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- PDB-6en7: Crystal structure of the ribosome assembly factor Nsa1 -

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Basic information

Entry
Database: PDB / ID: 6en7
TitleCrystal structure of the ribosome assembly factor Nsa1
ComponentsRibosome biogenesis protein NSA1
KeywordsCHAPERONE / Ribosome / biogenesis
Function / homologyWDR74/Nsa1 / preribosome, large subunit precursor / ribosomal large subunit biogenesis / rRNA processing / WD40-repeat-containing domain superfamily / nucleolus / nucleus / Ribosome biogenesis protein NSA1
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.403 Å
AuthorsAltegoer, F. / Bange, G.
CitationJournal: Cell / Year: 2017
Title: Visualizing the Assembly Pathway of Nucleolar Pre-60S Ribosomes.
Authors: Lukas Kater / Matthias Thoms / Clara Barrio-Garcia / Jingdong Cheng / Sherif Ismail / Yasar Luqman Ahmed / Gert Bange / Dieter Kressler / Otto Berninghausen / Irmgard Sinning / Ed Hurt / Roland Beckmann /
Abstract: Eukaryotic 60S ribosomal subunits are comprised of three rRNAs and ∼50 ribosomal proteins. The initial steps of their formation take place in the nucleolus, but, owing to a lack of structural ...Eukaryotic 60S ribosomal subunits are comprised of three rRNAs and ∼50 ribosomal proteins. The initial steps of their formation take place in the nucleolus, but, owing to a lack of structural information, this process is poorly understood. Using cryo-EM, we solved structures of early 60S biogenesis intermediates at 3.3 Å to 4.5 Å resolution, thereby providing insights into their sequential folding and assembly pathway. Besides revealing distinct immature rRNA conformations, we map 25 assembly factors in six different assembly states. Notably, the Nsa1-Rrp1-Rpf1-Mak16 module stabilizes the solvent side of the 60S subunit, and the Erb1-Ytm1-Nop7 complex organizes and connects through Erb1's meandering N-terminal extension, eight assembly factors, three ribosomal proteins, and three 25S rRNA domains. Our structural snapshots reveal the order of integration and compaction of the six major 60S domains within early nucleolar 60S particles developing stepwise from the solvent side around the exit tunnel to the central protuberance.
History
DepositionOct 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribosome biogenesis protein NSA1


Theoretical massNumber of molelcules
Total (without water)51,9821
Polymers51,9821
Non-polymers00
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.723, 81.100, 87.574
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ribosome biogenesis protein NSA1 / NOP7-associated protein 1


Mass: 51982.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NSA1, YGL111W, G2990 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P53136
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.31 Å3/Da / Density % sol: 46.83 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH 6.5, 25% w/v PEG-1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.4→59.5 Å / Num. obs: 15750 / % possible obs: 99.9 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.04384 / Net I/σ(I): 34.78
Reflection shellResolution: 2.4→2.489 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.1126 / Mean I/σ(I) obs: 14.02 / Num. unique obs: 1543 / CC1/2: 0.992 / % possible all: 99.23

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5SUM

5sum


Resolution: 2.403→46.408 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.26 / Phase error: 19.4
RfactorNum. reflection% reflection
Rfree0.2198 745 4.73 %
Rwork0.1781 --
obs0.1801 15750 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.403→46.408 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2955 0 0 230 3185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023008
X-RAY DIFFRACTIONf_angle_d0.5164052
X-RAY DIFFRACTIONf_dihedral_angle_d2.5481818
X-RAY DIFFRACTIONf_chiral_restr0.046460
X-RAY DIFFRACTIONf_plane_restr0.002512
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4027-2.58820.2491450.19582937X-RAY DIFFRACTION100
2.5882-2.84870.25541300.19752973X-RAY DIFFRACTION100
2.8487-3.26080.20531510.18752969X-RAY DIFFRACTION100
3.2608-4.10790.19681490.16442994X-RAY DIFFRACTION100
4.1079-46.41620.22411700.16813132X-RAY DIFFRACTION100

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