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- PDB-5w6v: The Structure of human Argonaute-1 in complex with the hook motif... -

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Basic information

Entry
Database: PDB / ID: 5w6v
TitleThe Structure of human Argonaute-1 in complex with the hook motif of human GW182
Components
  • Protein argonaute-1
  • RNA (5'-R(P*AP*AP*UP*AP*UP*UP*AP*AP*AP*A)-3')
  • Trinucleotide repeat-containing gene 6A protein
KeywordsGENE REGULATION/RNA / RNA interference / RNA binding proteins / GW motif / GENE REGULATION-RNA complex
Function / homology
Function and homology information


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 / Small interfering RNA (siRNA) biogenesis / Transcriptional Regulation by MECP2 / RNA secondary structure unwinding / RISC-loading complex / miRNA-mediated post-transcriptional gene silencing ...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 / Small interfering RNA (siRNA) biogenesis / Transcriptional Regulation by MECP2 / RNA secondary structure unwinding / RISC-loading complex / miRNA-mediated post-transcriptional gene silencing / endoderm development / RISC complex assembly / miRNA processing / pre-miRNA processing / miRNA-mediated gene silencing by inhibition of translation / RISC complex / miRNA binding / Regulation of RUNX1 Expression and Activity / nuclear-transcribed mRNA catabolic process / MicroRNA (miRNA) biogenesis / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / RNA polymerase II complex binding / Regulation of MECP2 expression and activity / Transcriptional Regulation by VENTX / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / core promoter sequence-specific DNA binding / cellular response to starvation / negative regulation of angiogenesis / P-body / TP53 Regulates Metabolic Genes / Transcriptional regulation by small RNAs / MAPK6/MAPK4 signaling / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Oncogene Induced Senescence / cytoplasmic ribonucleoprotein granule / Pre-NOTCH Transcription and Translation / double-stranded RNA binding / Ca2+ pathway / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / single-stranded RNA binding / intracellular membrane-bounded organelle / Golgi apparatus / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
TNRC6A, RNA recognition motif / TNRC6, PABC binding domain / TNRC6-PABC binding domain / Argonaute hook domain / Argonaute hook / paz domain / Protein argonaute, Mid domain / Argonaute-like, PIWI domain / Mid domain of argonaute / paz domain ...TNRC6A, RNA recognition motif / TNRC6, PABC binding domain / TNRC6-PABC binding domain / Argonaute hook domain / Argonaute hook / 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 / RNA-binding domain superfamily / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Trinucleotide repeat-containing gene 6A protein / Protein argonaute-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Spodoptera frugiperda (fall armyworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.828 Å
AuthorsElkayam, E. / Faehnle, C.R. / Joshua-Tor, L.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Mol. Cell / Year: 2017
Title: Multivalent Recruitment of Human Argonaute by GW182.
Authors: Elkayam, E. / Faehnle, C.R. / Morales, M. / Sun, J. / Li, H. / Joshua-Tor, L.
History
DepositionJun 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Aug 23, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Aug 30, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.5Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Oct 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-1
R: RNA (5'-R(P*AP*AP*UP*AP*UP*UP*AP*AP*AP*A)-3')
B: Trinucleotide repeat-containing gene 6A protein


Theoretical massNumber of molelcules
Total (without water)103,8943
Polymers103,8943
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-35 kcal/mol
Surface area38120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.750, 136.861, 86.054
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Protein argonaute-1 / hAgo1 / Argonaute RISC catalytic component 1 / Eukaryotic translation initiation factor 2C 1 / ...hAgo1 / Argonaute RISC catalytic component 1 / Eukaryotic translation initiation factor 2C 1 / eIF2C 1 / RNA-binding protein Q99


Mass: 97477.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGO1, EIF2C1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UL18
#2: RNA chain RNA (5'-R(P*AP*AP*UP*AP*UP*UP*AP*AP*AP*A)-3')


Mass: 4029.030 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spodoptera frugiperda (fall armyworm)
#3: Protein/peptide Trinucleotide repeat-containing gene 6A protein / CAG repeat protein 26 / EMSY interactor protein / GW182 autoantigen / Protein GW1 / Glycine- ...CAG repeat protein 26 / EMSY interactor protein / GW182 autoantigen / Protein GW1 / Glycine-tryptophan protein of 182 kDa


Mass: 2387.495 Da / Num. of mol.: 1 / Fragment: hook motif (UNP residues 820-841)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNRC6A, CAGH26, KIAA1460, TNRC6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NDV7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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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: 2.68 Å3/Da / Density % sol: 54.14 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 21.2% w/v PEG3350, 0.1 M di-ammonium tartrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 13, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.828→136.861 Å / Num. obs: 27125 / % possible obs: 99.9 % / Redundancy: 4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.045 / Rrim(I) all: 0.092 / Net I/σ(I): 16.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
2.828-2.8374.10.5492.50.7910.4140.634100
13.121-136.8610.0230.9990.0240.028

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XSCALEdata scaling
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4KRE

4kre


Resolution: 2.828→77.344 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2448 1393 5.14 %
Rwork0.2 --
obs0.2022 27079 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.828→77.344 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6533 215 0 4 6752
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026939
X-RAY DIFFRACTIONf_angle_d0.6279447
X-RAY DIFFRACTIONf_dihedral_angle_d12.1654182
X-RAY DIFFRACTIONf_chiral_restr0.0461047
X-RAY DIFFRACTIONf_plane_restr0.0041175
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8278-2.92880.30091460.27992509X-RAY DIFFRACTION100
2.9288-3.04610.29011340.27192526X-RAY DIFFRACTION100
3.0461-3.18470.33011570.26492530X-RAY DIFFRACTION100
3.1847-3.35260.25441330.23192533X-RAY DIFFRACTION100
3.3526-3.56270.28911340.21962542X-RAY DIFFRACTION100
3.5627-3.83780.28471300.19922545X-RAY DIFFRACTION100
3.8378-4.22390.2411390.17612575X-RAY DIFFRACTION100
4.2239-4.83510.18521380.15822585X-RAY DIFFRACTION100
4.8351-6.09130.22261450.17742604X-RAY DIFFRACTION100
6.0913-77.37290.21481370.1962737X-RAY DIFFRACTION99
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)
11.3740.16740.19842.75550.55752.87930.02130.3861-0.039-0.79820.05430.2044-0.199-0.3787-0.06490.4535-0.0224-0.0870.47610.09120.349217.42242.5765-16.4334
21.6298-0.03470.52653.49270.44582.6239-0.05820.2709-0.0831-0.56130.01020.1693-0.0511-0.08740.06110.3564-0.02560.02430.37170.01860.359621.329736.4499-12.1738
30.13740.107-0.13982.1342-1.79175.0698-0.1206-0.12460.00520.61510.15450.1755-0.1261-0.30150.01030.43470.02030.14580.34690.00910.62225.78570.6699-7.913
44.1194-0.57530.63714.8297-0.22883.9899-0.52970.4839-0.1676-1.42130.47810.50390.1988-0.15230.12221.0444-0.1007-0.0940.45640.04330.69920.6323-0.2687-22.9787
50.0317-0.0518-0.14621.53840.57681.6529-0.07380.0023-0.1475-0.04530.0869-0.25090.09390.2235-0.05470.2774-0.02120.04520.40770.05220.601730.513831.8969-4.4208
61.30380.31470.23213.29210.41171.91540.2799-0.4248-0.54370.7277-0.2019-0.25530.44730.1601-0.10370.6661-0.0756-0.16050.53260.15850.503320.586311.590632.4982
72.6479-0.38520.40274.0925-0.5692.40690.036-0.0447-0.05760.29020.0190.2868-0.04840.1072-0.08920.2895-0.06520.02550.38540.03830.31719.661527.430621.8026
84.88571.0802-1.33212.4286-0.47162.0956-0.00150.0370.1870.11230.04880.2443-0.1719-0.2236-0.06630.24920.011-0.01920.2484-0.0210.24611.707938.477815.2125
92.48991.7218-0.18256.57-0.17822.38580.1406-0.0932-0.34070.3557-0.0740.3350.2096-0.2405-0.01010.2674-0.0082-0.02180.40430.02540.33411.717323.470220.6494
101.40310.6528-1.18953.0208-0.23511.03640.13890.7922-0.4818-1.07410.3138-0.01210.7939-0.7356-0.5510.74540.0423-0.15870.71680.04530.498825.157822.171214.1015
114.902-2.48532.04611.3786-1.12191.0054-0.3579-0.6177-0.60590.43540.5521-0.20960.2135-0.46870.01610.6814-0.00490.15720.74060.04090.7475-3.258436.177836.2545
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 23:110)
2X-RAY DIFFRACTION2chain 'A' and (resseq 111:224)
3X-RAY DIFFRACTION3chain 'A' and (resseq 225:262)
4X-RAY DIFFRACTION4chain 'A' and (resseq 263:336)
5X-RAY DIFFRACTION5chain 'A' and (resseq 337:411)
6X-RAY DIFFRACTION6chain 'A' and (resseq 412:556)
7X-RAY DIFFRACTION7chain 'A' and (resseq 557:641)
8X-RAY DIFFRACTION8chain 'A' and (resseq 642:775)
9X-RAY DIFFRACTION9chain 'A' and (resseq 776:857)
10X-RAY DIFFRACTION10chain 'R' and (resseq 1:9)
11X-RAY DIFFRACTION11chain 'B' and (resseq 823:839)

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