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- PDB-5wwo: Crystal structure of Enp1 -

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Basic information

Entry
Database: PDB / ID: 5wwo
TitleCrystal structure of Enp1
Components
  • Essential nuclear protein 1
  • Protein LTV1
KeywordsRNA BINDING PROTEIN / component of 90S preribosome
Function / homology
Function and homology information


Ragulator complex / ATP export / endocytic recycling / poly(A)+ mRNA export from nucleus / response to osmotic stress / preribosome, small subunit precursor / snoRNA binding / Major pathway of rRNA processing in the nucleolus and cytosol / 90S preribosome / ribosomal small subunit export from nucleus ...Ragulator complex / ATP export / endocytic recycling / poly(A)+ mRNA export from nucleus / response to osmotic stress / preribosome, small subunit precursor / snoRNA binding / Major pathway of rRNA processing in the nucleolus and cytosol / 90S preribosome / ribosomal small subunit export from nucleus / 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 / ribosomal small subunit biogenesis / rRNA processing / protein transport / late endosome / late endosome membrane / cellular response to oxidative stress / nucleolus / nucleus / cytosol / cytoplasm
Similarity search - Function
Low temperature viability protein Ltv1 / Low temperature viability protein / Bystin / Bystin
Similarity search - Domain/homology
Protein LTV1 / Essential nuclear protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.4 Å
AuthorsYe, K. / Zhang, W.
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 3, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 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

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Assembly

Deposited unit
A: Essential nuclear protein 1
B: Essential nuclear protein 1
C: Protein LTV1


Theoretical massNumber of molelcules
Total (without water)98,2553
Polymers98,2553
Non-polymers00
Water1,38777
1
A: Essential nuclear protein 1
C: Protein LTV1


Theoretical massNumber of molelcules
Total (without water)56,7302
Polymers56,7302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-20 kcal/mol
Surface area14820 Å2
MethodPISA
2
B: Essential nuclear protein 1


Theoretical massNumber of molelcules
Total (without water)41,5251
Polymers41,5251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.220, 98.607, 109.728
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 Essential nuclear protein 1


Mass: 41524.859 Da / Num. of mol.: 2 / Fragment: UNP residues 121-483
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: ENP1, MEG1, YBR247C, YBR1635 / Production host: Escherichia coli (E. coli) / References: UniProt: P38333
#2: Protein Protein LTV1 / Low-temperature viability protein 1


Mass: 15205.630 Da / Num. of mol.: 1 / Fragment: UNP residues 333-463
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: LTV1, YKL143W, YKL2 / Production host: Escherichia coli (E. coli) / References: UniProt: P34078
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 1.91 Å3/Da / Density % sol: 35.45 % / Mosaicity: 0.658 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 7.2% PEG3350, 12% (v/v) Tacsimate pH 6.0, 8% (v/v) Tacsimate pH 8.0

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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: Feb 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 29903 / % possible obs: 99.7 % / Redundancy: 6.9 % / Biso Wilson estimate: 37.6 Å2 / Rmerge(I) obs: 0.111 / Χ2: 1.839 / Net I/av σ(I): 28.121 / Net I/σ(I): 11.4 / Num. measured all: 205522
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.4-2.446.70.57714301.13100
2.44-2.4970.5414741.174100
2.49-2.537.10.47514851.189100
2.53-2.5970.59214921.615100
2.59-2.646.80.49214762.854100
2.64-2.77.10.34314711.476100
2.7-2.777.10.30514901.308100
2.77-2.857.10.25214581.41499.9
2.85-2.937.10.20814871.465100
2.93-3.027.10.18414951.543100
3.02-3.137.10.15714841.577100
3.13-3.2670.13514921.65399.9
3.26-3.4170.11414861.736100
3.41-3.5870.10314862.064100
3.58-3.816.80.09415072.55699.9
3.81-4.16.70.08615232.76599.9
4.1-4.526.60.08115062.96999.9
4.52-5.176.60.07115292.456100
5.17-6.516.50.06315572.01100
6.51-506.30.04515751.96995.5

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Phasing

PhasingMethod: SIRAS

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: SIRAS / Resolution: 2.4→19.751 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 0.08 / Phase error: 21.41
RfactorNum. reflection% reflection
Rfree0.2297 1476 5.09 %
Rwork0.1673 --
obs0.1704 28977 96.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 104.2 Å2 / Biso mean: 42.6794 Å2 / Biso min: 19.51 Å2
Refinement stepCycle: final / Resolution: 2.4→19.751 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4603 0 0 77 4680
Biso mean---38.96 -
Num. residues----561
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094718
X-RAY DIFFRACTIONf_angle_d1.1116397
X-RAY DIFFRACTIONf_chiral_restr0.045712
X-RAY DIFFRACTIONf_plane_restr0.006808
X-RAY DIFFRACTIONf_dihedral_angle_d15.9221750
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4001-2.47740.26611170.21342261237889
2.4774-2.56580.25591280.20522375250393
2.5658-2.66830.27911240.19542333245791
2.6683-2.78940.24111260.18652444257096
2.7894-2.9360.24081520.18392482263497
2.936-3.11930.29521260.18622520264698
3.1193-3.35910.25321380.19042549268799
3.3591-3.69510.22861320.17572596272899
3.6951-4.22530.23241410.152525792720100
4.2253-5.30630.21131410.145826372778100
5.3063-19.75180.18031510.142927252876100

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