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- PDB-4m5d: Crystal structure of the Utp22 and Rrp7 complex from Saccharomyce... -

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Basic information

Entry
Database: PDB / ID: 4m5d
TitleCrystal structure of the Utp22 and Rrp7 complex from Saccharomyces cerevisiae
Components
  • Ribosomal RNA-processing protein 7
  • U3 small nucleolar RNA-associated protein 22
KeywordsRNA BINDING PROTEIN / Nucleolus
Function / homology
Function and homology information


regulation of ribosomal protein gene transcription by RNA polymerase II / CURI complex / UTP-C complex / tRNA export from nucleus / Major pathway of rRNA processing in the nucleolus and cytosol / nucleolar large rRNA transcription by RNA polymerase I / 90S preribosome / maturation of SSU-rRNA / small-subunit processome / rRNA processing ...regulation of ribosomal protein gene transcription by RNA polymerase II / CURI complex / UTP-C complex / tRNA export from nucleus / Major pathway of rRNA processing in the nucleolus and cytosol / nucleolar large rRNA transcription by RNA polymerase I / 90S preribosome / maturation of SSU-rRNA / small-subunit processome / rRNA processing / ribosomal small subunit assembly / rRNA binding / nucleolus / RNA binding / nucleoplasm / nucleus
Similarity search - Function
Alpha-Beta Plaits - #3020 / Alpha-Beta Plaits - #3030 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2760 / Poly(a)-polymerase, middle domain - #10 / NOL6/Upt22 / Nrap protein domain 1 / Nrap protein, domain 2 / Nrap protein, domain 3 / Nrap protein, domain 4 / Nrap protein, domain 5 ...Alpha-Beta Plaits - #3020 / Alpha-Beta Plaits - #3030 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2760 / Poly(a)-polymerase, middle domain - #10 / NOL6/Upt22 / Nrap protein domain 1 / Nrap protein, domain 2 / Nrap protein, domain 3 / Nrap protein, domain 4 / Nrap protein, domain 5 / Nrap protein, domain 6 / Nrap protein domain 1 / Nrap protein PAP/OAS-like domain / Nrap protein domain 3 / Nrap protein nucleotidyltransferase domain 4 / Nrap protein PAP/OAS1-like domain 5 / Nrap protein domain 6 / Ribosomal RNA-processing protein 7, C-terminal domain / Ribosomal RNA-processing protein 7 / Rrp7, RRM-like N-terminal domain / Ribosomal RNA-processing protein 7 (RRP7) C-terminal domain / Rrp7 RRM-like N-terminal domain / Poly(a)-polymerase, middle domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Ribosomal RNA-processing protein 7 / U3 small nucleolar RNA-associated protein 22
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.97 Å
AuthorsLin, J. / Ye, K.
CitationJournal: Plos Biol. / Year: 2013
Title: An RNA-Binding Complex Involved in Ribosome Biogenesis Contains a Protein with Homology to tRNA CCA-Adding Enzyme.
Authors: Lin, J. / Lu, J. / Feng, Y. / Sun, M. / Ye, K.
History
DepositionAug 8, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 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: U3 small nucleolar RNA-associated protein 22
B: Ribosomal RNA-processing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,69416
Polymers175,1872
Non-polymers1,50714
Water13,745763
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9020 Å2
ΔGint-184 kcal/mol
Surface area53710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.257, 129.560, 214.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1530-

HOH

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Components

#1: Protein U3 small nucleolar RNA-associated protein 22 / U3 snoRNA-associated protein 22 / U three protein 22


Mass: 140660.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: UTP22, YGR090W / Plasmid: pFastBac-1 / Cell line (production host): High 5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P53254
#2: Protein Ribosomal RNA-processing protein 7


Mass: 34526.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: RRP7, YCL031C, YCL184, YCL31C / Plasmid: pFastBac-1 / Cell line (production host): High 5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P25368
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 763 / 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: 50.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 100mM sodium cacodylate pH 6.2-6.5, 30% (w/v) PEG 400, 200mM lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 123322 / % possible obs: 99.3 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 15.9
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 2.4 / % possible all: 92.7

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Processing

Software
NameVersionClassification
SHARPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.97→19.94 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.574 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23847 6183 5 %RANDOM
Rwork0.20844 ---
obs0.20995 116965 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.707 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.97→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10238 0 78 763 11079
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02210550
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.111.97114269
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.29251258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55524.492472
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.055151872
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3351537
X-RAY DIFFRACTIONr_chiral_restr0.0760.21592
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217796
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_it0.5881.56335
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.146210291
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.75634215
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9734.53978
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.972→2.023 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 400 -
Rwork0.255 8497 -
obs--99.69 %

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