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- PDB-4ola: Crystal Structure of Human Argonaute2 -

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Basic information

Entry
Database: PDB / ID: 4ola
TitleCrystal Structure of Human Argonaute2
Components
  • 5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*U)-3'
  • Protein argonaute-2
KeywordsHYDROLASE/RNA / RNA-binding protein / RNA interference / protein-RNA complex / ago / 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 / Regulation of CDH11 mRNA translation by microRNAs / Regulation of NPAS4 mRNA translation / Post-transcriptional silencing by small RNAs / Competing endogenous RNAs (ceRNAs) regulate PTEN 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 / Regulation of CDH11 mRNA translation by microRNAs / Regulation of NPAS4 mRNA translation / Post-transcriptional silencing by small RNAs / Competing endogenous RNAs (ceRNAs) regulate PTEN translation / Regulation of PTEN mRNA translation / negative regulation of amyloid precursor protein biosynthetic process / Small interfering RNA (siRNA) biogenesis / Transcriptional Regulation by MECP2 / positive regulation of trophoblast cell migration / RNA secondary structure unwinding / miRNA metabolic process / RISC-loading complex / mRNA cap binding / regulatory ncRNA-mediated post-transcriptional gene silencing / : / RISC complex assembly / mRNA 3'-UTR AU-rich region binding / miRNA processing / pre-miRNA processing / miRNA-mediated gene silencing by inhibition of translation / siRNA processing / RNA 7-methylguanosine cap binding / siRNA binding / M-decay: degradation of maternal mRNAs by maternally stored factors / regulatory ncRNA-mediated gene silencing / RISC complex / miRNA binding / Regulation of RUNX1 Expression and Activity / 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 / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / negative regulation of translational initiation / core promoter sequence-specific DNA binding / RNA endonuclease activity / translation initiation factor activity / post-embryonic development / positive regulation of translation / P-body / TP53 Regulates Metabolic Genes / Transcriptional regulation by small RNAs / MAPK6/MAPK4 signaling / cytoplasmic ribonucleoprotein granule / Pre-NOTCH Transcription and Translation / positive regulation of angiogenesis / double-stranded RNA binding / Ca2+ pathway / Estrogen-dependent gene expression / single-stranded RNA binding / translation / dendrite / positive regulation of transcription by RNA polymerase II / RNA binding / extracellular exosome / nucleoplasm / membrane / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Protein argonaute-2 / paz domain / Protein argonaute, Mid domain / Argonaute-like, PIWI domain / Mid domain of argonaute / paz domain / Argonaute linker 2 domain / Protein argonaute, N-terminal / N-terminal domain of argonaute / Argonaute linker 2 domain ...Protein argonaute-2 / paz domain / Protein argonaute, Mid domain / Argonaute-like, PIWI domain / Mid domain of argonaute / paz domain / Argonaute linker 2 domain / Protein argonaute, N-terminal / N-terminal domain of argonaute / Argonaute linker 2 domain / DUF1785 / Argonaute, linker 1 domain / Argonaute linker 1 domain / Piwi domain / Piwi domain profile. / Piwi domain / Piwi / PAZ domain superfamily / PAZ / PAZ domain / PAZ domain / PAZ domain profile. / Response regulator / Beta Complex / Ribonuclease H-like superfamily/Ribonuclease H / 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
ISOPROPYL ALCOHOL / PHENOL / RNA / Protein argonaute-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsSchirle, N.T. / MacRae, I.J.
CitationJournal: Science / Year: 2012
Title: The crystal structure of human Argonaute2.
Authors: Schirle, N.T. / MacRae, I.J.
History
DepositionJan 23, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 5, 2014ID: 4EI1
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_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: 5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*U)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,7564
Polymers100,6022
Non-polymers1542
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-14 kcal/mol
Surface area35880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.157, 107.669, 68.522
Angle α, β, γ (deg.)90.00, 107.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein argonaute-2 / Argonaute2 / hAgo2 / Eukaryotic translation initiation factor 2C 2 / eIF-2C 2 / eIF2C 2 / PAZ Piwi ...Argonaute2 / hAgo2 / Eukaryotic translation initiation factor 2C 2 / eIF-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: EIF2C2, AGO2 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9
References: UniProt: Q9UKV8, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#2: RNA chain 5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*U)-3'


Mass: 3224.060 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9
#3: Chemical ChemComp-IPH / PHENOL / Phenol


Mass: 94.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6O
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE RNA STRAND BETWEEN RESIDUES A9 AND U21 IS DISORDERED. BOTH THE SEQUENCE AND LENGTH OF THE ...THE RNA STRAND BETWEEN RESIDUES A9 AND U21 IS DISORDERED. BOTH THE SEQUENCE AND LENGTH OF THE DISORDERED REGION ARE UNKNOWN.

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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: 2.21 Å3/Da / Density % sol: 44.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 16% PEG3350, 12% isopropanol, 0.1 M phenol, 0.1 M Tris, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL11-110.97926, 0.91837
SYNCHROTRONAPS 24-ID-E20.9792
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELDec 9, 2011
ADSC QUANTUM 3152CCDNov 19, 2011
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)MADMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979261
20.918371
30.97921
ReflectionResolution: 2.2→65.493 Å / Num. obs: 44375 / % possible obs: 99.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.057 / Χ2: 0.76 / Net I/σ(I): 11.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.2-2.283.70.74143720.8431,298.7
2.28-2.373.80.55144130.8431,298.9
2.37-2.483.80.38643940.891,299.3
2.48-2.613.80.26844540.9591,299.3
2.61-2.773.80.17444200.8651,299.3
2.77-2.993.80.10544340.8461,299.7
2.99-3.293.80.06344530.771,299.6
3.29-3.763.80.04744440.7121,299.7
3.76-4.743.80.04544690.6651,299.8
4.74-65.4933.70.02545220.2051,299.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→41.588 Å / SU ML: 0.34 / σ(F): 1.36 / Phase error: 27.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2529 1960 5.06 %
Rwork0.212 --
obs0.2141 38697 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→41.588 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6343 191 11 177 6722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036711
X-RAY DIFFRACTIONf_angle_d0.7769117
X-RAY DIFFRACTIONf_dihedral_angle_d14.3522552
X-RAY DIFFRACTIONf_chiral_restr0.0531022
X-RAY DIFFRACTIONf_plane_restr0.0031138
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.35750.34491370.25842615X-RAY DIFFRACTION99
2.3575-2.42130.35971390.25662597X-RAY DIFFRACTION99
2.4213-2.49250.31251440.24292598X-RAY DIFFRACTION99
2.4925-2.57290.34241370.23512592X-RAY DIFFRACTION99
2.5729-2.66490.28191460.2382624X-RAY DIFFRACTION99
2.6649-2.77160.29761390.23492621X-RAY DIFFRACTION99
2.7716-2.89770.2681420.23322633X-RAY DIFFRACTION100
2.8977-3.05040.31121320.24012612X-RAY DIFFRACTION100
3.0504-3.24150.29911570.23242611X-RAY DIFFRACTION100
3.2415-3.49160.28681250.22952658X-RAY DIFFRACTION100
3.4916-3.84280.22761200.20492633X-RAY DIFFRACTION100
3.8428-4.39830.23011510.19072648X-RAY DIFFRACTION100
4.3983-5.53930.20321410.18132648X-RAY DIFFRACTION100
5.5393-41.59460.20861500.19872647X-RAY DIFFRACTION98

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