG105 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14444
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 1.99 Å3/Da / Density % sol: 38.08 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.8M tri-ammonium citrate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.18057 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18057 Å / Relative weight: 1
ReflectionResolution: 2.88→48.42 Å / Num. obs: 6159 / % possible obs: 99.5 % / Redundancy: 4.5 % / CC1/2: 0.938 / Net I/σ(I): 4.5
Reflection shellResolution: 2.88→2.955 Å / Num. unique obs: 966 / CC1/2: 0.837

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q9O

3q9o


Resolution: 2.88→48.41 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.87 / SU B: 23.778 / SU ML: 0.454 / Cross valid method: THROUGHOUT / ESU R Free: 0.512 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27652 341 5.2 %RANDOM
Rwork0.18965 ---
obs0.19448 6159 97.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.789 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0 Å20.06 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.88→48.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2405 0 0 12 2417
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132460
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172222
X-RAY DIFFRACTIONr_angle_refined_deg1.61.643331
X-RAY DIFFRACTIONr_angle_other_deg1.2321.5825055
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3625304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.72422.34141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.85615373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6411515
X-RAY DIFFRACTIONr_chiral_restr0.0670.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022882
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02628
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_it2.913.9721231
X-RAY DIFFRACTIONr_mcbond_other2.93.9711230
X-RAY DIFFRACTIONr_mcangle_it4.7285.9391530
X-RAY DIFFRACTIONr_mcangle_other4.7275.941531
X-RAY DIFFRACTIONr_scbond_it2.7634.081229
X-RAY DIFFRACTIONr_scbond_other2.7624.0811230
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4486.0171802
X-RAY DIFFRACTIONr_long_range_B_refined7.07945.9632672
X-RAY DIFFRACTIONr_long_range_B_other7.07745.9622673
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.88→2.955 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.456 23 -
Rwork0.282 456 -
obs--99.38 %

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