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- PDB-1lj2: Recognition of eIF4G by Rotavirus NSP3 reveals a basis for mRNA c... -

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Basic information

Entry
Database: PDB / ID: 1lj2
TitleRecognition of eIF4G by Rotavirus NSP3 reveals a basis for mRNA circularization
Components
  • NONSTRUCTURAL RNA-BINDING PROTEIN 34
  • eukaryotic protein synthesis initiation factorEukaryote
KeywordsViral protein/ translation / NSP3 / homodimer / eIF4G / Rotavirus / translation / mRNA / closed loop / coiled coil / Viral protein- translation COMPLEX
Function / homology
Function and homology information


positive regulation of eukaryotic translation initiation factor 4F complex assembly / positive regulation of mRNA cap binding / positive regulation of translation in response to endoplasmic reticulum stress / cap-dependent translational initiation / macromolecule biosynthetic process / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / eukaryotic initiation factor 4E binding / regulation of cellular response to stress / eukaryotic translation initiation factor 4F complex / Z-decay: degradation of maternal mRNAs by zygotically expressed factors ...positive regulation of eukaryotic translation initiation factor 4F complex assembly / positive regulation of mRNA cap binding / positive regulation of translation in response to endoplasmic reticulum stress / cap-dependent translational initiation / macromolecule biosynthetic process / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / eukaryotic initiation factor 4E binding / regulation of cellular response to stress / eukaryotic translation initiation factor 4F complex / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / translation factor activity, RNA binding / Deadenylation of mRNA / miRNA-mediated gene silencing by inhibition of translation / M-decay: degradation of maternal mRNAs by maternally stored factors / positive regulation of protein localization to cell periphery / regulation of translational initiation / Ribosomal scanning and start codon recognition / Translation initiation complex formation / negative regulation of peptidyl-threonine phosphorylation / mTORC1-mediated signalling / cellular response to nutrient levels / regulation of presynapse assembly / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / positive regulation of G1/S transition of mitotic cell cycle / behavioral fear response / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / energy homeostasis / translation initiation factor binding / translational initiation / positive regulation of neuron differentiation / positive regulation of protein metabolic process / translation initiation factor activity / negative regulation of autophagy / AUF1 (hnRNP D0) binds and destabilizes mRNA / lung development / ISG15 antiviral mechanism / neuron differentiation / Regulation of expression of SLITs and ROBOs / cytoplasmic stress granule / regulation of translation / positive regulation of peptidyl-serine phosphorylation / postsynapse / positive regulation of cell growth / response to ethanol / host cell cytoplasm / molecular adaptor activity / ribosome / translation / mRNA binding / RNA binding / ATP binding / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Nonstructural RNA-binding protein / Rotavirus non-structural protein NSP3 / NSP3 superfamily / Non-structural protein NSP3, N-terminal, rotavirus / Rotavirus non-structural protein NSP3 / Initiation factor 4G / Initiation factor eIF-4 gamma, MA3 / MA3 domain / MI domain profile. / Domain in DAP-5, eIF4G, MA-3 and other proteins. ...Nonstructural RNA-binding protein / Rotavirus non-structural protein NSP3 / NSP3 superfamily / Non-structural protein NSP3, N-terminal, rotavirus / Rotavirus non-structural protein NSP3 / Initiation factor 4G / Initiation factor eIF-4 gamma, MA3 / MA3 domain / MI domain profile. / Domain in DAP-5, eIF4G, MA-3 and other proteins. / eIF4-gamma/eIF5/eIF2-epsilon / Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5 / W2 domain / W2 domain profile. / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Armadillo-type fold / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Non-structural protein 3 / Eukaryotic translation initiation factor 4 gamma 1
Similarity search - Component
Biological speciesSimian rotavirus A/SA11
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.38 Å
AuthorsGroft, C.M. / Burley, S.K.
CitationJournal: Mol.Cell / Year: 2002
Title: Recognition of eIF4G by rotavirus NSP3 reveals a basis for mRNA circularization.
Authors: Groft, C.M. / Burley, S.K.
History
DepositionApr 18, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NONSTRUCTURAL RNA-BINDING PROTEIN 34
B: NONSTRUCTURAL RNA-BINDING PROTEIN 34
C: eukaryotic protein synthesis initiation factor
D: eukaryotic protein synthesis initiation factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6837
Polymers32,0924
Non-polymers5913
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9590 Å2
ΔGint-95 kcal/mol
Surface area14180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.690, 74.040, 77.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
DetailsThe assembly consists of an NSP3 homodimer bound to two fragments of eIF4G.

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Components

#1: Protein NONSTRUCTURAL RNA-BINDING PROTEIN 34 / NSP3-C / NS34 / NCVP4 / non-structural protein NCVP4


Mass: 12842.396 Da / Num. of mol.: 2 / Fragment: C-terminal domain / Mutation: C306S C314S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian rotavirus A/SA11 / Species: Rotavirus A / Production host: Escherichia coli (E. coli) / References: UniProt: P03536
#2: Protein/peptide eukaryotic protein synthesis initiation factor / Eukaryote / eIF4GI


Mass: 3203.653 Da / Num. of mol.: 2 / Fragment: residues 132-159 of AAC82471 / Source method: obtained synthetically / Details: sequence appear naturally in Homo sapiens / References: UniProt: Q04637
#3: Chemical ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Au
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.67 Å3/Da / Density % sol: 53.88 %
Crystal growTemperature: 275 K / Method: vapor diffusion, hanging drop
Details: PEG-MME 550, glucose, theophylline, unbuffered, VAPOR DIFFUSION, HANGING DROP at 275K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
117 %PEG550 MME1reservoir
22.5 %(w/v)glucose1reservoir
31.5 mMtheophylline1reservoir
47 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 1.0447 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 1, 2001
RadiationMonochromator: crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0447 Å / Relative weight: 1
ReflectionResolution: 2.38→20 Å / Num. all: 26535 / Num. obs: 24286 / % possible obs: 99.9 % / Observed criterion σ(I): 1
Reflection shellResolution: 2.38→2.46 Å / % possible all: 99.9
Reflection
*PLUS
Num. obs: 26797 / Num. measured all: 110178 / Rmerge(I) obs: 0.074
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.316

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Processing

Software
NameVersionClassification
DENZOdata reduction
TRUNCATEdata reduction
MLPHAREphasing
CNSrefinement
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.38→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1589 6.5 %random
Rwork0.221 ---
all-26535 --
obs-24286 --
Refinement stepCycle: LAST / Resolution: 2.38→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2130 0 3 196 2329
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.01
Refinement
*PLUS
% reflection Rfree: 7 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.01

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