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- PDB-6emf: Crystal structure of Rrp1 from Chaetomium thermophilum in space g... -

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Basic information

Entry
Database: PDB / ID: 6emf
TitleCrystal structure of Rrp1 from Chaetomium thermophilum in space group C2
ComponentsG0S4M2
KeywordsRIBOSOME / Ribosome biogenesis / translation
Function / homologyRibosomal RNA processing protein 1-like / Nucleolar protein,Nop52 / preribosome, small subunit precursor / rRNA processing / nucleus / PROLINE / Ribosomal RNA-processing protein 1
Function and homology information
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 Å
AuthorsAhmed, Y.L. / Sinning, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation Germany
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 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Nov 13, 2019Group: Data collection / Database references / Category: pdbx_database_related / Item: _pdbx_database_related.content_type
Revision 1.4May 8, 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: G0S4M2
B: G0S4M2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,86811
Polymers66,2032
Non-polymers6659
Water2,108117
1
A: G0S4M2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4126
Polymers33,1021
Non-polymers3105
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: G0S4M2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4565
Polymers33,1021
Non-polymers3544
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.720, 74.675, 68.795
Angle α, β, γ (deg.)90.000, 90.530, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein G0S4M2


Mass: 33101.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0031510 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta 2 / References: UniProt: G0S4M2
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.56 Å3/Da / Density % sol: 51.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 200 mM Proline 100 mM HEPES pH 7.5 10% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→47.791 Å / Num. obs: 19400 / % possible obs: 99.24 % / Redundancy: 11.3 % / Biso Wilson estimate: 32.56 Å2 / Net I/σ(I): 6.88

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→47.791 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.59 / Phase error: 25.67
RfactorNum. reflection% reflection
Rfree0.2318 988 5.1 %
Rwork0.1987 --
obs0.2004 19376 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 136.09 Å2 / Biso mean: 40.4765 Å2 / Biso min: 6.99 Å2
Refinement stepCycle: final / Resolution: 2.65→47.791 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3711 0 44 117 3872
Biso mean--61.96 39.62 -
Num. residues----461
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023840
X-RAY DIFFRACTIONf_angle_d0.4955179
X-RAY DIFFRACTIONf_chiral_restr0.035585
X-RAY DIFFRACTIONf_plane_restr0.003644
X-RAY DIFFRACTIONf_dihedral_angle_d8.8322770
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6501-2.78980.30211410.24912499264096
2.7898-2.96460.27911350.24726342769100
2.9646-3.19350.30541300.23042635276599
3.1935-3.51470.24961470.197926292776100
3.5147-4.02310.20481480.180326342782100
4.0231-5.06780.18921480.164526592807100
5.0678-47.79920.21151390.197526982837100
Refinement TLS params.Method: refined / Origin x: -37.4124 Å / Origin y: 1.8168 Å / Origin z: 34.3928 Å
111213212223313233
T0.0825 Å20.0149 Å20.0138 Å2-0.0702 Å20.0026 Å2--0.0839 Å2
L0.168 °20.008 °20.3736 °2-0.5174 °2-0.1022 °2--0.9239 °2
S0.0008 Å °-0.0031 Å °-0.0303 Å °0.0069 Å °-0.0273 Å °-0.0155 Å °-0.0283 Å °0.0163 Å °-0.0027 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA6 - 259
2X-RAY DIFFRACTION1allB6 - 258
3X-RAY DIFFRACTION1allD1 - 9
4X-RAY DIFFRACTION1allF1 - 7
5X-RAY DIFFRACTION1allS1 - 117

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