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- PDB-6mfn: Human Argonaute2-miR-27a bound to HSUR1 target RNA -

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Basic information

Entry
Database: PDB / ID: 6mfn
TitleHuman Argonaute2-miR-27a bound to HSUR1 target RNA
Components
  • Protein argonaute-2
  • RNA (5'-R(P*UP*CP*UP*GP*UP*GP*AP*UP*AP*A)-3')
  • RNA (5'-R(P*UP*UP*CP*AP*CP*AP*GP*UP*G)-3')
KeywordsHYDROLASE/RNA / RNA-binding protein / microRNA / target directed microRNA decay / 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 / M-decay: degradation of maternal mRNAs by maternally stored factors / Regulation of MITF-M-dependent genes involved in apoptosis / mRNA 3'-UTR AU-rich region binding / 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 / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / Nuclear events stimulated by ALK signaling in cancer / negative regulation of translational initiation / translation initiation factor activity / 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 / cytosol / cytoplasm
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: 2.5 Å
AuthorsSheu-Gruttadauria, J. / MacRae, I.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM104475 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115649 United States
CitationJournal: Mol.Cell / Year: 2019
Title: Structural Basis for Target-Directed MicroRNA Degradation.
Authors: Sheu-Gruttadauria, J. / Pawlica, P. / Klum, S.M. / Wang, S. / Yario, T.A. / Schirle Oakdale, N.T. / Steitz, J.A. / MacRae, I.J.
History
DepositionSep 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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: Protein argonaute-2
C: RNA (5'-R(P*UP*UP*CP*AP*CP*AP*GP*UP*G)-3')
E: RNA (5'-R(P*UP*CP*UP*GP*UP*GP*AP*UP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,1464
Polymers111,0523
Non-polymers941
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-34 kcal/mol
Surface area38190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.948, 104.212, 152.858
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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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: 97358.188 Da / Num. of mol.: 1 / Mutation: D669A, 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 RNA (5'-R(P*UP*UP*CP*AP*CP*AP*GP*UP*G)-3')


Mass: 6665.980 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: RNA chain RNA (5'-R(P*UP*CP*UP*GP*UP*GP*AP*UP*AP*A)-3')


Mass: 7028.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-IPH / PHENOL


Mass: 94.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.58 Å3/Da / Density % sol: 52.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10% PEG3350, 50 mM Tris, pH 8.0, 20 mM magnesium chloride, 75 mM phenol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03323 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 21, 2017
RadiationMonochromator: double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03323 Å / Relative weight: 1
ReflectionResolution: 2.5→28.59 Å / Num. obs: 37628 / % possible obs: 99.3 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.039 / Net I/σ(I): 14.5
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.516 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4159 / Rpim(I) all: 0.323 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4W5O

4w5o


Resolution: 2.5→28.59 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.5
RfactorNum. reflection% reflection
Rfree0.2468 1875 4.99 %
Rwork0.209 --
obs0.2109 37587 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→28.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6448 368 7 87 6910
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037014
X-RAY DIFFRACTIONf_angle_d0.7069573
X-RAY DIFFRACTIONf_dihedral_angle_d13.1762695
X-RAY DIFFRACTIONf_chiral_restr0.0271079
X-RAY DIFFRACTIONf_plane_restr0.0031172
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4966-2.5640.36341470.30112653X-RAY DIFFRACTION98
2.564-2.63940.32791300.27312730X-RAY DIFFRACTION100
2.6394-2.72460.28711360.25822715X-RAY DIFFRACTION100
2.7246-2.82190.30881380.2582733X-RAY DIFFRACTION100
2.8219-2.93470.26051560.2542702X-RAY DIFFRACTION99
2.9347-3.06820.31881330.24152728X-RAY DIFFRACTION99
3.0682-3.22970.28081360.24252727X-RAY DIFFRACTION99
3.2297-3.43180.27681750.23742713X-RAY DIFFRACTION99
3.4318-3.69620.27791240.22162753X-RAY DIFFRACTION99
3.6962-4.06720.22741720.19772710X-RAY DIFFRACTION99
4.0672-4.65360.19151470.1722787X-RAY DIFFRACTION100
4.6536-5.85480.22471060.17382846X-RAY DIFFRACTION99
5.8548-28.59640.21051750.18052915X-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)
12.29930.795-0.71742.68480.0862.06080.21830.14450.7314-0.4768-0.0156-0.1158-0.80410.0875-0.21180.57820.01760.04950.39760.03670.62150.591240.2652-13.3395
20.89810.4617-2.6923-0.7398-0.88628.2461-0.17190.00860.00190.09610.11670.07590.5857-0.15470.03240.51940.00190.04120.480.04730.40496.288424.509-44.231
31.72610.3860.58081.41850.39331.46070.07460.2186-0.1761-0.4542-0.10150.27110.1056-0.1977-0.01520.43960.0881-0.09390.3394-0.03570.3571-29.2396.9548-25.5745
42.5101-0.57280.4211.5747-0.07951.43770.0699-0.07250.21-0.1788-0.10360.2316-0.1992-0.13540.04380.2671-0.0122-0.01220.3067-0.03320.3553-29.529522.1749-13.167
55.0705-4.6339-0.17644.4561-1.05886.2041-0.07380.44320.936-0.76250.0839-0.3143-1.06711.0006-0.07740.5783-0.11110.06790.44850.08270.4192-19.833611.0936-25.8325
64.36860.1308-1.01896.08360.32782.73230.14940.30530.3196-1.0697-0.07010.5238-0.05520.0563-0.0180.54490.0630.02810.5749-0.01490.4382-16.29382.9995-27.9053
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 183 )
2X-RAY DIFFRACTION2chain 'A' and (resid 184 through 371 )
3X-RAY DIFFRACTION3chain 'A' and (resid 372 through 570 )
4X-RAY DIFFRACTION4chain 'A' and (resid 571 through 859 )
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 9 )
6X-RAY DIFFRACTION6chain 'E' and (resid 13 through 22 )

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