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- PDB-5ica: Structure of the CTD complex of UTP12, Utp13, Utp1 and Utp21 -

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Basic information

Entry
Database: PDB / ID: 5ica
TitleStructure of the CTD complex of UTP12, Utp13, Utp1 and Utp21
Components
  • (Putative uncharacterized protein) x 2
  • Periodic tryptophan protein 2-like protein
  • Putative U3 snoRNP protein
KeywordsSTRUCTURAL PROTEIN / rRNA processing / 90S preribosome / protein binding
Function / homology
Function and homology information


Pwp2p-containing subcomplex of 90S preribosome / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / U3 snoRNA binding / snoRNA binding / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / rRNA processing ...Pwp2p-containing subcomplex of 90S preribosome / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / U3 snoRNA binding / snoRNA binding / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / rRNA processing / ribosomal small subunit assembly / nucleolus
Similarity search - Function
WDR3 second beta-propeller domain / WDR3 first beta-propeller domain / U3 small nucleolar RNA-associated protein 13, C-terminal / Periodic tryptophan protein 2 / Utp13 specific WD40 associated domain / : / Small-subunit processome, Utp12 / Dip2/Utp12 Family / Small-subunit processome, Utp21 / Utp21 specific WD40 associated putative domain ...WDR3 second beta-propeller domain / WDR3 first beta-propeller domain / U3 small nucleolar RNA-associated protein 13, C-terminal / Periodic tryptophan protein 2 / Utp13 specific WD40 associated domain / : / Small-subunit processome, Utp12 / Dip2/Utp12 Family / Small-subunit processome, Utp21 / Utp21 specific WD40 associated putative domain / WDR36/Utp21 second beta-propeller domain / WDR36/Utp21 first beta-propeller / Quinoprotein amine dehydrogenase, beta chain-like / Quinoprotein alcohol dehydrogenase-like superfamily / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Small-subunit processome Utp12 domain-containing protein / Putative U3 snoRNP protein / Periodic tryptophan protein 2-like 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: 3.507 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

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein
C: Putative U3 snoRNP protein
D: Periodic tryptophan protein 2-like protein


Theoretical massNumber of molelcules
Total (without water)80,1674
Polymers80,1674
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9150 Å2
ΔGint-65 kcal/mol
Surface area28180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.695, 121.695, 167.490
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 18434.656 Da / Num. of mol.: 1 / Fragment: UNP residues 769-931
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: 17371.770 Da / Num. of mol.: 1 / Fragment: UNP residues 738-889
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
#3: Protein Putative U3 snoRNP protein / U3 small nucleolar RNA-associated protein 21


Mass: 27201.953 Da / Num. of mol.: 1 / Fragment: UNP residues 806-1049
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_0037800 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-RIL / References: UniProt: G0S872
#4: Protein Periodic tryptophan protein 2-like protein / U3 small nucleolar RNA-associated protein 1


Mass: 17158.912 Da / Num. of mol.: 1 / Fragment: UNP residues 701-849
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_0061240 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-RIL / References: UniProt: G0SF93
Sequence detailsONLY WEAK ELECTRON DENSITY IS OBSERVED FOR RESIDUES 900-911 OF CHAIN C. AND THESE RESIDUES CANNOT ...ONLY WEAK ELECTRON DENSITY IS OBSERVED FOR RESIDUES 900-911 OF CHAIN C. AND THESE RESIDUES CANNOT BE DEFINED EXACTLY. ONLY C-CA ATOMS HAVE BEEN MODELLED. THESE RESIDUES CAN BE ANY POSITION BETWEEN RESIDUES 806-922.

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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: 4.47 Å3/Da / Density % sol: 72.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES Sodium, 45% w/v Poly(acrylic acid sodium salt) 5100, 0.02M Magnesium Chloride, 0.01M Spermidine

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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: Nov 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 34729 / % possible obs: 99.9 % / Redundancy: 20.7 % / Rmerge(I) obs: 0.172 / Rsym value: 0.172 / Net I/σ(I): 14.6
Reflection shellResolution: 3.5→3.56 Å / Redundancy: 20.6 % / Mean I/σ(I) obs: 1.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.507→34.382 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.31
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.275 3447 9.94 %
Rwork0.2438 --
obs0.247 34670 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 110.5 Å2
Refinement stepCycle: LAST / Resolution: 3.507→34.382 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4378 0 0 0 4378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074455
X-RAY DIFFRACTIONf_angle_d1.0696044
X-RAY DIFFRACTIONf_dihedral_angle_d15.7321652
X-RAY DIFFRACTIONf_chiral_restr0.036712
X-RAY DIFFRACTIONf_plane_restr0.004770
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5068-3.55470.41931300.35421246X-RAY DIFFRACTION99
3.5547-3.60550.28631440.35771236X-RAY DIFFRACTION100
3.6055-3.65920.42591360.40931255X-RAY DIFFRACTION100
3.6592-3.71630.43481440.43691244X-RAY DIFFRACTION100
3.7163-3.77720.39021480.37721269X-RAY DIFFRACTION100
3.7772-3.84230.32071340.31691244X-RAY DIFFRACTION100
3.8423-3.9120.39371410.32741253X-RAY DIFFRACTION99
3.912-3.98720.31121280.34111231X-RAY DIFFRACTION99
3.9872-4.06840.3571390.28041239X-RAY DIFFRACTION99
4.0684-4.15670.28731380.30631243X-RAY DIFFRACTION100
4.1567-4.25330.33421380.27521225X-RAY DIFFRACTION99
4.2533-4.35940.29931350.29431284X-RAY DIFFRACTION100
4.3594-4.47710.29781420.26341263X-RAY DIFFRACTION100
4.4771-4.60850.32071290.2631223X-RAY DIFFRACTION100
4.6085-4.75690.31321320.24571249X-RAY DIFFRACTION100
4.7569-4.92640.28721460.23761255X-RAY DIFFRACTION100
4.9264-5.12310.32841340.24541257X-RAY DIFFRACTION100
5.1231-5.35540.34581460.22881257X-RAY DIFFRACTION100
5.3554-5.63660.26351360.26391232X-RAY DIFFRACTION100
5.6366-5.9880.36031400.25051259X-RAY DIFFRACTION100
5.988-6.44750.29611350.2691269X-RAY DIFFRACTION100
6.4475-7.09130.2831340.21831256X-RAY DIFFRACTION100
7.0913-8.10560.20421410.17511241X-RAY DIFFRACTION100
8.1056-10.16820.17311310.12981255X-RAY DIFFRACTION100
10.1682-34.38380.15891460.16781238X-RAY DIFFRACTION99

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