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- PDB-2hww: Structure of PIN domain of human SMG6 -

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Basic information

Entry
Database: PDB / ID: 2hww
TitleStructure of PIN domain of human SMG6
ComponentsTelomerase-binding protein EST1A
KeywordsRNA BINDING PROTEIN / degradation / decay / NMD / EST1A / P bodies
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 / 5'-nuclease / Large family of predicted nucleotide-binding domains / PIN domain / PIN-like domain superfamily ...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 / 5'-nuclease / Large family of predicted nucleotide-binding domains / PIN domain / PIN-like domain superfamily / Tetratricopeptide-like helical domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Telomerase-binding protein EST1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGlavan, F. / Behm-Ansmant, I. / Izaurralde, E. / Conti, E.
CitationJournal: Embo J. / Year: 2006
Title: Structures of the PIN domains of SMG6 and SMG5 reveal a nuclease within the mRNA surveillance complex.
Authors: Glavan, F. / Behm-Ansmant, I. / Izaurralde, E. / Conti, E.
History
DepositionAug 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Telomerase-binding protein EST1A
B: Telomerase-binding protein EST1A
C: Telomerase-binding protein EST1A


Theoretical massNumber of molelcules
Total (without water)61,7783
Polymers61,7783
Non-polymers00
Water3,981221
1
A: Telomerase-binding protein EST1A


Theoretical massNumber of molelcules
Total (without water)20,5931
Polymers20,5931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Telomerase-binding protein EST1A


Theoretical massNumber of molelcules
Total (without water)20,5931
Polymers20,5931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Telomerase-binding protein EST1A


Theoretical massNumber of molelcules
Total (without water)20,5931
Polymers20,5931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.879, 71.216, 181.273
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 / Ever shorter telomeres 1A / Telomerase subunit EST1A / EST1-like protein A / hSmg5/7a


Mass: 20592.701 Da / Num. of mol.: 3 / Fragment: PIN Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EST1A / Plasmid: pGEXcs / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL 21 / References: UniProt: Q86US8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 1.93 Å3/Da / Density % sol: 36.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: Jeffamine 2000 32%, 0.1M Hepes pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9779 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 2, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 45496 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.9 / Redundancy: 5.2 % / Rsym value: 0.075
Reflection shellResolution: 1.8→1.9 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 2HWX

2hwx


Resolution: 1.8→28.8 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.921 / SU B: 3.271 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1.9 / ESU R: 0.149 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26748 2290 5 %RANDOM
Rwork0.22184 ---
all0.22184 45496 --
obs0.22417 43132 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.218 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.8→28.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3722 0 0 221 3943
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223580
X-RAY DIFFRACTIONr_bond_other_d0.0020.023483
X-RAY DIFFRACTIONr_angle_refined_deg1.841.9884840
X-RAY DIFFRACTIONr_angle_other_deg1.49437971
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1095448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.21122.993147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.42415616
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3941533
X-RAY DIFFRACTIONr_chiral_restr0.3220.2594
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023894
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02724
X-RAY DIFFRACTIONr_nbd_refined0.2390.2808
X-RAY DIFFRACTIONr_nbd_other0.1930.23648
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21778
X-RAY DIFFRACTIONr_nbtor_other0.090.22334
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2120.2210
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1390.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2690.278
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.28
X-RAY DIFFRACTIONr_mcbond_it1.5361.52917
X-RAY DIFFRACTIONr_mcbond_other0.321.5927
X-RAY DIFFRACTIONr_mcangle_it1.85223660
X-RAY DIFFRACTIONr_scbond_it3.05131420
X-RAY DIFFRACTIONr_scangle_it4.3854.51180
LS refinement shellResolution: 1.796→1.843 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 161 -
Rwork0.238 3054 -
obs--96.63 %

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