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- PDB-5ic9: Structure of the CTD complex of Utp12 and Utp13 -

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Basic information

Entry
Database: PDB / ID: 5ic9
TitleStructure of the CTD complex of Utp12 and Utp13
Components(Putative uncharacterized protein) x 2
KeywordsSTRUCTURAL PROTEIN / solenoid structure / rRNA processing / 90S preribosome / protein binding
Function / homology
Function and homology information


small-subunit processome / rRNA processing / ribosome biogenesis / nucleolus
Similarity search - Function
U3 small nucleolar RNA-associated protein 13, C-terminal / Utp13 specific WD40 associated domain / Small-subunit processome, Utp12 / Dip2/Utp12 Family / Quinoprotein alcohol dehydrogenase-like superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats ...U3 small nucleolar RNA-associated protein 13, C-terminal / Utp13 specific WD40 associated domain / Small-subunit processome, Utp12 / Dip2/Utp12 Family / Quinoprotein alcohol dehydrogenase-like superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / 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
Small-subunit processome Utp12 domain-containing protein / U3 small nucleolar RNA-associated protein 13 C-terminal domain-containing protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.7 Å
AuthorsZhang, C. / Ye, K.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Integrative structural analysis of the UTPB complex, an early assembly factor for eukaryotic small ribosomal subunits
Authors: Zhang, C. / Sun, Q. / Chen, R. / Chen, X. / Lin, J. / Ye, K.
History
DepositionFeb 23, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)87,2104
Polymers87,2104
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8270 Å2
ΔGint-52 kcal/mol
Surface area28240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.311, 160.311, 134.703
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Putative uncharacterized protein / U3 small nucleolar RNA-associated protein 12


Mass: 23876.555 Da / Num. of mol.: 2 / Fragment: UNP residues 748-956
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0003430 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-RIL / References: UniProt: G0RZL9
#2: Protein Putative uncharacterized protein / U3 small nucleolar RNA-associated protein 13


Mass: 19728.293 Da / Num. of mol.: 2 / Fragment: UNP residues 738-912
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0065530 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-RIL / References: UniProt: G0SG95

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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: 2.86 Å3/Da / Density % sol: 57.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-Tris-HCl, 50% Pentaerythritol, 0.35M Ammonium Sulfate, 0.2M Sodium Thiocyanate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.7→50 Å / Num. obs: 20816 / % possible obs: 99.9 % / Redundancy: 24.3 % / Rmerge(I) obs: 0.168 / Rsym value: 0.168 / Net I/σ(I): 19.2
Reflection shellResolution: 3.7→3.76 Å / Redundancy: 24.9 % / Mean I/σ(I) obs: 3.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8.4_1496phasing
RefinementMethod to determine structure: SAD / Resolution: 3.7→29.9 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.56
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2994 2051 9.93 %
Rwork0.2748 --
obs0.2773 20658 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.7→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4015 0 0 0 4015
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054077
X-RAY DIFFRACTIONf_angle_d0.9135524
X-RAY DIFFRACTIONf_dihedral_angle_d13.0061540
X-RAY DIFFRACTIONf_chiral_restr0.032667
X-RAY DIFFRACTIONf_plane_restr0.004696
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7001-3.7860.41391390.37191240X-RAY DIFFRACTION100
3.786-3.88050.35911350.34961256X-RAY DIFFRACTION100
3.8805-3.98520.36771330.33731236X-RAY DIFFRACTION100
3.9852-4.10220.35871370.30581236X-RAY DIFFRACTION100
4.1022-4.23420.32721350.30551248X-RAY DIFFRACTION100
4.2342-4.38510.34371390.30821209X-RAY DIFFRACTION100
4.3851-4.56010.30561360.28881261X-RAY DIFFRACTION100
4.5601-4.76680.28621410.25931233X-RAY DIFFRACTION100
4.7668-5.01710.24141360.26681239X-RAY DIFFRACTION100
5.0171-5.32970.32861400.26511233X-RAY DIFFRACTION100
5.3297-5.73860.33591370.31221239X-RAY DIFFRACTION100
5.7386-6.31120.3051370.32981247X-RAY DIFFRACTION100
6.3112-7.21320.32941340.28991240X-RAY DIFFRACTION100
7.2132-9.04590.25791360.23221244X-RAY DIFFRACTION100
9.0459-29.90060.26371360.2361246X-RAY DIFFRACTION100

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