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

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Basic information

Entry
Database: PDB / ID: 6emg
TitleCrystal structure of Rrp1 from Chaetomium thermophilum in space group P6322
ComponentsG0S4M2
KeywordsRIBOSOME / Ribosome biogenesis / translation
Function / homologyRibosomal RNA processing protein 1-like / Nucleolar protein,Nop52 / preribosome, small subunit precursor / rRNA processing / nucleus / PHOSPHATE ION / Ribosomal RNA-processing protein 1
Function and homology information
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.24 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 1.3May 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

Downloads & links

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Assembly

Deposited unit
A: G0S4M2
B: G0S4M2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,25614
Polymers66,2032
Non-polymers1,05312
Water3,405189
1
A: G0S4M2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,96411
Polymers33,1021
Non-polymers86310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: G0S4M2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2923
Polymers33,1021
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)214.259, 214.259, 124.785
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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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-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 6.24 Å3/Da / Density % sol: 80.3 % / Description: hexagonal
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.8M K-H2PO4 0.8M Na-H2PO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.99188 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99188 Å / Relative weight: 1
ReflectionResolution: 2.24→49.222 Å / Num. obs: 80956 / % possible obs: 99.96 % / Redundancy: 20.2 % / Biso Wilson estimate: 47.48 Å2 / Net I/σ(I): 24.62

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
SHELXDEphasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.24→49.222 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.04 / Phase error: 19.79
RfactorNum. reflection% reflection
Rfree0.2069 3988 4.93 %
Rwork0.1873 --
obs0.1882 80940 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 220.2 Å2 / Biso mean: 69.141 Å2 / Biso min: 29.64 Å2
Refinement stepCycle: final / Resolution: 2.24→49.222 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3694 0 63 189 3946
Biso mean--89.12 65.34 -
Num. residues----458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033838
X-RAY DIFFRACTIONf_angle_d0.6435177
X-RAY DIFFRACTIONf_chiral_restr0.039578
X-RAY DIFFRACTIONf_plane_restr0.004640
X-RAY DIFFRACTIONf_dihedral_angle_d8.3743213
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.24-2.26730.27181260.258127402866
2.2673-2.2960.24471260.253727132839
2.296-2.32630.28181610.244726632824
2.3263-2.35810.27311330.23127452878
2.3581-2.39180.21681430.224126852828
2.3918-2.42750.21261490.22527022851
2.4275-2.46540.27511350.213927312866
2.4654-2.50590.23751570.205626892846
2.5059-2.54910.22731360.205727252861
2.5491-2.59540.23621220.200227252847
2.5954-2.64530.22281410.18727362877
2.6453-2.69930.19181500.194827082858
2.6993-2.7580.22751490.198827162865
2.758-2.82220.19981340.190227292863
2.8222-2.89270.23061390.196927282867
2.8927-2.97090.22441370.204727362873
2.9709-3.05830.20071590.201627342893
3.0583-3.1570.2271610.194827052866
3.157-3.26990.24251220.188327532875
3.2699-3.40080.21061510.194627582909
3.4008-3.55550.20561390.184227432882
3.5555-3.74290.18431520.175927502902
3.7429-3.97730.1831390.160127732912
3.9773-4.28420.17421320.154927962928
4.2842-4.7150.15511400.15427912931
4.715-5.39660.17751480.164828232971
5.3966-6.79630.20841460.20528422988
6.7963-49.23340.2431610.203730133174
Refinement TLS params.Method: refined / Origin x: 62.8368 Å / Origin y: 71.1197 Å / Origin z: 18.2993 Å
111213212223313233
T0.3706 Å20.1441 Å2-0.0395 Å2-0.3808 Å2-0.0564 Å2--0.323 Å2
L0.3923 °20.0115 °20.1499 °2-1.6624 °2-0.646 °2--1.0692 °2
S0.019 Å °0.1135 Å °0.0108 Å °-0.2278 Å °-0.031 Å °0.1787 Å °0.3252 Å °0.0829 Å °0.001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA5 - 258
2X-RAY DIFFRACTION1allB7 - 259
3X-RAY DIFFRACTION1allC1 - 4
4X-RAY DIFFRACTION1allD1 - 7
5X-RAY DIFFRACTION1allE1
6X-RAY DIFFRACTION1allS1 - 189

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