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- PDB-7y16: Crystal structure of rRNA-processing protein Las1 -

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Basic information

Entry
Database: PDB / ID: 7y16
TitleCrystal structure of rRNA-processing protein Las1
ComponentsLAS1 protein
KeywordsRNA BINDING PROTEIN / RNA processing / Nuclease
Function / homologyLas1 / Las1-like / Las1 complex / maturation of 5.8S rRNA / preribosome, large subunit precursor / maturation of LSU-rRNA / endonuclease activity / LAS1 protein
Function and homology information
Biological speciesCyberlindnera jadinii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChen, J. / Liu, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171286 China
CitationJournal: Elife / Year: 2024
Title: Structural and mechanistic insights into ribosomal ITS2 RNA processing by nuclease-kinase machinery.
Authors: Jiyun Chen / Hong Chen / Shanshan Li / Xiaofeng Lin / Rong Hu / Kaiming Zhang / Liang Liu /
Abstract: Precursor ribosomal RNA (pre-rRNA) processing is a key step in ribosome biosynthesis and involves numerous RNases. A HEPN (higher eukaryote and prokaryote nucleotide binding) nuclease Las1 and a ...Precursor ribosomal RNA (pre-rRNA) processing is a key step in ribosome biosynthesis and involves numerous RNases. A HEPN (higher eukaryote and prokaryote nucleotide binding) nuclease Las1 and a polynucleotide kinase Grc3 assemble into a tetramerase responsible for rRNA maturation. Here, we report the structures of full-length and Las1-Grc3 complexes, and Las1. The Las1-Grc3 structures show that the central coiled-coil domain of Las1 facilitates pre-rRNA binding and cleavage, while the Grc3 C-terminal loop motif directly binds to the HEPN active center of Las1 and regulates pre-rRNA cleavage. Structural comparison between Las1 and Las1-Grc3 complex exhibits that Grc3 binding induces conformational rearrangements of catalytic residues associated with HEPN nuclease activation. Biochemical assays identify that Las1 processes pre-rRNA at the two specific sites (C2 and C2'), which greatly facilitates rRNA maturation. Our structures and specific pre-rRNA cleavage findings provide crucial insights into the mechanism and pathway of pre-rRNA processing in ribosome biosynthesis.
History
DepositionJun 7, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Jan 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LAS1 protein
B: LAS1 protein
C: LAS1 protein


Theoretical massNumber of molelcules
Total (without water)54,7833
Polymers54,7833
Non-polymers00
Water3,819212
1
A: LAS1 protein
B: LAS1 protein


Theoretical massNumber of molelcules
Total (without water)36,5222
Polymers36,5222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-11 kcal/mol
Surface area15150 Å2
MethodPISA
2
C: LAS1 protein


Theoretical massNumber of molelcules
Total (without water)18,2611
Polymers18,2611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.495, 58.975, 158.688
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein LAS1 protein


Mass: 18260.857 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyberlindnera jadinii (fungus)
Strain: ATCC 18201 / CBS 1600 / BCRC 20928 / JCM 3617 / NBRC 0987 / NRRL Y-1542
Gene: LAS1, BN1211_1791 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A0H5CBH3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.2 Å3/Da / Density % sol: 44.07 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-HCl, pH 8.0, 0.2 M MgCl2, and 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 44296 / % possible obs: 97.7 % / Redundancy: 10.1 % / Biso Wilson estimate: 18.13 Å2 / Rpim(I) all: 0.033 / Net I/σ(I): 22
Reflection shellResolution: 1.8→1.83 Å / Num. unique obs: 2147 / Rpim(I) all: 0.305

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Processing

Software
NameVersionClassification
HKL-30007.21data scaling
PHENIX1.17.1_3660refinement
HKL-30007.21data reduction
Coot0.7.2.1model building
PHENIX1.17.1_3660phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OF4

6of4


Resolution: 1.8→48.98 Å / SU ML: 0.189 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 21.9489
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2334 2164 4.89 %
Rwork0.212 42132 -
obs0.213 44296 97.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.6 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3657 0 0 212 3869
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153741
X-RAY DIFFRACTIONf_angle_d1.49965070
X-RAY DIFFRACTIONf_chiral_restr0.439573
X-RAY DIFFRACTIONf_plane_restr0.0067639
X-RAY DIFFRACTIONf_dihedral_angle_d28.62921354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.29621390.2692509X-RAY DIFFRACTION87.77
1.84-1.890.30551450.25032657X-RAY DIFFRACTION94.92
1.89-1.940.29281440.24732743X-RAY DIFFRACTION96.33
1.94-20.24091570.22622762X-RAY DIFFRACTION96.91
2-2.060.2531250.21512777X-RAY DIFFRACTION95.55
2.06-2.140.23131560.20982746X-RAY DIFFRACTION97.55
2.14-2.220.23791540.20722800X-RAY DIFFRACTION97.88
2.22-2.320.21951320.20162836X-RAY DIFFRACTION98.28
2.32-2.440.28081580.21142828X-RAY DIFFRACTION98.39
2.44-2.60.26751380.21112810X-RAY DIFFRACTION97.49
2.6-2.80.22631460.21022879X-RAY DIFFRACTION98.92
2.8-3.080.23611450.21452870X-RAY DIFFRACTION99.28
3.08-3.520.24441410.21082885X-RAY DIFFRACTION97.83
3.52-4.440.16981530.18852938X-RAY DIFFRACTION99.58
4.44-48.980.22491310.21553092X-RAY DIFFRACTION98.23

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