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- PDB-5t16: Crystal structure of yeast RNase III (Rnt1p) complexed with a non... -

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Basic information

Entry
Database: PDB / ID: 5t16
TitleCrystal structure of yeast RNase III (Rnt1p) complexed with a non-hydrolyzable RNA substrate analog
Components
  • (Ribonuclease 3) x 2
  • RNA substrate analog
Keywordshydrolase/rna / Rnt1p / RNase III / substrate-loaded complex / hydrolase-rna complex
Function / homology
Function and homology information


box C/D sno(s)RNA processing / box H/ACA sno(s)RNA processing / regulation of fungal-type cell wall organization / termination of RNA polymerase II transcription, exosome-dependent / U1 snRNA 3'-end processing / U5 snRNA 3'-end processing / U4 snRNA 3'-end processing / ribonuclease III / ribonuclease III activity / termination of RNA polymerase II transcription ...box C/D sno(s)RNA processing / box H/ACA sno(s)RNA processing / regulation of fungal-type cell wall organization / termination of RNA polymerase II transcription, exosome-dependent / U1 snRNA 3'-end processing / U5 snRNA 3'-end processing / U4 snRNA 3'-end processing / ribonuclease III / ribonuclease III activity / termination of RNA polymerase II transcription / rRNA transcription / rRNA processing / double-stranded RNA binding / chromatin organization / nucleolus / nucleoplasm / nucleus
Similarity search - Function
Ribonuclease III, N-terminal domain / Rnt1/Pac1, double-stranded RNA binding domain, fungi / Ribonuclease III N-terminal domain / Ribonuclease III family signature. / Ribonuclease III domain / Ribonuclease III family domain profile. / Ribonuclease III family / Ribonuclease III domain / Double-stranded RNA binding motif / Double-stranded RNA binding motif ...Ribonuclease III, N-terminal domain / Rnt1/Pac1, double-stranded RNA binding domain, fungi / Ribonuclease III N-terminal domain / Ribonuclease III family signature. / Ribonuclease III domain / Ribonuclease III family domain profile. / Ribonuclease III family / Ribonuclease III domain / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Ribonuclease III, endonuclease domain superfamily / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain
Similarity search - Domain/homology
RNA / RNA (> 10) / Ribonuclease 3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.783 Å
AuthorsSong, H. / Ji, X.
Citation
Journal: Structure / Year: 2017
Title: The Functional Cycle of Rnt1p: Five Consecutive Steps of Double-Stranded RNA Processing by a Eukaryotic RNase III.
Authors: Song, H. / Fang, X. / Jin, L. / Shaw, G.X. / Wang, Y.X. / Ji, X.
#1: Journal: Mol. Cell / Year: 2014
Title: Structure of a eukaryotic RNase III postcleavage complex reveals a double-ruler mechanism for substrate selection.
Authors: Liang, Y.H. / Lavoie, M. / Comeau, M.A. / Abou Elela, S. / Ji, X.
History
DepositionAug 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2017Group: Database references
Revision 1.2Aug 30, 2023Group: Data collection / Database references / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / database_2
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 4, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease 3
B: Ribonuclease 3
C: Ribonuclease 3
D: Ribonuclease 3
E: Ribonuclease 3
F: Ribonuclease 3
G: RNA substrate analog
H: RNA substrate analog
I: Ribonuclease 3
J: Ribonuclease 3
K: Ribonuclease 3
L: Ribonuclease 3
M: Ribonuclease 3
N: Ribonuclease 3
O: RNA substrate analog
P: RNA substrate analog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)282,11626
Polymers281,49516
Non-polymers62110
Water6,449358
1
A: Ribonuclease 3
B: Ribonuclease 3
C: Ribonuclease 3
D: Ribonuclease 3
E: Ribonuclease 3
F: Ribonuclease 3
G: RNA substrate analog
H: RNA substrate analog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,99612
Polymers140,7478
Non-polymers2484
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29690 Å2
ΔGint-217 kcal/mol
Surface area58550 Å2
MethodPISA
2
I: Ribonuclease 3
J: Ribonuclease 3
K: Ribonuclease 3
L: Ribonuclease 3
M: Ribonuclease 3
N: Ribonuclease 3
O: RNA substrate analog
P: RNA substrate analog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,12014
Polymers140,7478
Non-polymers3726
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30490 Å2
ΔGint-206 kcal/mol
Surface area58710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.037, 164.065, 176.855
Angle α, β, γ (deg.)90.00, 96.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ribonuclease 3 / Ribonuclease III / RNase III


Mass: 31481.312 Da / Num. of mol.: 4 / Fragment: unp residues 184-499
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RNT1, YMR239C, YM9408.01C, YM9959.21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q02555, ribonuclease III
#2: Protein
Ribonuclease 3 / Ribonuclease III / RNase III


Mass: 13975.908 Da / Num. of mol.: 8 / Fragment: unp residues 41-199
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: RNT1, YMR239C, YM9408.01C, YM9959.21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q02555, ribonuclease III
#3: RNA chain
RNA substrate analog


Mass: 10940.617 Da / Num. of mol.: 4 / Source method: obtained synthetically
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 3.19 Å3/Da / Density % sol: 61.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2 M di ammonium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 6, 2015
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.78→38.99 Å / Num. obs: 86174 / % possible obs: 99.3 % / Redundancy: 4.5 % / Net I/σ(I): 6.79
Reflection shellResolution: 2.78→2.9 Å / Redundancy: 3.8 % / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX(dev_2376: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OOG

4oog


Resolution: 2.783→38.985 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.92
RfactorNum. reflection% reflection
Rfree0.2653 995 1.15 %
Rwork0.2259 --
obs0.2263 86174 98.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.783→38.985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16286 2884 40 358 19568
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7828-2.92950.44641260.379211044X-RAY DIFFRACTION89
2.9295-3.1130.39721520.34412201X-RAY DIFFRACTION99
3.113-3.35320.31771370.287912311X-RAY DIFFRACTION100
3.3532-3.69040.30711480.24812354X-RAY DIFFRACTION100
3.6904-4.22390.24621380.201912412X-RAY DIFFRACTION100
4.2239-5.31950.25351470.18712415X-RAY DIFFRACTION100
5.3195-38.98910.18431470.178412442X-RAY DIFFRACTION99

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