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- PDB-9bf0: MID domain of human Argo2 bound to UTP -

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Basic information

Entry
Database: PDB / ID: 9bf0
TitleMID domain of human Argo2 bound to UTP
ComponentsProtein argonaute-2
KeywordsRNA BINDING PROTEIN / MID domain / Argonaute2
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 / Regulation of CDH11 mRNA translation by microRNAs / miRNA-mediated gene silencing by mRNA destabilization / 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 / Regulation of CDH11 mRNA translation by microRNAs / miRNA-mediated gene silencing by mRNA destabilization / 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 / positive regulation of trophoblast cell migration / Transcriptional Regulation by MECP2 / RNA secondary structure unwinding / RISC-loading complex / miRNA metabolic process / mRNA cap binding / RISC complex assembly / regulatory ncRNA-mediated post-transcriptional gene silencing / miRNA processing / miRNA-mediated gene silencing by inhibition of translation / regulation of synapse maturation / pre-miRNA processing / RNA 7-methylguanosine cap binding / mRNA 3'-UTR AU-rich region binding / siRNA binding / siRNA processing / Regulation of MITF-M-dependent genes involved in apoptosis / M-decay: degradation of maternal mRNAs by maternally stored factors / P-body assembly / regulatory ncRNA-mediated gene silencing / RISC complex / Regulation of RUNX1 Expression and Activity / MicroRNA (miRNA) biogenesis / miRNA binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA polymerase II complex binding / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Regulation of MECP2 expression and activity / Nuclear events stimulated by ALK signaling in cancer / core promoter sequence-specific DNA binding / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / negative regulation of translational initiation / RNA endonuclease activity / translation initiation factor activity / post-embryonic development / positive regulation of translation / TP53 Regulates Metabolic Genes / Transcriptional regulation by small RNAs / P-body / MAPK6/MAPK4 signaling / Pre-NOTCH Transcription and Translation / cytoplasmic ribonucleoprotein granule / positive regulation of angiogenesis / double-stranded RNA binding / Ca2+ pathway / Estrogen-dependent gene expression / postsynapse / single-stranded RNA binding / translation / glutamatergic synapse / dendrite / positive regulation of transcription by RNA polymerase II / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Protein argonaute-2 / Protein argonaute, Mid domain / Argonaute-like, PIWI domain / Mid domain of argonaute / Argonaute linker 2 domain / Protein argonaute, N-terminal / N-terminal domain of argonaute / Argonaute linker 2 domain / DUF1785 / Argonaute, linker 1 domain ...Protein argonaute-2 / Protein argonaute, Mid domain / Argonaute-like, PIWI domain / Mid domain of argonaute / 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 profile. / PAZ domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
URIDINE 5'-TRIPHOSPHATE / Protein argonaute-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsHarp, J.M. / Egli, M.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Curr Protoc / Year: 2024
Title: Structure and Stability of Ago2 MID-Nucleotide Complexes: All-in-One (Drop) His 6 -SUMO Tag Removal, Nucleotide Binding, and Crystal Growth.
Authors: Lei, L. / Harp, J.M. / Chaput, J.C. / Wassarman, K. / Schlegel, M.K. / Manoharan, M. / Egli, M.
History
DepositionApr 16, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 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-2
B: Protein argonaute-2
C: Protein argonaute-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0556
Polymers44,6023
Non-polymers1,4523
Water6,485360
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.106, 46.511, 65.240
Angle α, β, γ (deg.)87.78, 74.53, 85.41
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Protein argonaute-2 / Argonaute2 / hAgo2 / Argonaute RISC catalytic component 2 / Eukaryotic translation initiation ...Argonaute2 / hAgo2 / Argonaute RISC catalytic component 2 / Eukaryotic translation initiation factor 2C 2 / eIF-2C 2 / eIF2C 2 / PAZ Piwi domain protein / PPD / Protein slicer


Mass: 14867.465 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGO2, EIF2C2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UKV8, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#2: Chemical ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE


Mass: 484.141 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: UTP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.62 Å3/Da / Density % sol: 53.07 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: drop was 1:1 15 mg/ml protein with RNA: 1.4 M Sodium citrate tribasic dihydrate, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: Excillum MetalJet D2+ 70 kV / Wavelength: 1.3418 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Aug 19, 2022
RadiationMonochromator: Helios MX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3418 Å / Relative weight: 1
ReflectionResolution: 1.78→20.53 Å / Num. obs: 86315 / % possible obs: 98.88 % / Redundancy: 3.9 % / CC1/2: 0.994 / CC star: 0.999 / Net I/σ(I): 5.72
Reflection shellResolution: 1.78→1.844 Å / Num. unique obs: 8459 / CC1/2: 0.273 / CC star: 0.655

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
PROTEUM PLUSdata reduction
SAINTdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→20.53 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2336 4221 4.92 %
Rwork0.1884 --
obs0.1905 85818 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.78→20.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3076 0 87 360 3523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063233
X-RAY DIFFRACTIONf_angle_d0.7374395
X-RAY DIFFRACTIONf_dihedral_angle_d18.2751199
X-RAY DIFFRACTIONf_chiral_restr0.051506
X-RAY DIFFRACTIONf_plane_restr0.005546
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.80.48661450.39042662X-RAY DIFFRACTION97
1.8-1.820.42691390.37852725X-RAY DIFFRACTION98
1.82-1.840.37471450.34832632X-RAY DIFFRACTION98
1.84-1.870.34331800.34962641X-RAY DIFFRACTION99
1.87-1.890.3871380.33252738X-RAY DIFFRACTION99
1.89-1.920.34741760.31742708X-RAY DIFFRACTION99
1.92-1.940.34511620.3142640X-RAY DIFFRACTION98
1.94-1.970.34971740.28752682X-RAY DIFFRACTION98
1.97-20.30611560.27712738X-RAY DIFFRACTION99
2-2.040.351320.26562708X-RAY DIFFRACTION98
2.04-2.070.28371770.24622597X-RAY DIFFRACTION98
2.07-2.110.27931390.22862782X-RAY DIFFRACTION99
2.11-2.150.25511680.2262633X-RAY DIFFRACTION99
2.15-2.190.21891280.20172772X-RAY DIFFRACTION99
2.19-2.240.26881500.19592719X-RAY DIFFRACTION99
2.24-2.290.24781160.20052689X-RAY DIFFRACTION99
2.29-2.350.23661200.19722826X-RAY DIFFRACTION99
2.35-2.420.24641340.19412682X-RAY DIFFRACTION99
2.42-2.490.2621360.19332776X-RAY DIFFRACTION100
2.49-2.570.26361200.19812788X-RAY DIFFRACTION100
2.57-2.660.27411360.19792704X-RAY DIFFRACTION99
2.66-2.760.20331620.19112691X-RAY DIFFRACTION99
2.76-2.890.26831040.18252803X-RAY DIFFRACTION100
2.89-3.040.22021080.17252775X-RAY DIFFRACTION100
3.04-3.230.251440.17372699X-RAY DIFFRACTION100
3.23-3.480.19951400.14492752X-RAY DIFFRACTION100
3.48-3.830.18361000.13412762X-RAY DIFFRACTION99
3.83-4.380.12371000.12042784X-RAY DIFFRACTION100
4.38-5.50.13011320.12162778X-RAY DIFFRACTION100
5.5-20.530.16881600.15782711X-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)
10.9770.26250.35182.2320.62781.2259-0.06330.02420.0156-0.09370.08070.0045-0.00480.0825-0.00130.1181-0.00930.00930.0880.00630.113328.942837.998431.7333
21.7587-0.96390.01161.3399-0.04581.20950.02410.0011-0.0337-0.1102-0.03010.03070.0141-0.0827-0.00220.0920.00350.01350.0992-0.00860.10349.761518.955449.4523
31.58970.11060.28391.3999-0.11712.39280.0766-0.0193-0.0590.13130.00290.08870.0696-0.31120.00770.1093-0.0082-0.00240.15470.00610.130113.29714.509113.3125
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resseq 442:572
2X-RAY DIFFRACTION2chain B and resseq 442:572
3X-RAY DIFFRACTION3chain C and resseq 442:575

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