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- PDB-5wxm: Crystal structure of the Imp3 and Mpp10 complex -

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Basic information

Entry
Database: PDB / ID: 5wxm
TitleCrystal structure of the Imp3 and Mpp10 complex
Components
  • U3 small nucleolar RNA-associated protein MPP10
  • U3 small nucleolar ribonucleoprotein protein IMP3
KeywordsRIBOSOMAL PROTEIN / protein complex / components of 90S preribosome
Function / homology
Function and homology information


Mpp10 complex / RNA folding chaperone / 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) / sno(s)RNA-containing ribonucleoprotein complex / snoRNA binding / Major pathway of rRNA processing in the nucleolus and cytosol / 90S preribosome / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA ...Mpp10 complex / RNA folding chaperone / 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) / sno(s)RNA-containing ribonucleoprotein complex / snoRNA binding / Major pathway of rRNA processing in the nucleolus and cytosol / 90S preribosome / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / rRNA processing / ribosomal small subunit biogenesis / rRNA binding / nucleolus / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
U3 small nucleolar ribonucleoprotein complex, subunit Mpp10 / Mpp10 protein / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S4/S9 / S4 RNA-binding domain profile. / S4 RNA-binding domain / S4 domain / RNA-binding S4 domain / RNA-binding S4 domain superfamily
Similarity search - Domain/homology
U3 small nucleolar ribonucleoprotein protein IMP3 / U3 small nucleolar RNA-associated protein MPP10
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.304 Å
AuthorsYe, K. / Zheng, S.
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 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: U3 small nucleolar ribonucleoprotein protein IMP3
U: U3 small nucleolar RNA-associated protein MPP10
B: U3 small nucleolar ribonucleoprotein protein IMP3
V: U3 small nucleolar RNA-associated protein MPP10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0999
Polymers45,6194
Non-polymers4805
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7150 Å2
ΔGint-116 kcal/mol
Surface area17290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.565, 86.951, 88.720
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein U3 small nucleolar ribonucleoprotein protein IMP3 / U3 snoRNP protein IMP3 / Interacting with MPP10 protein 3


Mass: 19053.246 Da / Num. of mol.: 2 / Fragment: UNP residues 26-183
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: IMP3, YHR148W / Production host: Escherichia coli (E. coli) / References: UniProt: P32899
#2: Protein/peptide U3 small nucleolar RNA-associated protein MPP10 / U3 snoRNA-associated protein MPP10 / M phase phosphoprotein 10


Mass: 3756.327 Da / Num. of mol.: 2 / Fragment: UNP residues 430-461
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: MPP10, YJR002W, J1411, YJR83.5 / Production host: Escherichia coli (E. coli) / References: UniProt: P47083
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.18 Å3/Da / Density % sol: 43.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.2 M potassium sodium tartrate, 0.1 M sodium citrate, 1.7 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 18226 / % possible obs: 99.9 % / Redundancy: 6.2 % / Net I/σ(I): 15.4

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Processing

Software
NameVersionClassification
PHENIX(1.11rc1_2513: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.304→33.629 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2372 855 4.7 %
Rwork0.1941 17322 -
obs0.1962 18177 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.87 Å2 / Biso mean: 26.6306 Å2 / Biso min: 7.97 Å2
Refinement stepCycle: final / Resolution: 2.304→33.629 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2686 0 25 192 2903
Biso mean--46.4 29.44 -
Num. residues----328
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082755
X-RAY DIFFRACTIONf_angle_d0.9173725
X-RAY DIFFRACTIONf_chiral_restr0.051423
X-RAY DIFFRACTIONf_plane_restr0.005468
X-RAY DIFFRACTIONf_dihedral_angle_d6.7121696
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3038-2.44810.28851350.21912811294699
2.4481-2.63710.31631330.20628462979100
2.6371-2.90230.24461600.197628372997100
2.9023-3.3220.24811620.195828513013100
3.322-4.18410.22791260.167529313057100
4.1841-33.63210.19041390.20263046318599

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