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- PDB-4w5n: The Crystal Structure of Human Argonaute2 Bound to a Defined Guide RNA -

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Basic information

Entry
Database: PDB / ID: 4w5n
TitleThe Crystal Structure of Human Argonaute2 Bound to a Defined Guide RNA
Components
  • Protein argonaute-2
  • RNA (5'-R(P*UP*UP*CP*AP*CP*AP*UP*UP*CP*AP*AP*GP*UP*CP*UP*CP*UP*U)-3')
KeywordsHYDROLASE/RNA / AGO2 / RNase / RNAi / RNA / 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 / TGFBR3 expression / regulatory ncRNA-mediated gene silencing / 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: 2.9 Å
AuthorsSchirle, N.T. / Sheu-Gruttadauria, J. / MacRae, I.J.
CitationJournal: Science / Year: 2014
Title: Gene regulation. Structural basis for microRNA targeting.
Authors: Schirle, N.T. / Sheu-Gruttadauria, J. / MacRae, I.J.
History
DepositionAug 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_validate_symm_contact / software / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_atom_id_1 / _pdbx_validate_symm_contact.auth_atom_id_2 / _pdbx_validate_symm_contact.auth_comp_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2 / _software.classification / _struct_keywords.text
Revision 1.2Sep 27, 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 / refine_hist
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: Protein argonaute-2
B: RNA (5'-R(P*UP*UP*CP*AP*CP*AP*UP*UP*CP*AP*AP*GP*UP*CP*UP*CP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,2336
Polymers103,9262
Non-polymers3074
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-43 kcal/mol
Surface area38650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.117, 108.870, 68.071
Angle α, β, γ (deg.)90.00, 106.93, 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 / Details (production host): baculovirus / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9UKV8, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#2: RNA chain RNA (5'-R(P*UP*UP*CP*AP*CP*AP*UP*UP*CP*AP*AP*GP*UP*CP*UP*CP*UP*U)-3')


Mass: 6547.876 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-IPH / PHENOL


Mass: 94.111 Da / Num. of mol.: 3 / 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.: 34 / 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: 2.15 Å3/Da / Density % sol: 42.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: PEG, Tris, Isopropanol, Phenol, Magnesium

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.9→38.98 Å / Num. obs: 19381 / % possible obs: 98.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.6
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.6 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OLA

4ola


Resolution: 2.9→38.98 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / Phase error: 27.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2533 970 5.01 %copy from 4OLA
Rwork0.2173 ---
obs0.2192 19358 98.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→38.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6461 355 22 34 6872
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017025
X-RAY DIFFRACTIONf_angle_d1.0359574
X-RAY DIFFRACTIONf_dihedral_angle_d14.3662701
X-RAY DIFFRACTIONf_chiral_restr0.0671074
X-RAY DIFFRACTIONf_plane_restr0.0051176
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.0520.37331280.3072618X-RAY DIFFRACTION99
3.052-3.24310.32781540.27362600X-RAY DIFFRACTION99
3.2431-3.49330.30891240.26032612X-RAY DIFFRACTION97
3.4933-3.84460.27291230.22142631X-RAY DIFFRACTION100
3.8446-4.40030.21491480.19712623X-RAY DIFFRACTION99
4.4003-5.54140.21161420.18532645X-RAY DIFFRACTION99
5.5414-38.97970.2371510.19742659X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.54881.37470.69254.09051.39321.97130.07840.0464-0.56610.09230.1851-0.36040.56020.2366-0.24480.4970.08160.04640.46180.03670.5512-33.2165-11.632551.8684
20.3481-0.1293-0.23641.51672.62095.16680.01120.03050.0181-0.3844-0.02330.0327-0.51920.09970.01030.3395-0.01430.05590.31450.02740.4066-37.02460.335327.8613
32.8715-0.20770.18151.7255-0.2872.0223-0.01810.67970.5735-0.3181-0.0889-0.2334-0.16160.22720.10.3058-0.01490.07990.43560.09570.5677-15.723327.517441.6665
44.70390.4844-2.67164.231-0.43355.51880.29770.57630.6395-0.3472-0.10290.261-0.6353-0.2837-0.24020.35210.05880.0750.38270.11080.5408-26.275330.205135.7178
51.5251-0.237-0.48110.04790.00750.81360.2370.5099-1.3186-1.4039-0.2190.16041.09430.5527-0.01640.91780.03120.05120.6715-0.21790.9064-29.89379.522439.9471
60.05450.2720.43731.33882.24253.79970.09250.3206-1.21060.14810.3327-0.66610.58080.6026-0.34671.3063-0.0753-0.06120.79-0.33211.1855-29.9614-15.287827.688
73.00661.801-3.47521.6794-3.42547.01560.3882-0.4785-1.02350.9690.33040.87320.7933-0.0933-0.72060.9108-0.15310.0480.50050.11260.7325-32.6779-21.220714.0014
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 173 )
2X-RAY DIFFRACTION2chain 'A' and (resid 174 through 412 )
3X-RAY DIFFRACTION3chain 'A' and (resid 413 through 859 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 5 )
5X-RAY DIFFRACTION5chain 'B' and (resid 6 through 13 )
6X-RAY DIFFRACTION6chain 'B' and (resid 14 through 18 )
7X-RAY DIFFRACTION7chain 'B' and (resid 19 through 21 )

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