- PDB-4m5d: Crystal structure of the Utp22 and Rrp7 complex from Saccharomyce... -
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Basic information
Entry
Database: PDB / ID: 4m5d
Title
Crystal structure of the Utp22 and Rrp7 complex from Saccharomyces cerevisiae
Components
Ribosomal RNA-processing protein 7
U3 small nucleolar RNA-associated protein 22
Keywords
RNA 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 species
Saccharomyces cerevisiae (brewer's yeast)
Method
X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.97 Å
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1 Å / Relative weight: 1
Reflection
Resolution: 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 shell
Resolution: 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
Name
Version
Classification
SHARP
phasing
REFMAC
5.5.0109
refinement
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method 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
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.23847
6183
5 %
RANDOM
Rwork
0.20844
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obs
0.20995
116965
99.96 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK