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- PDB-4cek: Crystal structure of the second MIF4G domain of human nonsense me... -

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Basic information

Entry
Database: PDB / ID: 4cek
TitleCrystal structure of the second 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 repeat DNA binding / mRNA export from nucleus / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Regulation of expression of SLITs and ROBOs / perinuclear region of cytoplasm / RNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Up-frameshift suppressor 2, C-terminal / Nonsense-mediated mRNA decay protein Nmd2/UPF2 / Up-frameshift suppressor 2 / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / Armadillo-type fold
Similarity search - Domain/homology
Regulator of nonsense transcripts 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 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
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: REGULATOR OF NONSENSE TRANSCRIPTS 2


Theoretical massNumber of molelcules
Total (without water)35,6111
Polymers35,6111
Non-polymers00
Water57632
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.880, 56.600, 142.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 35610.613 Da / Num. of mol.: 1 / Fragment: MIF4G2, RESIDUES 455-757
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.: 32 / 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: 2.41 Å3/Da / Density % sol: 49.1 % / Description: NONE
Crystal growpH: 6
Details: 100 MM MES PH 6.0, 19% PEG 3350 AND AT A PROTEIN CONCENTRATION OF 8 MG/ML

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 14361 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.95 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.8
Reflection shellResolution: 2.35→2.4 Å / Redundancy: 4.09 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 1.9 / % possible all: 99.4

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Processing

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

Resolution: 2.35→71.07 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.936 / SU B: 7.504 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.292 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25083 723 5 %RANDOM
Rwork0.20623 ---
obs0.2085 13638 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.713 Å2
Baniso -1Baniso -2Baniso -3
1-2.09 Å20 Å20 Å2
2---1.3 Å20 Å2
3----0.78 Å2
Refinement stepCycle: LAST / Resolution: 2.35→71.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1958 0 0 32 1990
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021991
X-RAY DIFFRACTIONr_bond_other_d0.0010.021394
X-RAY DIFFRACTIONr_angle_refined_deg1.4621.9682672
X-RAY DIFFRACTIONr_angle_other_deg0.92933385
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1515235
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69223.54296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.94115384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2951516
X-RAY DIFFRACTIONr_chiral_restr0.0780.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022142
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02410
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: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 63 -
Rwork0.286 885 -
obs--99.27 %

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