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- PDB-5js1: Human Argonaute2 Bound to an siRNA -

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Basic information

Entry
Database: PDB / ID: 5js1
TitleHuman Argonaute2 Bound to an siRNA
Components
  • Protein argonaute-2
  • siRNA
KeywordsHYDROLASE/RNA / Argonaute / siRNA / RNAi / nuclease / HYDROLASE-RNA complex
Function / homology
Function and homology information


: / endoribonuclease activity, cleaving miRNA-paired mRNA / endoribonuclease activity, cleaving siRNA-paired mRNA / siRNA-mediated gene silencing by mRNA destabilization / miRNA-mediated gene silencing by mRNA destabilization / Post-transcriptional silencing by small RNAs / Competing endogenous RNAs (ceRNAs) regulate PTEN translation / Regulation of CDH11 mRNA translation by microRNAs / Regulation of NPAS4 mRNA translation / Regulation of PTEN mRNA translation ...: / endoribonuclease activity, cleaving miRNA-paired mRNA / endoribonuclease activity, cleaving siRNA-paired mRNA / siRNA-mediated gene silencing by mRNA destabilization / miRNA-mediated gene silencing by mRNA destabilization / Post-transcriptional silencing by small RNAs / Competing endogenous RNAs (ceRNAs) regulate PTEN translation / Regulation of CDH11 mRNA translation by microRNAs / Regulation of NPAS4 mRNA translation / Regulation of PTEN mRNA translation / negative regulation of amyloid precursor protein biosynthetic process / Small interfering RNA (siRNA) biogenesis / positive regulation of trophoblast cell migration / Transcriptional Regulation by MECP2 / RISC-loading complex / miRNA metabolic process / mRNA cap binding / RISC complex assembly / regulatory ncRNA-mediated post-transcriptional gene silencing / miRNA processing / miRNA-mediated gene silencing by inhibition of translation / pre-miRNA processing / RNA 7-methylguanosine cap binding / siRNA processing / siRNA binding / regulation of synapse maturation / mRNA 3'-UTR AU-rich region binding / M-decay: degradation of maternal mRNAs by maternally stored factors / Regulation of MITF-M-dependent genes involved in apoptosis / RISC complex / regulatory ncRNA-mediated gene silencing / TGFBR3 expression / Regulation of RUNX1 Expression and Activity / miRNA binding / P-body assembly / MicroRNA (miRNA) biogenesis / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / RNA polymerase II complex binding / Regulation of MECP2 expression and activity / core promoter sequence-specific DNA binding / Nuclear events stimulated by ALK signaling in cancer / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / translation initiation factor activity / negative regulation of translational initiation / RNA endonuclease activity / positive regulation of translation / post-embryonic development / TP53 Regulates Metabolic Genes / P-body / Transcriptional regulation by small RNAs / MAPK6/MAPK4 signaling / Pre-NOTCH Transcription and Translation / cytoplasmic ribonucleoprotein granule / positive regulation of angiogenesis / double-stranded RNA binding / Ca2+ pathway / Estrogen-dependent gene expression / single-stranded RNA binding / postsynapse / translation / dendrite / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / RNA binding / extracellular exosome / nucleoplasm / metal ion binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Protein argonaute-2 / paz domain / paz domain / Protein argonaute, Mid domain / Mid domain of argonaute / Argonaute linker 2 domain / Protein argonaute, N-terminal / Argonaute-like, PIWI domain / N-terminal domain of argonaute / Argonaute linker 2 domain ...Protein argonaute-2 / paz domain / paz domain / Protein argonaute, Mid domain / Mid domain of argonaute / Argonaute linker 2 domain / Protein argonaute, N-terminal / Argonaute-like, PIWI domain / N-terminal domain of argonaute / Argonaute linker 2 domain / DUF1785 / Argonaute, linker 1 domain / Argonaute linker 1 domain / Piwi domain profile. / Piwi domain / Piwi domain / Piwi / PAZ domain superfamily / PAZ / PAZ domain / PAZ domain profile. / PAZ domain / Response regulator / Ribonuclease H-like superfamily/Ribonuclease H / Beta Complex / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHENOL / RNA / RNA (> 10) / Protein argonaute-2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.499 Å
AuthorsSchirle, N.T. / MacRae, I.J.
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: Structural Analysis of Human Argonaute-2 Bound to a Modified siRNA Guide.
Authors: Schirle, N.T. / Kinberger, G.A. / Murray, H.F. / Lima, W.F. / Prakash, T.P. / MacRae, I.J.
History
DepositionMay 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein argonaute-2
B: siRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,2755
Polymers104,0622
Non-polymers2133
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-30 kcal/mol
Surface area37360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.932, 107.119, 68.198
Angle α, β, γ (deg.)90.00, 106.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein argonaute-2 / hAgo2 / Argonaute RISC catalytic component 2 / Eukaryotic translation initiation factor 2C 2 / ...hAgo2 / Argonaute RISC catalytic component 2 / Eukaryotic translation initiation factor 2C 2 / eIF2C 2 / PAZ Piwi domain protein / PPD / Protein slicer


Mass: 97378.180 Da / Num. of mol.: 1 / Mutation: S387D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGO2, EIF2C2 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9UKV8, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#2: RNA chain siRNA


Mass: 6683.997 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: siRNA / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-IPH / PHENOL


Mass: 94.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6O
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.19 Å3/Da / Density % sol: 43.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 16% PEG 3350, 50mM Phenol, 10% Isopropanol, 5mM Magnesium Chloride, 100mM Tris

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.499→38.83 Å / Num. obs: 29397 / % possible obs: 98.1 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.049 / Rsym value: 0.044 / Net I/σ(I): 17.2
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.438 / Rsym value: 0.39

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ola

4ola


Resolution: 2.499→31.531 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.97
RfactorNum. reflection% reflection
Rfree0.2475 1491 5.08 %
Rwork0.2165 --
obs0.2181 29366 97.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.499→31.531 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6439 209 15 52 6715
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016834
X-RAY DIFFRACTIONf_angle_d1.2889288
X-RAY DIFFRACTIONf_dihedral_angle_d17.232607
X-RAY DIFFRACTIONf_chiral_restr0.0831039
X-RAY DIFFRACTIONf_plane_restr0.0061163
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4994-2.580.35311280.28862471X-RAY DIFFRACTION97
2.58-2.67220.34131410.26842528X-RAY DIFFRACTION98
2.6722-2.77910.30231400.25642518X-RAY DIFFRACTION97
2.7791-2.90550.29091330.25632510X-RAY DIFFRACTION98
2.9055-3.05860.28261370.25522553X-RAY DIFFRACTION99
3.0586-3.250.30431500.24752564X-RAY DIFFRACTION99
3.25-3.50070.27281150.24272508X-RAY DIFFRACTION97
3.5007-3.85240.24841210.22212576X-RAY DIFFRACTION99
3.8524-4.40850.21241480.19332541X-RAY DIFFRACTION98
4.4085-5.54940.21551350.18512556X-RAY DIFFRACTION98
5.5494-31.53360.20611430.18362550X-RAY DIFFRACTION97

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