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- PDB-3uah: Structure of the Shq1 specific domain from Saccharomyces cerevisiae -

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Basic information

Entry
Database: PDB / ID: 3uah
TitleStructure of the Shq1 specific domain from Saccharomyces cerevisiae
ComponentsProtein SHQ1
KeywordsCHAPERONE / All alpha helix / H/ACA RNP assembly factor / Cbf5-binding / Nuclear
Function / homology
Function and homology information


Telomere Extension By Telomerase / box H/ACA snoRNP assembly / unfolded protein binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Shq1 protein domain / Protein Shq1 / : / SHQ1 protein, Shq1 domain / SHQ1-like, CS domain / CS domain / CS domain profile. / HSP20-like chaperone
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.6 Å
AuthorsYe, K.
CitationJournal: Embo J. / Year: 2011
Title: Structure of the Shq1-Cbf5-Nop10-Gar1 complex and implications for H/ACA RNP biogenesis and dyskeratosis congenita
Authors: Li, S. / Duan, J. / Li, D. / Ma, S. / Ye, K.
History
DepositionOct 21, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein SHQ1


Theoretical massNumber of molelcules
Total (without water)42,9281
Polymers42,9281
Non-polymers00
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.087, 50.126, 53.951
Angle α, β, γ (deg.)102.19, 93.75, 97.97
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Protein SHQ1 / Small nucleolar RNAs of the box H/ACA family quantitative accumulation protein 1


Mass: 42928.047 Da / Num. of mol.: 1 / Fragment: Shq1-specific domain, residues 147-507
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: SHQ1 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: P40486
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.37 Å3/Da / Density % sol: 48.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M tri-sodium citrate, 0.2M ammonium acetate, 20%(w/v) PEG 4000, 9% isopropanol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorDetector: CCD / Date: Jun 26, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 50317 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 42.5
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 4 % / Rmerge(I) obs: 0.132 / Mean I/σ(I) obs: 14.1 / % possible all: 95.3

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Processing

Software
NameVersionClassification
SHARPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MIR / Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.091 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19826 2563 5.1 %RANDOM
Rwork0.16821 ---
obs0.16972 47740 96.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.584 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20.09 Å20.03 Å2
2--0.37 Å20.23 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2599 0 0 330 2929
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222652
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2121.9623586
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.265309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.70724.928138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.50615493
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.241514
X-RAY DIFFRACTIONr_chiral_restr0.0880.2396
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211992
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.7671.51555
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.53922532
X-RAY DIFFRACTIONr_scbond_it2.40131097
X-RAY DIFFRACTIONr_scangle_it3.9154.51054
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.201 190 -
Rwork0.173 3414 -
obs--93.34 %

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