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- PDB-7ki3: Human Argonaute2:miR-122 bound to the HCV genotype 1a site-1 RNA -

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Basic information

Entry
Database: PDB / ID: 7ki3
TitleHuman Argonaute2:miR-122 bound to the HCV genotype 1a site-1 RNA
Components
  • HCV genotype 1a miR-122 site-1
  • Protein argonaute-2
  • miR-122
KeywordsHYDROLASE/RNA / Argonaute / miR-122 / HCV / complex / 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 / Regulation of RUNX1 Expression and Activity / MicroRNA (miRNA) biogenesis / miRNA binding / 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 / negative regulation of translational initiation / RNA endonuclease activity / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / 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 / Protein argonaute, Mid domain / Argonaute-like, PIWI domain / Mid domain of argonaute / Argonaute linker 2 domain / Protein argonaute, N-terminal / N-terminal domain of argonaute / Argonaute linker 2 domain / DUF1785 / Argonaute, linker 1 domain ...Protein argonaute-2 / Protein argonaute, Mid domain / Argonaute-like, PIWI domain / Mid domain of argonaute / 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. / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
: / RNA / RNA (> 10) / Protein argonaute-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Hepacivirus C
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGebert, L.F.R. / MacRae, I.J.
Funding support United States, Switzerland, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM127090 United States
Swiss National Science FoundationP300PA 177860 Switzerland
CitationJournal: Nat Commun / Year: 2021
Title: A structured RNA motif locks Argonaute2:miR-122 onto the 5' end of the HCV genome.
Authors: Gebert, L.F.R. / Law, M. / MacRae, I.J.
History
DepositionOct 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein argonaute-2
B: miR-122
C: HCV genotype 1a miR-122 site-1
D: Protein argonaute-2
E: miR-122
F: HCV genotype 1a miR-122 site-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,6729
Polymers228,2606
Non-polymers4123
Water0
1
A: Protein argonaute-2
B: miR-122
C: HCV genotype 1a miR-122 site-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,4055
Polymers114,1303
Non-polymers2752
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8750 Å2
ΔGint-87 kcal/mol
Surface area40710 Å2
MethodPISA
2
D: Protein argonaute-2
E: miR-122
F: HCV genotype 1a miR-122 site-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,2684
Polymers114,1303
Non-polymers1371
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-59 kcal/mol
Surface area39600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.313, 112.963, 207.684
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 97402.195 Da / Num. of mol.: 2 / Mutation: S387D, S824A, S828D, S831D, S834A
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 miR-122 /


Mass: 7439.394 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: RNA chain HCV genotype 1a miR-122 site-1


Mass: 9288.604 Da / Num. of mol.: 2 / Mutation: C8G, G17C / Source method: obtained synthetically / Source: (synth.) Hepacivirus C
#4: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ba
Has ligand of interestN

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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: 2.24 Å3/Da / Density % sol: 45.18 % / Description: Flat, elongated hexagon
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG8000, barium chloride, Tris-HCl

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 7, 2017
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→99.234 Å / Num. obs: 58923 / % possible obs: 99.96 % / Redundancy: 12.6 % / CC1/2: 0.885 / Net I/σ(I): 12.52
Reflection shellResolution: 3→3.107 Å / Mean I/σ(I) obs: 1.58 / Num. unique obs: 50608 / CC1/2: 0.537

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Processing

Software
NameVersionClassification
PHENIX1.14rc1_3161refinement
PDB_EXTRACT3.25data extraction
DIALS2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4W5R MID and PIWI domains

4w5r


Resolution: 3→99.234 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.276 3916 4.93 %
Rwork0.2327 75485 -
obs0.2349 41923 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 212.68 Å2 / Biso mean: 64.0142 Å2 / Biso min: 12.33 Å2
Refinement stepCycle: final / Resolution: 3→99.234 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12699 1715 3 0 14417
Biso mean--84.47 --
Num. residues----1667
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
3-3.03660.35291410.32592731
3.0366-3.0750.39941310.31352653
3.075-3.11550.36341520.30492715
3.1155-3.15820.31731560.29462654
3.1582-3.20330.34461060.29042729
3.2033-3.25110.32841330.2822718
3.2511-3.30190.32551370.26242685
3.3019-3.35610.28291780.25872673
3.3561-3.41390.28631410.26742699
3.4139-3.4760.29671380.25492699
3.476-3.54290.34141220.26792688
3.5429-3.61520.31991490.25072688
3.6152-3.69380.27791610.24142661
3.6938-3.77970.27611410.22372736
3.7797-3.87430.25891640.21462667
3.8743-3.9790.26151020.21422718
3.979-4.09610.23351340.22022703
4.0961-4.22830.21351100.20712715
4.2283-4.37940.25671270.21022742
4.3794-4.55480.28341570.19822647
4.5548-4.76210.25591380.20242730
4.7621-5.01310.2951540.20682643
5.0131-5.32720.22881410.20512712
5.3272-5.73850.26291610.21542685
5.7385-6.31590.30921320.21792700
6.3159-7.22960.26231360.2332703
7.2296-9.10750.23051320.21332700

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