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- PDB-5vm9: Human Argonaute3 bound to guide RNA -

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Basic information

Entry
Database: PDB / ID: 5vm9
TitleHuman Argonaute3 bound to guide RNA
Components
  • Protein argonaute-3
  • RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*UP*U)-3')
  • RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*UP*U)-3')
KeywordsHydrolase/RNA / protein / complex / RNA Binding protein-RNA complex / Hydrolase-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 / regulation of stem cell proliferation / 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 / 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 / positive regulation of non-canonical NF-kappaB signal transduction / MAPK6/MAPK4 signaling / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / 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 / cytoplasm / cytosol
Similarity search - Function
Protein argonaute-3 / 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-3 / 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
RNA / RNA (> 10) / Protein argonaute-3
Similarity search - Component
Biological speciesHomo sapiens (human)
Insect cell expression vector pTIE1 (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.28 Å
AuthorsPark, M.S. / Nakanishi, K.
Funding support United States, Japan, 5items
OrganizationGrant numberCountry
The Ohio State UniversityStart-up United States
Department of Energy (DOE, United States)GUP-41799 United States
Department of Energy (DOE, United States)GUP-51294 United States
JSTJPMJPR13L7 Japan
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM124320 United States
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Human Argonaute3 has slicer activity.
Authors: Park, M.S. / Phan, H.D. / Busch, F. / Hinckley, S.H. / Brackbill, J.A. / Wysocki, V.H. / Nakanishi, K.
History
DepositionApr 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 29, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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-3
B: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*UP*U)-3')
C: Protein argonaute-3
D: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)204,3274
Polymers204,3274
Non-polymers00
Water00
1
A: Protein argonaute-3
B: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)101,8342
Polymers101,8342
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-23 kcal/mol
Surface area37960 Å2
MethodPISA
2
C: Protein argonaute-3
D: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)102,4922
Polymers102,4922
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-27 kcal/mol
Surface area37210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.414, 68.414, 408.802
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGO3, EIF2C3
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q9H9G7
#2: RNA chain RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*UP*U)-3')


Mass: 4188.638 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Insect cell expression vector pTIE1 (others)
#3: RNA chain RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*UP*U)-3')


Mass: 4847.050 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Insect cell expression vector pTIE1 (others)

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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: 2.34 Å3/Da / Density % sol: 47.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM succinate-phosphateglycine buffer pH 4.4, 23% PEG2,000 and 4% PEG400

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Data collection

DiffractionMean temperature: 100 K
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: 3.28→67.48 Å / Num. obs: 28649 / % possible obs: 100 % / Redundancy: 13.6 % / Rpim(I) all: 0.086 / Net I/σ(I): 1.72
Reflection shellHighest resolution: 3.28 Å / Rpim(I) all: 0.408

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OLA

4ola


Resolution: 3.28→67.476 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 38.11 / Stereochemistry target values: TWIN_LSQ_F
Details: Author states that protein co-purified with endogenous microRNAs (miRNAs) which were from insect cells. This protein usually uptake the endogenous miRNAs during the overexpression and do not ...Details: Author states that protein co-purified with endogenous microRNAs (miRNAs) which were from insect cells. This protein usually uptake the endogenous miRNAs during the overexpression and do not release the RNA from the protein. They do not know the precise sequence or length of the RNA and the RNA were tightly bound to protein with the middle of the nucleotides disordered.
RfactorNum. reflection% reflection
Rfree0.2391 1996 6.99 %
Rwork0.1871 --
obs0.1922 28557 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.28→67.476 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12557 564 0 0 13121
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00513485
X-RAY DIFFRACTIONf_angle_d0.84618381
X-RAY DIFFRACTIONf_dihedral_angle_d16.1368093
X-RAY DIFFRACTIONf_chiral_restr0.0512067
X-RAY DIFFRACTIONf_plane_restr0.0062255
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2808-3.36280.31841460.27751868X-RAY DIFFRACTION93
3.3628-3.45370.30861430.27751901X-RAY DIFFRACTION93
3.4537-3.55530.30411420.25481903X-RAY DIFFRACTION93
3.5553-3.670.31471400.23591864X-RAY DIFFRACTION93
3.67-3.80110.261430.2121942X-RAY DIFFRACTION93
3.8011-3.95320.23051420.20011841X-RAY DIFFRACTION93
3.9532-4.1330.26131500.19431909X-RAY DIFFRACTION93
4.133-4.35080.22871390.17041886X-RAY DIFFRACTION93
4.3508-4.62320.18451390.16471927X-RAY DIFFRACTION93
4.6232-4.97980.24231430.161876X-RAY DIFFRACTION93
4.9798-5.48030.24311460.16911883X-RAY DIFFRACTION93
5.4803-6.27190.25131430.18411914X-RAY DIFFRACTION93
6.2719-7.89620.24771380.18341896X-RAY DIFFRACTION93
7.8962-48.04590.18811420.16721920X-RAY DIFFRACTION93
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)
12.2149-0.33330.3512.23290.32431.43640.10590.1439-0.51770.0148-0.24010.73480.5854-0.22770.23950.7579-0.06180.14860.61980.21890.9452-40.4476-44.055234.0976
21.0964-0.9515-1.10211.44041.4231.2111-0.1402-0.2817-0.18780.1150.18070.04980.190.1860.03730.76190.03730.04980.79490.28370.5789-19.204-44.060923.9282
32.82390.4365-0.57781.9178-0.99172.31920.1318-0.43620.1322-0.0667-0.2938-0.4522-0.30840.53960.06680.3786-0.01570.10881.05160.20010.6004-1.6689-10.866646.7796
41.8745-0.6693-0.28532.1227-1.14973.0164-0.0251-0.8124-0.2562-0.032-0.10180.30630.05230.12040.11490.27810.00190.15191.17170.21950.5291-20.6044-21.64253.1281
5-0.6362-0.5404-0.33290.221.45420.21830.6849-0.2877-0.417-2.7861-1.0041.57572.1355-0.13150.3529-0.0730.07630.2081.53840.04881.0131-15.1926-31.834733.4416
60.73540.0716-0.84180.1798-0.15691.4274-0.05080.1967-0.19440.0439-0.00970.27570.2061-0.34220.03070.6257-0.0346-0.11410.63580.2450.9639-38.9633-37.4833-1.076
71.8899-2.28870.16242.7092-0.26942.16420.46630.2251-0.3971-0.0999-0.25870.57490.1224-0.2404-0.12160.53670.04370.0090.57280.18210.9651-44.5255-22.52839.057
80.97850.1054-0.05672.4827-0.20342.3341-0.06890.12180.3935-0.32160.0913-0.2451-0.36450.73920.12240.5725-0.101-0.15520.66260.06650.6435-1.4008-6.26-12.6038
91.8073-0.61561.28612.9389-0.22031.8041-0.10750.3060.8415-0.7159-0.1355-0.0032-0.24350.18010.17290.8066-0.1574-0.0890.45760.20490.5264-13.2125-6.808-18.0076
103.32430.74980.53710.59290.22413.6582-0.18360.2443-0.063-0.47540.06930.071-0.05870.18140.03840.84720.0716-0.03820.35460.15560.3774-18.6338-24.587-21.6126
11-0.1978-1.0953-1.25510.36290.55091.1217-1.3527-1.057-0.4224-0.18430.5913-0.38920.7098-0.24520.11990.93830.2196-0.04990.63460.37630.8777-34.0957-19.8573-0.0435
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 196 )
2X-RAY DIFFRACTION2chain 'A' and (resid 197 through 413 )
3X-RAY DIFFRACTION3chain 'A' and (resid 414 through 618 )
4X-RAY DIFFRACTION4chain 'A' and (resid 619 through 860 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 21 )
6X-RAY DIFFRACTION6chain 'C' and (resid 15 through 263 )
7X-RAY DIFFRACTION7chain 'C' and (resid 264 through 406 )
8X-RAY DIFFRACTION8chain 'C' and (resid 407 through 500 )
9X-RAY DIFFRACTION9chain 'C' and (resid 501 through 618 )
10X-RAY DIFFRACTION10chain 'C' and (resid 619 through 860 )
11X-RAY DIFFRACTION11chain 'D' and (resid 1 through 21 )

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