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- PDB-5the: Crystal structure of the C-terminal lobe of a budding yeast Argonaute -

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Basic information

Entry
Database: PDB / ID: 5the
TitleCrystal structure of the C-terminal lobe of a budding yeast Argonaute
Components
  • RNA (5'-R(P*UP*AP*AP*AP*AP*AP*AP*A)-3')
  • Uncharacterized protein
KeywordsRNA BINDING PROTEIN/RNA / RNA-binding protein / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


Argonaute, N domain / Argonaute, N-terminal / Argonaute N domain / Fungal Argonaute N-terminal domain / Piwi domain / Piwi domain profile. / Piwi domain / Piwi / PAZ domain superfamily / PAZ domain ...Argonaute, N domain / Argonaute, N-terminal / Argonaute N domain / Fungal Argonaute N-terminal domain / Piwi domain / Piwi domain profile. / Piwi domain / Piwi / PAZ domain superfamily / PAZ domain / PAZ domain profile. / PAZ domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
RNA / Piwi domain-containing protein
Similarity search - Component
Biological speciesVanderwaltozyma polyspora (fungus)
Escherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.097 Å
AuthorsDayeh, D.M. / Nakanishi, K.
Funding support United States, 1items
OrganizationGrant numberCountry
The Ohio State University Center for RNA Biology Seed Grant United States
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural and functional analyses reveal the contributions of the C- and N-lobes of Argonaute protein to selectivity of RNA target cleavage.
Authors: Dayeh, D.M. / Kruithoff, B.C. / Nakanishi, K.
History
DepositionSep 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 9, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Uncharacterized protein
B: RNA (5'-R(P*UP*AP*AP*AP*AP*AP*AP*A)-3')
C: Uncharacterized protein
D: RNA (5'-R(P*UP*AP*AP*AP*AP*AP*AP*A)-3')
E: Uncharacterized protein
F: RNA (5'-R(P*UP*AP*AP*AP*AP*AP*AP*A)-3')
G: Uncharacterized protein
H: RNA (5'-R(P*UP*AP*AP*AP*AP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)254,4758
Polymers254,4758
Non-polymers00
Water25,6351423
1
A: Uncharacterized protein
B: RNA (5'-R(P*UP*AP*AP*AP*AP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)63,6192
Polymers63,6192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-23 kcal/mol
Surface area21060 Å2
MethodPISA
2
C: Uncharacterized protein
D: RNA (5'-R(P*UP*AP*AP*AP*AP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)63,6192
Polymers63,6192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-22 kcal/mol
Surface area21020 Å2
MethodPISA
3
E: Uncharacterized protein
F: RNA (5'-R(P*UP*AP*AP*AP*AP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)63,6192
Polymers63,6192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-23 kcal/mol
Surface area21250 Å2
MethodPISA
4
G: Uncharacterized protein
H: RNA (5'-R(P*UP*AP*AP*AP*AP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)63,6192
Polymers63,6192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-23 kcal/mol
Surface area21200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.609, 85.565, 127.864
Angle α, β, γ (deg.)90.00, 89.81, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11E-1610-

HOH

21G-1599-

HOH

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Components

#1: Protein
Uncharacterized protein


Mass: 61053.172 Da / Num. of mol.: 4 / Fragment: residues 728-1251
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vanderwaltozyma polyspora (fungus) / Strain: ATCC 22028 / DSM 70294 / Gene: Kpol_520p25 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A7TMA9
#2: RNA chain
RNA (5'-R(P*UP*AP*AP*AP*AP*AP*AP*A)-3')


Mass: 2565.649 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1423 / 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: 2.57 Å3/Da / Density % sol: 52.16 %
Crystal growTemperature: 293 K / Method: evaporation / Details: Sodium citrate 100 mM, pH 5.5 PEG4000 18% / PH range: 5.5

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.097→49.02 Å / Num. obs: 150631 / % possible obs: 99.9 % / Redundancy: 3.8 % / Net I/σ(I): 27.19
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 4.18

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Processing

Software
NameVersionClassification
PHENIX(1.10.1-2155)refinement
Cootmodel building
HKL-2000data scaling
MOLREPphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F1N

4f1n


Resolution: 2.097→47.125 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.97
RfactorNum. reflection% reflection
Rfree0.2058 2003 1.33 %
Rwork0.1576 --
obs0.1582 150594 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.097→47.125 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16180 628 0 1423 18231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00817218
X-RAY DIFFRACTIONf_angle_d0.91423438
X-RAY DIFFRACTIONf_dihedral_angle_d13.41210344
X-RAY DIFFRACTIONf_chiral_restr0.0632629
X-RAY DIFFRACTIONf_plane_restr0.0052921
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.097-2.14940.25111400.19299980X-RAY DIFFRACTION95
2.1494-2.20750.21971260.183510624X-RAY DIFFRACTION100
2.2075-2.27250.2371440.178310551X-RAY DIFFRACTION100
2.2725-2.34580.25351490.183610593X-RAY DIFFRACTION100
2.3458-2.42970.23041410.183210616X-RAY DIFFRACTION100
2.4297-2.52690.26671420.180210621X-RAY DIFFRACTION100
2.5269-2.64190.25661410.172110608X-RAY DIFFRACTION100
2.6419-2.78120.21841400.172610698X-RAY DIFFRACTION100
2.7812-2.95540.241500.160610626X-RAY DIFFRACTION100
2.9554-3.18360.20111460.155210654X-RAY DIFFRACTION100
3.1836-3.50390.18091440.153910671X-RAY DIFFRACTION100
3.5039-4.01070.15611430.139510699X-RAY DIFFRACTION100
4.0107-5.05210.18421440.129610738X-RAY DIFFRACTION100
5.0521-47.13660.20221530.158510912X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -64.1584 Å / Origin y: 97.4847 Å / Origin z: 287.6705 Å
111213212223313233
T0.1945 Å2-0.003 Å2-0.0075 Å2-0.183 Å20.0076 Å2--0.1595 Å2
L0.0914 °2-0.0057 °2-0.0041 °2-0.0751 °20.0127 °2--0.0355 °2
S0.0124 Å °-0.0075 Å °0.0056 Å °0.0078 Å °-0.0133 Å °0.0112 Å °0.0074 Å °0.0028 Å °0.0003 Å °
Refinement TLS groupSelection details: all

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