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- PDB-4cem: Crystal structure of the first MIF4G domain of human nonsense med... -

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Basic information

Entry
Database: PDB / ID: 4cem
TitleCrystal structure of the first MIF4G domain of human nonsense mediated decay factor UPF2
ComponentsREGULATOR OF NONSENSE TRANSCRIPTS 2
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


exon-exon junction complex / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / telomeric DNA binding / animal organ regeneration / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / mRNA export from nucleus / liver development / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / perinuclear region of cytoplasm ...exon-exon junction complex / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / telomeric DNA binding / animal organ regeneration / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / mRNA export from nucleus / liver development / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / perinuclear region of cytoplasm / RNA binding / nucleus / cytoplasm / cytosol
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 / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Regulator of nonsense transcripts 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsClerici, M. / Deniaud, A. / Boehm, V. / Gehring, N.H. / Schaffitzel, C. / Cusack, S.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Structural and Functional Analysis of the Three Mif4G Domains of Nonsense-Mediated Decay Factor Upf2.
Authors: Clerici, M. / Deniaud, A. / Boehm, V. / Gehring, N.H. / Schaffitzel, C. / Cusack, S.
History
DepositionNov 11, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: REGULATOR OF NONSENSE TRANSCRIPTS 2
B: REGULATOR OF NONSENSE TRANSCRIPTS 2


Theoretical massNumber of molelcules
Total (without water)85,9322
Polymers85,9322
Non-polymers00
Water97354
1
A: REGULATOR OF NONSENSE TRANSCRIPTS 2


Theoretical massNumber of molelcules
Total (without water)42,9661
Polymers42,9661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: REGULATOR OF NONSENSE TRANSCRIPTS 2


Theoretical massNumber of molelcules
Total (without water)42,9661
Polymers42,9661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.080, 101.080, 158.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein REGULATOR OF NONSENSE TRANSCRIPTS 2 / NONSENSE MRNA REDUCING FACTOR 2 / UP-FRAMESHIFT SUPPRESSOR 2 HOMOLOG / HUPF2 / UPF2


Mass: 42965.867 Da / Num. of mol.: 2 / Fragment: MIF4G1, RESIDUES 121-486
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: Q9HAU5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL GAMG LEFT AFTER HIS-TAG CLEAVAGE

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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: 2.85 Å3/Da / Density % sol: 56.8 % / Description: NONE
Crystal growpH: 9
Details: 100 MM BICINE PH 9, 100 MM NACL, 11% PEG 6000 AND AT A PROTEIN CONCENTRATION OF 16 MG/ML

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9788
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 28216 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 2.86 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.9
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 2.37 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.7 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.6.0116refinement
XDSdata reduction
XSCALEdata scaling
SHELXDSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.6→87.54 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.906 / SU B: 9.404 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.489 / ESU R Free: 0.29 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25087 1428 5.1 %RANDOM
Rwork0.20532 ---
obs0.20761 26788 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.044 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20.17 Å20 Å2
2--0.34 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.6→87.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5061 0 0 54 5115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0195159
X-RAY DIFFRACTIONr_bond_other_d0.0010.023662
X-RAY DIFFRACTIONr_angle_refined_deg1.0591.9596938
X-RAY DIFFRACTIONr_angle_other_deg0.81838927
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.645615
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.33624.382267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.82915984
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3391538
X-RAY DIFFRACTIONr_chiral_restr0.060.2757
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025651
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021023
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 97 -
Rwork0.327 1942 -
obs--100 %

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