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- PDB-4oog: Crystal structure of yeast RNase III (Rnt1p) complexed with the p... -

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Basic information

Entry
Database: PDB / ID: 4oog
TitleCrystal structure of yeast RNase III (Rnt1p) complexed with the product of dsRNA processing
Components
  • (Ribonuclease 3) x 2
  • 34-mer RNA
KeywordsHYDROLASE/RNA / RNase:RNA complex / ribonuclease III domain / double-stranded RNA-binding domain / endoribonuclease / dsRNA-specific RNase / double-stranded RNA / 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 / apoptotic DNA fragmentation / deoxyribonuclease I activity ...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 / apoptotic DNA fragmentation / deoxyribonuclease I activity / ribonuclease III activity / pre-miRNA processing / siRNA processing / RISC complex / termination of RNA polymerase II transcription / rRNA transcription / rRNA processing / double-stranded RNA binding / chromatin organization / nucleolus / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Ribonuclease III, N-terminal domain / Rnt1/Pac1, double-stranded RNA binding domain, fungi / Ribonuclease III N-terminal domain / Ribonuclease III domain / Ribonuclease iii, N-terminal Endonuclease Domain; Chain A / Ribonuclease III family signature. / Ribonuclease III domain / Ribonuclease III family domain profile. / Ribonuclease III family / Ribonuclease III domain ...Ribonuclease III, N-terminal domain / Rnt1/Pac1, double-stranded RNA binding domain, fungi / Ribonuclease III N-terminal domain / Ribonuclease III domain / Ribonuclease iii, N-terminal Endonuclease Domain; Chain A / Ribonuclease III family signature. / Ribonuclease III domain / Ribonuclease III family domain profile. / Ribonuclease III family / Ribonuclease III domain / Double Stranded RNA Binding Domain - #20 / 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 / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
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: 2.5 Å
AuthorsLiang, Y.-H. / Ji, X.
CitationJournal: 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
DepositionFeb 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1May 28, 2014Group: Database references
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 20, 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: 34-mer RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5498
Polymers66,4524
Non-polymers974
Water1,76598
1
A: Ribonuclease 3
B: Ribonuclease 3
C: Ribonuclease 3
D: 34-mer RNA
hetero molecules

A: Ribonuclease 3
B: Ribonuclease 3
C: Ribonuclease 3
D: 34-mer RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,09916
Polymers132,9048
Non-polymers1948
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area31080 Å2
ΔGint-325 kcal/mol
Surface area51400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.972, 183.804, 61.289
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 12804.515 Da / Num. of mol.: 2 / Fragment: N-terminal domain (UNP residues 42-151)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: RNT1, YM9408.01C, YM9959.21, YMR239C / Plasmid: pQE31 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q02555
#2: Protein Ribonuclease 3 / Ribonuclease III / RNase III


Mass: 29934.600 Da / Num. of mol.: 1
Fragment: endonuclease domain and double-stranded RNA binding domain (UNP residues 197-457)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: RNT1, YM9408.01C, YM9959.21, YMR239C / Plasmid: pQE31 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q02555, ribonuclease III
#3: RNA chain 34-mer RNA


Mass: 10908.486 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Derived from U5 snRNA 3' end cleavage product
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 3.35 Å3/Da / Density % sol: 63.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% PEG1000, 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 2, 2011 / Details: mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. obs: 31418 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 50.22 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 14.45
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
2.5-2.654.30.7841.82207634870487097.5
2.65-2.834.90.453.41227564673467399.7
2.83-3.0650.2016.29217214382438299.9
3.06-3.354.90.10811.16198694039403999.9
3.35-3.744.70.08214.8165433536353695.8
3.74-4.314.70.05123.41150733191319197.5
4.31-5.274.70.03731.34132682795279599.9
5.27-7.384.70.03435.27102342195219599.9
7.38-404.30.02544.1257361329132998.2

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3RV0, 3RV1, 1YYW, 2NUG, 1O0W, 3N3W, 3O2R, 3C4T, AND 1T4O

3rv0

3rv1

1yyw

2nug

1o0w

3n3w

3o2r

3c4t

1t4o


Resolution: 2.5→39.719 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 33.23 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2394 1015 3.26 %RANDOM
Rwork0.216 ---
obs0.2168 31130 99.16 %-
all-31130 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.64 Å2 / ksol: 0.338 e/Å3
Displacement parametersBiso max: 193.34 Å2 / Biso mean: 78.4156 Å2 / Biso min: 32.74 Å2
Baniso -1Baniso -2Baniso -3
1--20.7225 Å2-0 Å20 Å2
2--42.6053 Å20 Å2
3----21.8827 Å2
Refinement stepCycle: LAST / Resolution: 2.5→39.719 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3897 725 4 98 4724
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014826
X-RAY DIFFRACTIONf_angle_d0.7776655
X-RAY DIFFRACTIONf_chiral_restr0.059786
X-RAY DIFFRACTIONf_plane_restr0.003726
X-RAY DIFFRACTIONf_dihedral_angle_d14.2751974
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.5-2.63160.40781350.410241664301430197
2.6316-2.79640.35481560.3417424243984398100
2.7964-3.01230.39231130.2683433244454445100
3.0123-3.31530.2781580.2135428544434443100
3.3153-3.79470.25241370.219342664403440398
3.7947-4.77960.22651560.169643124468446899
4.7796-39.72360.16751600.1794451246724672100

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