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- PDB-5z1g: Structure of the Brx1 and Ebp2 complex -

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Basic information

Entry
Database: PDB / ID: 5z1g
TitleStructure of the Brx1 and Ebp2 complex
Components
  • Ribosome biogenesis protein BRX1
  • rRNA-processing protein EBP2
KeywordsRIBOSOME / BRIX domain / pre-60S / pre-ribosome
Function / homology
Function and homology information


nuclear division / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA primary transcript binding / Major pathway of rRNA processing in the nucleolus and cytosol / preribosome, large subunit precursor / ribosomal large subunit biogenesis / nuclear periphery / ribosomal large subunit assembly / rRNA processing ...nuclear division / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA primary transcript binding / Major pathway of rRNA processing in the nucleolus and cytosol / preribosome, large subunit precursor / ribosomal large subunit biogenesis / nuclear periphery / ribosomal large subunit assembly / rRNA processing / 5S rRNA binding / mRNA binding / nucleolus / RNA binding / identical protein binding
Similarity search - Function
Eukaryotic rRNA processing / Eukaryotic rRNA processing protein EBP2 / Ribosome biogenesis protein BRX1 / Brix domain / Brix domain / Brix domain profile. / Brix
Similarity search - Domain/homology
rRNA-processing protein EBP2 / Ribosome biogenesis protein BRX1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.294 Å
AuthorsZheng, S. / Ye, K.
CitationJournal: Protein Cell / Year: 2019
Title: Cryo-EM structure of an early precursor of large ribosomal subunit reveals a half-assembled intermediate.
Authors: Dejian Zhou / Xing Zhu / Sanduo Zheng / Dan Tan / Meng-Qiu Dong / Keqiong Ye /
Abstract: Assembly of eukaryotic ribosome is a complicated and dynamic process that involves a series of intermediates. It is unknown how the highly intertwined structure of 60S large ribosomal subunits is ...Assembly of eukaryotic ribosome is a complicated and dynamic process that involves a series of intermediates. It is unknown how the highly intertwined structure of 60S large ribosomal subunits is established. Here, we report the structure of an early nucleolar pre-60S ribosome determined by cryo-electron microscopy at 3.7 Å resolution, revealing a half-assembled subunit. Domains I, II and VI of 25S/5.8S rRNA pack tightly into a native-like substructure, but domains III, IV and V are not assembled. The structure contains 12 assembly factors and 19 ribosomal proteins, many of which are required for early processing of large subunit rRNA. The Brx1-Ebp2 complex would interfere with the assembly of domains IV and V. Rpf1, Mak16, Nsa1 and Rrp1 form a cluster that consolidates the joining of domains I and II. Our structure reveals a key intermediate on the path to establishing the global architecture of 60S subunits.
History
DepositionDec 26, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: rRNA-processing protein EBP2
B: Ribosome biogenesis protein BRX1
C: rRNA-processing protein EBP2
D: Ribosome biogenesis protein BRX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8005
Polymers80,7044
Non-polymers961
Water5,549308
1
A: rRNA-processing protein EBP2
D: Ribosome biogenesis protein BRX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4483
Polymers40,3522
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-52 kcal/mol
Surface area15360 Å2
MethodPISA
2
B: Ribosome biogenesis protein BRX1
C: rRNA-processing protein EBP2


Theoretical massNumber of molelcules
Total (without water)40,3522
Polymers40,3522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-32 kcal/mol
Surface area15630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.934, 47.353, 100.695
Angle α, β, γ (deg.)90.00, 94.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein rRNA-processing protein EBP2 / EBNA1-binding protein homolog


Mass: 13053.873 Da / Num. of mol.: 2 / Fragment: UNP residues 186-295
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: EBP2, YKL172W, YKL636 / Production host: Escherichia coli (E. coli) / References: UniProt: P36049
#2: Protein Ribosome biogenesis protein BRX1 /


Mass: 27298.133 Da / Num. of mol.: 2 / Fragment: UNP residues 26-259
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: BRX1, YOL077C / Production host: Escherichia coli (E. coli) / References: UniProt: Q08235
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.38 Å3/Da / Density % sol: 48.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1M Bis-Tris, pH 5.5 and 1.8M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.294→30 Å / Num. obs: 33644 / % possible obs: 97.5 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 17.8
Reflection shellResolution: 2.294→2.34 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 4 / Num. unique obs: 1715 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.294→24.909 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.21
RfactorNum. reflection% reflection
Rfree0.2974 1680 5.06 %
Rwork0.2295 --
obs0.2331 33214 96.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.294→24.909 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5146 0 5 308 5459
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085268
X-RAY DIFFRACTIONf_angle_d1.0917102
X-RAY DIFFRACTIONf_dihedral_angle_d18.2283216
X-RAY DIFFRACTIONf_chiral_restr0.065770
X-RAY DIFFRACTIONf_plane_restr0.006910
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2942-2.36160.3941300.27782616X-RAY DIFFRACTION96
2.3616-2.43780.33551340.26012684X-RAY DIFFRACTION99
2.4378-2.52480.36571480.26452706X-RAY DIFFRACTION99
2.5248-2.62580.31491550.25512642X-RAY DIFFRACTION99
2.6258-2.74520.31761440.24962672X-RAY DIFFRACTION99
2.7452-2.88970.37391440.23912714X-RAY DIFFRACTION100
2.8897-3.07050.29611250.24132725X-RAY DIFFRACTION100
3.0705-3.3070.28191560.22752699X-RAY DIFFRACTION100
3.307-3.63890.32341530.22312692X-RAY DIFFRACTION98
3.6389-4.16340.31771070.24481867X-RAY DIFFRACTION69
4.1634-5.23740.21921340.17662705X-RAY DIFFRACTION97
5.2374-24.91010.23881500.21292812X-RAY DIFFRACTION99

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