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- PDB-8vaj: Human Argonaute3 bound to cityRNA and target RNA -

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Basic information

Entry
Database: PDB / ID: 8vaj
TitleHuman Argonaute3 bound to cityRNA and target RNA
Components
  • Protein argonaute-3
  • RNA (5'-R(P*(SRA)P*AP*GP*CP*AP*CP*UP*UP*UP*AP*AP*A)-3')
  • RNA (5'-R(P*UP*AP*AP*AP*GP*UP*GP*CP*UP*UP*AP*G)-3')
KeywordsRNA BINDING PROTEIN/RNA / Tiny RNA / Argonaute3 / cityRNA / RISC / gene silencing / RNA interference / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


: / endoribonuclease activity, cleaving miRNA-paired mRNA / 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 / Small interfering RNA (siRNA) biogenesis / Transcriptional Regulation by MECP2 / RISC-loading complex ...: / endoribonuclease activity, cleaving miRNA-paired mRNA / 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 / Small interfering RNA (siRNA) biogenesis / Transcriptional Regulation by MECP2 / RISC-loading complex / regulatory ncRNA-mediated post-transcriptional gene silencing / regulation of stem cell proliferation / RISC complex assembly / miRNA processing / miRNA-mediated gene silencing by inhibition of translation / pre-miRNA processing / Regulation of MITF-M-dependent genes involved in apoptosis / RISC complex / TGFBR3 expression / Regulation of RUNX1 Expression and Activity / miRNA binding / MicroRNA (miRNA) biogenesis / mRNA catabolic process / Transcriptional Regulation by VENTX / Regulation of MECP2 expression and activity / Nuclear events stimulated by ALK signaling in cancer / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / RNA endonuclease activity / condensed nuclear chromosome / TP53 Regulates Metabolic Genes / P-body / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / MAPK6/MAPK4 signaling / positive regulation of non-canonical NF-kappaB signal transduction / Oncogene Induced Senescence / Pre-NOTCH Transcription and Translation / cytoplasmic ribonucleoprotein granule / double-stranded RNA binding / Ca2+ pathway / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / single-stranded RNA binding / positive regulation of gene expression / RNA binding / nucleoplasm / metal ion binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Protein argonaute-3 / 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 ...Protein argonaute-3 / 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 / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / Protein argonaute-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 Å
AuthorsZhang, H. / Sim, G. / Adhav, V.A. / Nakanishi, K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM138997 United States
CitationJournal: Cell Rep / Year: 2024
Title: Target cleavage and gene silencing by Argonautes with cityRNAs.
Authors: Zhang, H. / Sim, G. / Kehling, A.C. / Adhav, V.A. / Savidge, A. / Pastore, B. / Tang, W. / Nakanishi, K.
History
DepositionDec 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein argonaute-3
E: RNA (5'-R(P*UP*AP*AP*AP*GP*UP*GP*CP*UP*UP*AP*G)-3')
F: RNA (5'-R(P*(SRA)P*AP*GP*CP*AP*CP*UP*UP*UP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)107,1993
Polymers107,1993
Non-polymers00
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-39 kcal/mol
Surface area40930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.142, 138.126, 143.533
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein Protein argonaute-3 / hAgo3 / Argonaute RISC catalytic component 3 / Eukaryotic translation initiation factor 2C 3 / eIF2C 3


Mass: 97645.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGO3, EIF2C3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9H9G7
#2: RNA chain RNA (5'-R(P*UP*AP*AP*AP*GP*UP*GP*CP*UP*UP*AP*G)-3')


Mass: 4472.699 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: RNA chain RNA (5'-R(P*(SRA)P*AP*GP*CP*AP*CP*UP*UP*UP*AP*AP*A)-3')


Mass: 5081.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.05 Å3/Da / Density % sol: 59.65 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.8
Details: 0.14 M sodium citrate, 0.1 M Bis-Tris propane pH 8.8, and 18% (w/v) PEG 3350 supplemented with 4% (v/v) 1,3-Propanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 3.45→48.23 Å / Num. obs: 17731 / % possible obs: 99.5 % / Redundancy: 6.6 % / Biso Wilson estimate: 107.03 Å2 / Rrim(I) all: 0.239 / Net I/σ(I): 7.1
Reflection shellResolution: 3.45→3.573 Å / Num. unique obs: 1724 / Rrim(I) all: 1.527

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
Cootmodel building
PHASERphasing
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.45→48.23 Å / SU ML: 0.4351 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.7428
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2543 1804 10.21 %
Rwork0.206 15857 -
obs0.2109 17661 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 137.61 Å2
Refinement stepCycle: LAST / Resolution: 3.45→48.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6617 485 0 25 7127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00367313
X-RAY DIFFRACTIONf_angle_d0.688410011
X-RAY DIFFRACTIONf_chiral_restr0.04391134
X-RAY DIFFRACTIONf_plane_restr0.00581205
X-RAY DIFFRACTIONf_dihedral_angle_d16.69532867
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.45-3.540.42771080.37431199X-RAY DIFFRACTION99.47
3.54-3.640.38771440.31961203X-RAY DIFFRACTION99.63
3.64-3.760.33511420.29351187X-RAY DIFFRACTION99.63
3.76-3.90.28281500.24361171X-RAY DIFFRACTION99.1
3.9-4.050.30791220.22861231X-RAY DIFFRACTION99.56
4.05-4.240.25771370.20191192X-RAY DIFFRACTION99.25
4.24-4.460.23091340.19041194X-RAY DIFFRACTION98.66
4.46-4.740.24811310.18221230X-RAY DIFFRACTION99.85
4.74-5.10.23671620.18171213X-RAY DIFFRACTION100
5.1-5.620.23811290.17641221X-RAY DIFFRACTION99.93
5.62-6.430.29161360.2131253X-RAY DIFFRACTION100
6.43-8.090.22561460.20231251X-RAY DIFFRACTION99.57
8.09-48.230.20741630.17061312X-RAY DIFFRACTION99.26
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)
10.355009956312-0.06197956174970.06197326144292.06401857604-0.2491986646811.14791634610.0899579994479-0.0469444704530.2232101102620.09274388853150.07627548199180.150738805586-1.156572941340.07975644139393.80379228558E-51.7148407916-0.118539765215-0.02303863677450.933799194489-0.03449003452841.03498810457-29.401-18.1318.466
20.397400116806-0.443800797407-0.4066263369330.9545241001031.676329192382.29805260032-0.151503941978-0.0390907550565-0.01282592420320.07136269381190.04976720066040.2185290026470.25255967466-0.0650946636962-9.08705197046E-51.18278550225-0.137556890243-0.05566065053120.8508457313940.03154602076840.943998522883-36.526-27.17833.833
31.548473611460.1081751964730.05161910905361.483193603330.2216702569331.117201657080.0263527405636-0.1781765482580.02646927873580.674401400446-0.0220139324933-0.440791945902-0.006494537906310.6088309338091.7205802503E-51.13523575057-0.11883308054-0.3325673859041.249289224860.08222768141831.14999616688-4.249-52.47921.85
42.193879283480.336850037560.3746860607031.43099434145-0.3154849919780.1295394791680.017898508481-0.2168330929040.3122477846930.788991177342-0.323101805914-0.308646275612-0.25831777780.245460015038-6.66583169868E-51.26723337115-0.248623047463-0.2530271950511.094156015340.1277926324751.03146414457-10.954-45.06916.407
50.9177827079990.280719020081-0.250503541120.1513237229170.0635169115950.2952963203770.12339376653-0.2267452484041.244564843930.99439859683-0.682488539932-0.873882932301-1.569415076680.0671590493841-0.001339702556342.12637365807-0.123330523329-0.2949662782061.31095790290.007491496097221.26407502277-21.457-43.98925.534
60.01402198159090.005085660449160.009561708128420.005081484494680.009851708544330.03637068214430.0342235436313-0.571892075081-0.1533962852580.0653487069188-0.334949697062-0.823165707906-0.5063633515910.222211921623-0.0007683928112211.398848832780.296585745637-0.07688393914461.34001585994-0.07841948533481.32423998217-24.93-68.48423.656
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 13:196 )A13 - 196
2X-RAY DIFFRACTION2( CHAIN A AND RESID 197:421 )A197 - 421
3X-RAY DIFFRACTION3( CHAIN A AND RESID 422:723 )A422 - 723
4X-RAY DIFFRACTION4( CHAIN A AND RESID 724:861 )A724 - 861
5X-RAY DIFFRACTION5( CHAIN E AND RESID 1:14 )E1 - 14
6X-RAY DIFFRACTION6( CHAIN F AND RESID 12:16 )F12 - 16

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