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- PDB-4um2: Crystal structure of the TPR domain of SMG6 -

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Basic information

Entry
Database: PDB / ID: 4um2
TitleCrystal structure of the TPR domain of SMG6
ComponentsTELOMERASE-BINDING PROTEIN EST1A
KeywordsTELOMERASE-BINDING PROTEIN / NONSENSE MEDIATED MRNA DECAY (NMD) / TPR DOMAIN
Function / homology
Function and homology information


regulation of dephosphorylation / regulation of telomerase activity / negative regulation of telomere capping / regulation of telomere maintenance via telomerase / telomerase RNA binding / telomerase holoenzyme complex / regulation of telomere maintenance / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / telomeric DNA binding / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) ...regulation of dephosphorylation / regulation of telomerase activity / negative regulation of telomere capping / regulation of telomere maintenance via telomerase / telomerase RNA binding / telomerase holoenzyme complex / regulation of telomere maintenance / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / telomeric DNA binding / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ribonucleoprotein complex binding / mRNA export from nucleus / DNA polymerase binding / RNA endonuclease activity / chromosome, telomeric region / Hydrolases; Acting on ester bonds / nucleolus / RNA binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Est1/Ebs1-like / Telomerase activating protein Est1-like, N-terminal / Telomerase activating protein Est1 / DNA/RNA-binding domain, Est1-type / Est1 DNA/RNA binding domain / PIN domain / Large family of predicted nucleotide-binding domains / PIN domain / PIN-like domain superfamily / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Telomerase-binding protein EST1A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsChakrabarti, S. / Bonneau, F. / Schuessler, S. / Eppinger, E. / Conti, E.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Phospho-Dependent and Phospho-Independent Interactions of the Helicase Upf1 with the Nmd Factors Smg5-Smg7 and Smg6.
Authors: Chakrabarti, S. / Bonneau, F. / Schussler, S. / Eppinger, E. / Conti, E.
History
DepositionMay 14, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TELOMERASE-BINDING PROTEIN EST1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3732
Polymers67,2811
Non-polymers921
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.080, 80.676, 124.729
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 TELOMERASE-BINDING PROTEIN EST1A / SMG6 / EST1-LIKE PROTEIN A / EVER SHORTER TELOMERES 1A / SMG-6 HOMOLOG / TELOMERASE SUBUNIT EST1A / HSMG5/7A


Mass: 67280.852 Da / Num. of mol.: 1 / Fragment: TETRATRICOPEPTIDE REPEAT, RESIDUES 580-1166
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): PLYSS
References: UniProt: Q86US8, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSTRUCTURE COVERS RESIDUES 580-1159 OF THE ABOVE SEQUENCE

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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: 2.32 Å3/Da / Density % sol: 46.95 % / Description: NONE
Crystal growpH: 5.5
Details: 50MM MES PH 5.5, 200MM AMMONIUM ACETATE, 2.5% 2-METHYL-2,4-PENTANEDIOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Aug 12, 2012 / Details: MIRRORS
RadiationMonochromator: SI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.1→49.3 Å / Num. obs: 37397 / % possible obs: 100 % / Observed criterion σ(I): 2.9 / Redundancy: 6.4 % / Biso Wilson estimate: 43.4 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.8
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.9 / % possible all: 99.8

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
SHELXphasing
PHENIXAUTOSOLphasing
PHENIXrefinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.1→49.2 Å / SU ML: 0.27 / σ(F): 0.84 / Phase error: 26.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2371 3537 5 %
Rwork0.2062 --
obs0.2078 37317 99.79 %
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48 Å2
Refinement stepCycle: LAST / Resolution: 2.1→49.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3820 0 6 64 3890
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083899
X-RAY DIFFRACTIONf_angle_d1.0815310
X-RAY DIFFRACTIONf_dihedral_angle_d13.5651378
X-RAY DIFFRACTIONf_chiral_restr0.044631
X-RAY DIFFRACTIONf_plane_restr0.005677
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.12880.32451410.29042752X-RAY DIFFRACTION100
2.1288-2.15920.341330.2732643X-RAY DIFFRACTION100
2.1592-2.19140.29541330.26832689X-RAY DIFFRACTION100
2.1914-2.22570.33591230.26472726X-RAY DIFFRACTION100
2.2257-2.26210.33881430.28482647X-RAY DIFFRACTION99
2.2621-2.30120.27561290.24882704X-RAY DIFFRACTION100
2.3012-2.3430.24951430.22932649X-RAY DIFFRACTION100
2.343-2.38810.26571490.23142691X-RAY DIFFRACTION100
2.3881-2.43680.27361260.22182687X-RAY DIFFRACTION100
2.4368-2.48980.26581210.22892703X-RAY DIFFRACTION100
2.4898-2.54770.28171650.22282654X-RAY DIFFRACTION100
2.5477-2.61140.33031240.2312683X-RAY DIFFRACTION100
2.6114-2.6820.32151560.23652700X-RAY DIFFRACTION100
2.682-2.76090.31491320.24942631X-RAY DIFFRACTION100
2.7609-2.850.27671670.23962676X-RAY DIFFRACTION100
2.85-2.95190.29011540.24032652X-RAY DIFFRACTION100
2.9519-3.07010.34331370.23782698X-RAY DIFFRACTION100
3.0701-3.20980.20231180.22572705X-RAY DIFFRACTION100
3.2098-3.37890.22551150.2182716X-RAY DIFFRACTION100
3.3789-3.59060.24811460.20792654X-RAY DIFFRACTION100
3.5906-3.86770.21911500.18882695X-RAY DIFFRACTION100
3.8677-4.25670.2121330.172689X-RAY DIFFRACTION100
4.2567-4.87220.16261570.1582656X-RAY DIFFRACTION100
4.8722-6.13660.20021670.19962666X-RAY DIFFRACTION100
6.1366-49.21320.20561750.17452642X-RAY DIFFRACTION100

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