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- PDB-4lun: Structure of the N-terminal mIF4G domain from S. cerevisiae Upf2,... -

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Basic information

Entry
Database: PDB / ID: 4lun
TitleStructure of the N-terminal mIF4G domain from S. cerevisiae Upf2, a protein involved in the degradation of mRNAs containing premature stop codons
ComponentsNonsense-mediated mRNA decay protein 2Nonsense-mediated decay
KeywordsRNA BINDING PROTEIN / HEAT-repeat / mRNA decay
Function / homology
Function and homology information


exon-exon junction complex / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / : / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / DNA recombination / RNA binding / cytoplasm
Similarity search - Function
: / Up-frameshift suppressor 2, C-terminal / Nonsense-mediated mRNA decay protein Nmd2/UPF2 / Up-frameshift suppressor 2 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe ...: / Up-frameshift suppressor 2, C-terminal / Nonsense-mediated mRNA decay protein Nmd2/UPF2 / Up-frameshift suppressor 2 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Nonsense-mediated mRNA decay protein 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.641 Å
AuthorsFourati, Z. / Roy, B. / Millan, C. / Courreux, P.D. / Kervestin, S. / van Tilbeurgh, H. / He, F. / Uson, I. / Jacobson, A. / Graille, M.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: A highly conserved region essential for NMD in the Upf2 N-terminal domain.
Authors: Fourati, Z. / Roy, B. / Millan, C. / Coureux, P.D. / Kervestin, S. / van Tilbeurgh, H. / He, F. / Uson, I. / Jacobson, A. / Graille, M.
History
DepositionJul 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2017Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2May 5, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / struct_ref_seq_dif / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _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 / _citation_author.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 28, 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
U: Nonsense-mediated mRNA decay protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6742
Polymers36,6381
Non-polymers351
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.813, 50.927, 71.993
Angle α, β, γ (deg.)90.00, 99.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Nonsense-mediated mRNA decay protein 2 / Nonsense-mediated decay / Up-frameshift suppressor 2


Mass: 36638.141 Da / Num. of mol.: 1 / Fragment: Upf2 domain, UNP residues 1-310
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288C / Gene: IFS1, NMD2, SUA1, UPF2, YHR077C / Plasmid: pMG567 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codon+ / References: UniProt: P38798
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 165 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.0640.31
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2911vapor diffusion, sitting drop8.5100mM Tris-HCl pH 8.5 and 30% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 291K
2912vapor diffusion, sitting drop9100mM NaCl, 100 mM Bicine pH9 and 30% PEG MME 550, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9791 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. all: 36645 / Num. obs: 36059 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rsym value: 0.052 / Net I/σ(I): 14.6
Reflection shellResolution: 1.64→1.74 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.626 / % possible all: 95.9

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Processing

Software
NameVersionClassification
Arcimboldophasing
PHENIX(phenix.refine: 1.7.2_869)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.641→41.183 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 2.01 / Phase error: 23.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2297 1803 5 %RANDOM
Rwork0.1909 ---
all0.23 36645 --
obs0.1929 36056 98.47 %-
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.748 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.6915 Å20 Å2-1.2267 Å2
2--8.8125 Å2-0 Å2
3----4.1211 Å2
Refinement stepCycle: LAST / Resolution: 1.641→41.183 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2544 0 1 165 2710
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062622
X-RAY DIFFRACTIONf_angle_d0.9933530
X-RAY DIFFRACTIONf_dihedral_angle_d14.9841003
X-RAY DIFFRACTIONf_chiral_restr0.071394
X-RAY DIFFRACTIONf_plane_restr0.003452
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6414-1.68580.3281290.28622463X-RAY DIFFRACTION92
1.6858-1.73540.31331390.27192631X-RAY DIFFRACTION99
1.7354-1.79140.3491370.23932617X-RAY DIFFRACTION99
1.7914-1.85540.24941400.21942642X-RAY DIFFRACTION100
1.8554-1.92970.27981390.19742658X-RAY DIFFRACTION99
1.9297-2.01750.24291410.19622663X-RAY DIFFRACTION100
2.0175-2.12390.23681390.1892658X-RAY DIFFRACTION99
2.1239-2.25690.21071390.17932641X-RAY DIFFRACTION99
2.2569-2.43120.20871400.18242645X-RAY DIFFRACTION99
2.4312-2.67580.25011390.19182656X-RAY DIFFRACTION99
2.6758-3.06290.23591400.20292643X-RAY DIFFRACTION98
3.0629-3.85850.22351400.18312659X-RAY DIFFRACTION98
3.8585-41.19640.19381410.16922677X-RAY DIFFRACTION97

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