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- PDB-5wyl: Crystal structure of Chaetomium thermophilum Utp10 N-terminal dom... -

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Basic information

Entry
Database: PDB / ID: 5wyl
TitleCrystal structure of Chaetomium thermophilum Utp10 N-terminal domain in complex with Utp17 C-terminal helices
Components(Putative uncharacterized protein) x 2
KeywordsRIBOSOMAL PROTEIN/NUCLEAR PROTEIN / nucleolar protein / protein complex / components of 90S preribosome / RIBOSOMAL PROTEIN-NUCLEAR PROTEIN complex
Function / homology
Function and homology information


rRNA processing / ribonucleoprotein complex / nucleolus
Similarity search - Function
BP28, C-terminal domain / U3 small nucleolar RNA-associated protein 10, N-terminal / U3 small nucleolar RNA-associated protein 10 / BP28CT (NUC211) domain / U3 small nucleolar RNA-associated protein 10 / BP28CT (NUC211) domain / Armadillo-like helical / Armadillo-type fold / WD domain, G-beta repeat / WD40 repeats ...BP28, C-terminal domain / U3 small nucleolar RNA-associated protein 10, N-terminal / U3 small nucleolar RNA-associated protein 10 / BP28CT (NUC211) domain / U3 small nucleolar RNA-associated protein 10 / BP28CT (NUC211) domain / Armadillo-like helical / Armadillo-type fold / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
U3 small nucleolar RNA-associated protein 10 / Uncharacterized protein
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.638 Å
AuthorsChen, R. / Zhu, X. / Ye, K.
CitationJournal: Elife / Year: 2017
Title: Molecular architecture of the 90S small subunit pre-ribosome.
Authors: Qi Sun / Xing Zhu / Jia Qi / Weidong An / Pengfei Lan / Dan Tan / Rongchang Chen / Bing Wang / Sanduo Zheng / Cheng Zhang / Xining Chen / Wei Zhang / Jing Chen / Meng-Qiu Dong / Keqiong Ye /
Abstract: Eukaryotic small ribosomal subunits are first assembled into 90S pre-ribosomes. The complete 90S is a gigantic complex with a molecular mass of approximately five megadaltons. Here, we report the ...Eukaryotic small ribosomal subunits are first assembled into 90S pre-ribosomes. The complete 90S is a gigantic complex with a molecular mass of approximately five megadaltons. Here, we report the nearly complete architecture of 90S determined from three cryo-electron microscopy single particle reconstructions at 4.5 to 8.7 angstrom resolution. The majority of the density maps were modeled and assigned to specific RNA and protein components. The nascent ribosome is assembled into isolated native-like substructures that are stabilized by abundant assembly factors. The 5' external transcribed spacer and U3 snoRNA nucleate a large subcomplex that scaffolds the nascent ribosome. U3 binds four sites of pre-rRNA, including a novel site on helix 27 but not the 3' side of the central pseudoknot, and crucially organizes the 90S structure. The 90S model provides significant insight into the principle of small subunit assembly and the function of assembly factors.
History
DepositionJan 13, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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: Putative uncharacterized protein
B: Putative uncharacterized protein
C: Putative uncharacterized protein
D: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)116,3024
Polymers116,3024
Non-polymers00
Water99155
1
A: Putative uncharacterized protein
B: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)58,1512
Polymers58,1512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-20 kcal/mol
Surface area20240 Å2
MethodPISA
2
C: Putative uncharacterized protein
D: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)58,1512
Polymers58,1512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-20 kcal/mol
Surface area20670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.309, 98.309, 235.653
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Putative uncharacterized protein / Utp10


Mass: 52228.414 Da / Num. of mol.: 2 / Fragment: N-terminal domain, UNP residues 1-471
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / Gene: CTHT_0024640 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S5L1
#2: Protein Putative uncharacterized protein / Utp17


Mass: 5922.624 Da / Num. of mol.: 2 / Fragment: C-terminal domain, UNP residues 907-960
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / Gene: CTHT_0058290 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SCS8
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.45 Å3/Da / Density % sol: 49.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M Hepes-Na, 20% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.64→49.154 Å / Num. obs: 34951 / % possible obs: 100 % / Redundancy: 26.992 % / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.078 / Χ2: 0.996 / Net I/σ(I): 35.46 / Num. measured all: 943385
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.64-2.80.18515.87161583552155180.9970.18899.9
2.8-2.990.13922.86151429521352130.9980.141100
2.99-3.230.11129.76137629486948680.9990.113100
3.23-3.530.08638.35120229449444940.9990.088100
3.53-3.950.07644.31104596409740970.9990.078100
3.95-4.560.06948.2991462364736460.9990.071100
4.56-5.570.06750.0679024312731270.9990.068100
5.57-7.820.06550.6561653248024800.9980.066100
7.82-49.1540.07850.1435780151915080.9970.0899.3

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHENIXphasing
PHENIX(1.11rc1_2513: ???)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WY4

5wy4


Resolution: 2.638→39.01 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 28.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2667 1998 5.72 %
Rwork0.2118 32912 -
obs0.215 34910 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.35 Å2 / Biso mean: 62.3908 Å2 / Biso min: 31.45 Å2
Refinement stepCycle: final / Resolution: 2.638→39.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7031 0 0 55 7086
Biso mean---54.87 -
Num. residues----909
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097163
X-RAY DIFFRACTIONf_angle_d1.0299726
X-RAY DIFFRACTIONf_chiral_restr0.0521156
X-RAY DIFFRACTIONf_plane_restr0.0061239
X-RAY DIFFRACTIONf_dihedral_angle_d3.1684373
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6376-2.70350.39261390.277222902429100
2.7035-2.77660.34991410.261523152456100
2.7766-2.85830.30491390.256322962435100
2.8583-2.95050.33961400.263423152455100
2.9505-3.05590.34991410.269223142455100
3.0559-3.17820.33541410.258823312472100
3.1782-3.32280.31421420.252123232465100
3.3228-3.49790.29471410.242323402481100
3.4979-3.71690.28291410.22823212462100
3.7169-4.00360.28891430.204923472490100
4.0036-4.4060.25451430.181223712514100
4.406-5.04240.21261450.170523832528100
5.0424-6.34850.23521480.198324222570100
6.3485-39.01420.20941540.19042544269899

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