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- PDB-5wea: Human Argonaute2 Helix-7 Mutant -

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Basic information

Entry
Database: PDB / ID: 5wea
TitleHuman Argonaute2 Helix-7 Mutant
Components
  • Protein argonaute-2
  • RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*U)-3')
KeywordsHYDROLASE/RNA / Argonaute / RNA binding / RNA silencing / microRNA / HYDROLASE / 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 / 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
PHENOL / RNA / Protein argonaute-2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.12 Å
AuthorsSchirle, N.T. / Klum, S.M. / 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: EMBO J. / Year: 2018
Title: Helix-7 in Argonaute2 shapes the microRNA seed region for rapid target recognition.
Authors: Klum, S.M. / Chandradoss, S.D. / Schirle, N.T. / Joo, C. / MacRae, I.J.
History
DepositionJul 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 17, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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-2
B: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,9603
Polymers99,8662
Non-polymers941
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-13 kcal/mol
Surface area35960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.261, 107.880, 68.723
Angle α, β, γ (deg.)90.000, 107.460, 90.000
Int Tables number4
Space group name H-MP1211

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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: 97300.000 Da / Num. of mol.: 1 / Mutation: M364A, I365A, S387D
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*AP*AP*AP*AP*AP*AP*AP*U)-3')


Mass: 2565.649 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-IPH / PHENOL / Phenol


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


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAuthors state that the protein is bound to a heterogenous mix of RNAs, so RNA was modeled as a poly- ...Authors state that the protein is bound to a heterogenous mix of RNAs, so RNA was modeled as a poly-A (other than the 3'-terminal U), as that fits in the density. The central part of the RNA is disordered, and because the protein is bound to many different RNA sequences, a defined RNA sequence can not be provided.

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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: 2.24 Å3/Da / Density % sol: 45.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 12% PEG 3350, 0.1 M phenol, 12% isopropanol, 0.1 M tris, pH 9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.1→66 Å / Num. obs: 14855 / % possible obs: 94.5 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 9
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.4 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
SCALAdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OLA

4ola


Resolution: 3.12→65.555 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.32
RfactorNum. reflection% reflectionSelection details
Rfree0.2822 739 4.99 %Random selection
Rwork0.2522 ---
obs0.2537 14815 94.15 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 178.81 Å2 / Biso mean: 76.5462 Å2 / Biso min: 12.88 Å2
Refinement stepCycle: final / Resolution: 3.12→65.555 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6139 155 23 23 6340
Biso mean--125.81 39.86 -
Num. residues----771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026484
X-RAY DIFFRACTIONf_angle_d0.578807
X-RAY DIFFRACTIONf_chiral_restr0.039986
X-RAY DIFFRACTIONf_plane_restr0.0041099
X-RAY DIFFRACTIONf_dihedral_angle_d14.0343903
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1201-3.3610.35711500.30452845299596
3.361-3.69920.32571390.28752864300396
3.6992-4.23440.30261480.25712836298495
4.2344-5.33450.25441460.22072814296094
5.3345-65.56970.24821560.24182717287390
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)
11.6990.73810.49380.3556-0.09111.91180.038-0.5336-0.57760.3159-0.3834-0.18880.56690.0783-0.31920.3584-0.0617-0.23640.52-0.07170.3499-9.18610.781292.394
23.92392.742-1.4943.5845-2.25924.21070.68140.2264-0.2374-0.6524-0.5460.92270.1319-0.3921-0.09491.320.2804-0.02350.42330.08550.9254-19.4318-20.895677.9956
35.1157-1.65212.23556.21561.44912.9302-0.2130.2145-0.7347-0.36790.19630.66721.00690.086-0.16950.50070.155-0.06380.39730.02810.4443-14.1766-17.813585.6291
47.16171.1369-0.16058.03070.93942.0132-0.14650.3421-0.27990.1641-0.36980.18520.2329-1.16970.25661.35430.1174-0.56610.9402-0.29371.175-13.2938-29.783778.0262
52.5753-0.1798-0.42534.0192-0.30842.25180.4117-0.165-0.2771-0.35290.1014-0.92060.1150.6594-0.24350.55970.0117-0.17730.4005-0.00210.419-13.9219-3.60183.9327
63.5222-1.8229-0.53353.05971.8683.69420.0412-0.7536-0.0698-0.13840.1182-0.4008-0.34850.3532-0.18480.61330.0041-0.13320.49930.04520.3435-12.3929-4.78846.724
72.63070.0110.75873.93060.71670.4771-0.15210.06660.76480.05330.06760.65280.0042-0.2490.08150.37040.0014-0.0610.4666-0.08380.3731-15.251619.214386.8453
81.4333-0.73150.64521.45830.05192.941-0.0581.41221.4013-1.021-0.3913-0.3839-0.70490.63690.27290.94710.0286-0.09461.05380.45290.80554.32438.269857.2942
92.9608-0.7780.75743.1464-1.06251.786-0.1080.15140.7827-0.4348-0.2321-0.7341-0.08050.65910.29330.33180.122-0.08450.62990.04920.73559.966726.575279.1717
101.64581.81710.15942.03630.55643.30930.3901-0.30540.30140.37090.24740.04310.0650.97840.04521.34780.37740.32330.8307-0.16910.50959.2576.092868.7912
114.38080.76270.14112.3867-0.24932.2673-0.1221-0.0652-0.48930.0016-0.0214-0.18520.12050.060.14270.33460.0457-0.14360.2466-0.08230.31734.419116.028285.4132
122.766-1.66070.05014.73211.42623.13820.3850.68230.3336-1.2452-0.1102-0.5682-0.65670.24760.6990.17760.0071-0.20260.46820.12640.63986.920423.3674.7814
135.6966-0.2362-2.6430.8745-0.63165.6128-0.1651.38330.1582-1.78350.3471-0.11141.7663-0.7477-0.27490.7636-0.0471-0.0950.5970.0680.5279-7.336525.692669.3841
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 23:64)A23 - 64
2X-RAY DIFFRACTION2(chain A and resid 65:90)A65 - 90
3X-RAY DIFFRACTION3(chain A and resid 91:108)A91 - 108
4X-RAY DIFFRACTION4(chain A and resid 109:127)A109 - 127
5X-RAY DIFFRACTION5(chain A and resid 128:224)A128 - 224
6X-RAY DIFFRACTION6(chain A and resid 225:369)A225 - 369
7X-RAY DIFFRACTION7(chain A and resid 370:440)A370 - 440
8X-RAY DIFFRACTION8(chain A and resid 441:565)A441 - 565
9X-RAY DIFFRACTION9(chain A and resid 566:629)A566 - 629
10X-RAY DIFFRACTION10(chain A and resid 630:637)A630 - 637
11X-RAY DIFFRACTION11(chain A and resid 638:772)A638 - 772
12X-RAY DIFFRACTION12(chain A and resid 773:859)A773 - 859
13X-RAY DIFFRACTION13(chain B and resid 1:7)B1 - 7

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