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- PDB-6oon: Human Argonaute4 bound to guide RNA -

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Basic information

Entry
Database: PDB / ID: 6oon
TitleHuman Argonaute4 bound to guide RNA
Components
  • Protein argonaute-4
  • RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*UP*U)-3')
KeywordsHYDROLASE/RNA / RNA / miRNA / RNA BINDING PROTEIN / HYDROLASE-RNA complex
Function / homology
Function and homology information


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 / synaptonemal complex assembly / male meiotic nuclear division / RNA secondary structure unwinding ...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 / synaptonemal complex assembly / male meiotic nuclear division / RNA secondary structure unwinding / RISC-loading complex / miRNA metabolic process / RISC complex assembly / regulatory ncRNA-mediated post-transcriptional gene silencing / miRNA processing / miRNA-mediated gene silencing by inhibition of translation / pre-miRNA processing / Regulation of MITF-M-dependent genes involved in apoptosis / RISC complex / regulation of cell morphogenesis / TGFBR3 expression / Regulation of RUNX1 Expression and Activity / miRNA binding / MicroRNA (miRNA) biogenesis / mRNA catabolic process / Regulation of MECP2 expression and activity / Transcriptional Regulation by VENTX / Nuclear events stimulated by ALK signaling in cancer / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / RNA endonuclease activity / TP53 Regulates Metabolic Genes / P-body / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / MAPK6/MAPK4 signaling / Oncogene Induced Senescence / Pre-NOTCH Transcription and Translation / cytoplasmic ribonucleoprotein granule / male gonad development / double-stranded RNA binding / Ca2+ pathway / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / single-stranded RNA binding / negative regulation of apoptotic process / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Protein argonaute-4 / 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-4 / 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 / Piwi domain profile. / Piwi domain / Piwi / PAZ domain superfamily / PAZ / PAZ domain / PAZ domain profile. / PAZ domain / 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-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPark, M.S. / Brackbill, J.A. / Nakanishi, K.
Funding support United States, Japan, 4items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)GUP-41799 United States
Japan Science and TechnologyJPMJPR13L7 Japan
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM124320 United States
Other government
CitationJournal: Mol.Cell / Year: 2019
Title: Multidomain Convergence of Argonaute during RISC Assembly Correlates with the Formation of Internal Water Clusters.
Authors: Park, M.S. / Araya-Secchi, R. / Brackbill, J.A. / Phan, H.D. / Kehling, A.C. / Abd El-Wahab, E.W. / Dayeh, D.M. / Sotomayor, M. / Nakanishi, K.
History
DepositionApr 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 10, 2021Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.4Oct 11, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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-4
B: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)101,2332
Polymers101,2332
Non-polymers00
Water8,359464
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-23 kcal/mol
Surface area35790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)213.980, 68.011, 83.270
Angle α, β, γ (deg.)90.00, 102.68, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1083-

HOH

21A-1311-

HOH

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Components

#1: Protein Protein argonaute-4 / hAgo4 / Argonaute RISC catalytic component 4 / Eukaryotic translation initiation factor 2C 4 / eIF2C 4


Mass: 97373.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGO4, EIF2C4, KIAA1567
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q9HCK5
#2: RNA chain RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*UP*U)-3')


Mass: 3859.432 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Insect cell expression vector pTIE1 (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 464 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe protein was co-purified with endogenous RNA from insect cells. Therefore, the precise sequence ...The protein was co-purified with endogenous RNA from insect cells. Therefore, the precise sequence or length of the RNA is unknown. The 5' end and 3' end of the RNA are tightly bound to the protein but the middle nucleotides were disordered.

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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: 2.92 Å3/Da / Density % sol: 57.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG5000, 0.1 M MES, pH=6, 1 M LiCl, 100 mM Trimethylamine Hydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.9→49.082 Å / Num. obs: 91128 / % possible obs: 98.9 % / Redundancy: 4.1 % / Net I/σ(I): 1.91
Reflection shellResolution: 1.9→1.95 Å / Num. unique obs: 14243

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OLA

4ola


Resolution: 1.9→49.082 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.64
RfactorNum. reflection% reflection
Rfree0.2024 4550 4.99 %
Rwork0.1714 --
obs0.173 91128 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→49.082 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6281 243 0 464 6988
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086736
X-RAY DIFFRACTIONf_angle_d1.1179180
X-RAY DIFFRACTIONf_dihedral_angle_d14.4712576
X-RAY DIFFRACTIONf_chiral_restr0.0481029
X-RAY DIFFRACTIONf_plane_restr0.0061137
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92160.32031400.28062857X-RAY DIFFRACTION98
1.9216-1.94420.28221340.26812888X-RAY DIFFRACTION98
1.9442-1.96790.27061540.24882797X-RAY DIFFRACTION98
1.9679-1.99280.27011510.24272877X-RAY DIFFRACTION98
1.9928-2.0190.2541460.22932828X-RAY DIFFRACTION98
2.019-2.04670.26011550.21682869X-RAY DIFFRACTION98
2.0467-2.07590.27171430.2072870X-RAY DIFFRACTION98
2.0759-2.10690.24081670.2012808X-RAY DIFFRACTION99
2.1069-2.13990.2281400.19752896X-RAY DIFFRACTION99
2.1399-2.17490.21931470.18822833X-RAY DIFFRACTION99
2.1749-2.21240.2041670.17412857X-RAY DIFFRACTION99
2.2124-2.25270.19251550.1732901X-RAY DIFFRACTION99
2.2527-2.2960.21631520.17082835X-RAY DIFFRACTION99
2.296-2.34290.18131310.16772924X-RAY DIFFRACTION99
2.3429-2.39380.20471590.16922877X-RAY DIFFRACTION99
2.3938-2.44950.19371450.17112887X-RAY DIFFRACTION99
2.4495-2.51070.2141620.17152868X-RAY DIFFRACTION99
2.5107-2.57860.19811510.16872859X-RAY DIFFRACTION99
2.5786-2.65450.1781690.16382868X-RAY DIFFRACTION99
2.6545-2.74020.2121520.17012916X-RAY DIFFRACTION99
2.7402-2.83810.19761660.17192888X-RAY DIFFRACTION99
2.8381-2.95170.2211440.17322909X-RAY DIFFRACTION99
2.9517-3.0860.20761460.17062901X-RAY DIFFRACTION99
3.086-3.24870.19871430.17592915X-RAY DIFFRACTION100
3.2487-3.45220.23441720.16362896X-RAY DIFFRACTION100
3.4522-3.71870.18151460.16342933X-RAY DIFFRACTION100
3.7187-4.09270.18821640.15032913X-RAY DIFFRACTION100
4.0927-4.68450.161350.13682972X-RAY DIFFRACTION100
4.6845-5.90040.18481590.15692952X-RAY DIFFRACTION100
5.9004-49.09810.17931550.17232984X-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)
12.65930.17330.98621.4648-0.03391.4607-0.30670.76330.2783-0.27860.1017-0.3121-0.23280.7640.12830.2653-0.1185-0.01020.5390.08710.271-13.10240.811426.2868
21.2350.51560.10141.4344-0.43733.0564-0.27310.48950.2245-0.57390.25650.0811-0.56020.22630.00210.5912-0.1309-0.01520.4639-0.00070.3117-28.64134.4412.9092
31.5852-0.38850.10421.1739-0.04560.96820.09670.3119-0.1479-0.35110.02460.3785-0.1795-0.1357-0.11750.30440.0095-0.08080.22460.00170.2359-63.27128.454718.2042
41.4793-0.48090.04431.67770.41340.7911-0.02280.02310.0715-0.14910.0708-0.0332-0.13280.0857-0.0230.1415-0.02350.01570.12990.02090.1348-48.113610.766232.4528
50.0135-0.04720.00160.03020.05580.048-0.09090.67940.1903-0.2666-0.1029-0.3866-0.47870.57480.17950.4548-0.12680.01660.75780.11330.5428-41.6056.087110.5668
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 137 )
2X-RAY DIFFRACTION2chain 'A' and (resid 138 through 374 )
3X-RAY DIFFRACTION3chain 'A' and (resid 375 through 562 )
4X-RAY DIFFRACTION4chain 'A' and (resid 563 through 861 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 21 )

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