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- PDB-1ya0: Crystal structure of the N-terminal domain of human SMG7 -

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Basic information

Entry
Database: PDB / ID: 1ya0
TitleCrystal structure of the N-terminal domain of human SMG7
ComponentsSMG-7 transcript variant 2
KeywordsSIGNALING PROTEIN / alpha-helical repeat / tetratricopetide repeat (TPR) / 14-3-3
Function / homology
Function and homology information


regulation of dephosphorylation / telomerase RNA binding / telomerase holoenzyme complex / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / telomeric DNA binding / mRNA export from nucleus / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / protein phosphatase 2A binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Telomerase activating protein Est1-like, N-terminal / Telomerase activating protein Est1 / DNA/RNA-binding domain, Est1-type / Est1/Ebs1-like / Est1 DNA/RNA binding domain / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Nonsense-mediated mRNA decay factor SMG7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.55 Å
AuthorsFukuhara, N. / Ebert, J. / Unterholzner, L. / Lindner, D. / Izaurralde, E. / Conti, E.
CitationJournal: Mol.Cell / Year: 2005
Title: SMG7 Is a 14-3-3-like Adaptor in the Nonsense-Mediated mRNA Decay Pathway.
Authors: Fukuhara, N. / Ebert, J. / Unterholzner, L. / Lindner, D. / Izaurralde, E. / Conti, E.
History
DepositionDec 17, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SMG-7 transcript variant 2
B: SMG-7 transcript variant 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,6285
Polymers114,3402
Non-polymers2883
Water5,747319
1
A: SMG-7 transcript variant 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2662
Polymers57,1701
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SMG-7 transcript variant 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3623
Polymers57,1701
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.018, 100.0497, 208.6214
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 SMG-7 transcript variant 2


Mass: 57169.891 Da / Num. of mol.: 2 / Fragment: N-terminal domain (1-497)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pProEx / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q92540
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Fragment: SO4 ion from crystallization solution / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 1.1 M ammonium sulfate, 0.1 M Hepes, pH 6.5 to 7.5, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 3, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→30 Å / Num. obs: 44344 / % possible obs: 99.7 % / Redundancy: 7.9 % / Rsym value: 0.082 / Net I/σ(I): 6.9
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 6407 / Rsym value: 0.324 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MIR / Resolution: 2.55→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.287 2219 RANDOM
Rwork0.246 --
all0.2503 44289 -
obs0.2503 44289 -
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.55→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7520 0 15 319 7854
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009336
X-RAY DIFFRACTIONc_angle_deg1.61316
X-RAY DIFFRACTIONc_dihedral_angle_d20.04816
X-RAY DIFFRACTIONc_improper_angle_d1.11441

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