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- PDB-6nit: Human Argonaute2-miR-122 bound to a target RNA with four central ... -

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Basic information

Entry
Database: PDB / ID: 6nit
TitleHuman Argonaute2-miR-122 bound to a target RNA with four central mismatches (bu4)
Components
  • Protein argonaute-2
  • RNA (5'-R(P*AP*AP*CP*AP*CP*CP*AP*UP*CP*CP*AP*AP*CP*AP*CP*UP*CP*CP*AP*AP*A)-3')
  • RNA (5'-R(P*UP*GP*GP*AP*GP*UP*GP*UP*GP*AP*CP*AP*AP*UP*GP*GP*UP*GP*UP*UP*U)-3')
Keywordsrna binding protein/rna / RNA-binding protein / microRNA / target directed microRNA decay / HYDROLASE / RNA BINDING PROTEIN / rna binding protein-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
RNA / RNA (> 10) / Protein argonaute-2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 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
DepositionDec 31, 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 / _citation.page_last
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Protein argonaute-2
C: RNA (5'-R(P*UP*GP*GP*AP*GP*UP*GP*UP*GP*AP*CP*AP*AP*UP*GP*GP*UP*GP*UP*UP*U)-3')
D: RNA (5'-R(P*UP*GP*GP*AP*GP*UP*GP*UP*GP*AP*CP*AP*AP*UP*GP*GP*UP*GP*UP*UP*U)-3')
E: RNA (5'-R(P*AP*AP*CP*AP*CP*CP*AP*UP*CP*CP*AP*AP*CP*AP*CP*UP*CP*CP*AP*AP*A)-3')
F: RNA (5'-R(P*AP*AP*CP*AP*CP*CP*AP*UP*CP*CP*AP*AP*CP*AP*CP*UP*CP*CP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)222,8536
Polymers222,8536
Non-polymers00
Water0
1
A: Protein argonaute-2
C: RNA (5'-R(P*UP*GP*GP*AP*GP*UP*GP*UP*GP*AP*CP*AP*AP*UP*GP*GP*UP*GP*UP*UP*U)-3')
E: RNA (5'-R(P*AP*AP*CP*AP*CP*CP*AP*UP*CP*CP*AP*AP*CP*AP*CP*UP*CP*CP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)111,4273
Polymers111,4273
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-57 kcal/mol
Surface area41790 Å2
MethodPISA
2
B: Protein argonaute-2
D: RNA (5'-R(P*UP*GP*GP*AP*GP*UP*GP*UP*GP*AP*CP*AP*AP*UP*GP*GP*UP*GP*UP*UP*U)-3')
F: RNA (5'-R(P*AP*AP*CP*AP*CP*CP*AP*UP*CP*CP*AP*AP*CP*AP*CP*UP*CP*CP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)111,4273
Polymers111,4273
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-52 kcal/mol
Surface area39690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.712, 137.086, 154.064
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 97358.188 Da / Num. of mol.: 2 / 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*GP*GP*AP*GP*UP*GP*UP*GP*AP*CP*AP*AP*UP*GP*GP*UP*GP*UP*UP*U)-3')


Mass: 6788.021 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: miR-122 21mer / Source: (synth.) Homo sapiens (human)
#3: RNA chain RNA (5'-R(P*AP*AP*CP*AP*CP*CP*AP*UP*CP*CP*AP*AP*CP*AP*CP*UP*CP*CP*AP*AP*A)-3')


Mass: 7280.480 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct

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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: 2.53 Å3/Da / Density % sol: 51.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10% PEG3350, 50mM Tris pH8, 20mM MgCl2, 75mM Phenol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.79→39.56 Å / Num. obs: 23149 / % possible obs: 98.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.283 / Rpim(I) all: 0.112 / Net I/σ(I): 5.8
Reflection shellResolution: 3.79→4.1 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.068 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4605 / Rpim(I) all: 0.43 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.8→39.301 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.07
RfactorNum. reflection% reflection
Rfree0.2941 1163 5.04 %
Rwork0.2427 --
obs0.2453 23073 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.8→39.301 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12758 1448 0 0 14206
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314664
X-RAY DIFFRACTIONf_angle_d0.82120158
X-RAY DIFFRACTIONf_dihedral_angle_d14.455708
X-RAY DIFFRACTIONf_chiral_restr0.0322305
X-RAY DIFFRACTIONf_plane_restr0.0042345
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7748-3.94640.35551460.32762647X-RAY DIFFRACTION97
3.9464-4.15430.2991530.29242699X-RAY DIFFRACTION100
4.1543-4.41420.3031390.26012681X-RAY DIFFRACTION99
4.4142-4.75450.29591530.24932708X-RAY DIFFRACTION99
4.7545-5.2320.26551350.23992753X-RAY DIFFRACTION100
5.232-5.98680.32321430.24872756X-RAY DIFFRACTION99
5.9868-7.5340.31361530.24772785X-RAY DIFFRACTION100
7.534-39.3030.25341410.19012881X-RAY DIFFRACTION98
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)
16.37242.3231-1.864.5226-1.66031.9904-0.3479-0.2289-1.3922-0.74950.29870.26480.965-0.69690.09471.3083-0.1615-0.18071.2059-0.0041.2211231.2476139.43647.0509
23.77431.30560.11380.5488-0.10826.30890.1962-0.4513-0.1555-0.2219-0.00810.74160.5264-0.8548-0.43191.329-0.1114-0.02960.98860.20661.647229.6254135.203752.564
32.18831.006-4.04211.9758-1.58217.13330.5828-0.41340.43070.1042-0.30.1029-0.89310.9049-0.38081.1367-0.05510.1071.39950.06591.0109241.2418129.075187.248
42.8797-0.10960.23963.4802-1.08913.2637-0.1711-0.42760.23230.4914-0.03340.0385-0.15640.27990.28550.85390.03110.09030.8238-0.03280.7724252.4641166.230454.587
53.93932.46030.33245.423-0.07422.0503-0.242-0.3397-0.0078-0.16110.14841.53070.5348-0.8298-0.07870.9736-0.05950.01941.0666-0.10971.3961226.155566.994453.0215
60.2270.2086-2.6711.9759-3.88158.50790.2036-0.4661-0.01530.48720.12860.1345-0.65730.6569-0.05531.1204-0.11650.08151.1585-0.00660.9789242.680361.380482.7787
73.36060.70550.19962.13570.11712.21360.0012-0.45950.518-0.0056-0.01630.1725-0.10040.1240.0280.59040.03830.07890.697-0.0570.8248252.43597.238860.042
85.6186-0.9179-4.04765.4112-1.85564.75760.4285-1.9036-0.54252.1271-0.2259-1.61961.0878-0.64530.04411.45830.0582-0.23171.28420.11930.7596258.3886157.774461.6552
99.15160.0965-4.14435.45770.52968.1334-0.7757-2.25650.8559-0.49650.24432.3808-1.8443-0.70950.3712.23570.1169-0.44982.4112-0.11061.936226.0454148.66572.4194
102.3862-0.53043.26892.3464-4.04879.48660.2167-1.3227-0.5260.6199-0.1068-0.58730.63550.48560.50470.77590.0368-0.03021.0924-0.14510.9203260.277190.934767.3147
113.4651.9812-4.54291.3263-2.77055.8573-1.1631-0.92730.33051.0565-0.03920.4928-0.61490.47950.77771.37030.10130.28360.94960.09941.3899240.907679.791171.2823
123.60091.1772-1.21960.9221.03923.7390.7658-0.8666-0.5107-0.3619-1.0694-0.78320.8296-0.4201-0.07492.71660.06030.01792.71280.0371.6711230.6821148.962969.9537
133.19412.9901-0.3382.9678-0.79481.1225-0.7984-1.1402-0.07561.5864-0.2394-1.0287-0.71510.73990.86121.8765-0.0295-0.10961.42170.52511.334266.5224152.045963.2959
149.36923.6601-1.05431.5224-0.06043.64280.17230.19270.45871.10970.2642-0.47513.3408-0.3172-0.4011.84240.1358-0.65982.2012-0.83152.9291230.990878.017876.017
153.17763.7423-1.31377.0773.07048.2396-0.8089-0.9837-1.13260.55160.28610.1341-0.81820.27040.67891.06210.129-0.0120.96510.29181.2037264.822782.223468.4032
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 81 )
2X-RAY DIFFRACTION2chain 'A' and (resid 82 through 225 )
3X-RAY DIFFRACTION3chain 'A' and (resid 226 through 371 )
4X-RAY DIFFRACTION4chain 'A' and (resid 372 through 859 )
5X-RAY DIFFRACTION5chain 'B' and (resid 22 through 182 )
6X-RAY DIFFRACTION6chain 'B' and (resid 183 through 384 )
7X-RAY DIFFRACTION7chain 'B' and (resid 385 through 859 )
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 7 )
9X-RAY DIFFRACTION9chain 'C' and (resid 8 through 20 )
10X-RAY DIFFRACTION10chain 'D' and (resid 1 through 5 )
11X-RAY DIFFRACTION11chain 'D' and (resid 6 through 16 )
12X-RAY DIFFRACTION12chain 'E' and (resid 2 through 14 )
13X-RAY DIFFRACTION13chain 'E' and (resid 15 through 23 )
14X-RAY DIFFRACTION14chain 'F' and (resid 2 through 13 )
15X-RAY DIFFRACTION15chain 'F' and (resid 14 through 23 )

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