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- PDB-9bf2: MID domain of Ago2 bound to UMP -

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Basic information

Entry
Database: PDB / ID: 9bf2
TitleMID domain of Ago2 bound to UMP
ComponentsProtein argonaute-2
KeywordsRNA BINDING PROTEIN / Argonaute2 / RNA binding
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 / Transcriptional Regulation by MECP2 / positive regulation of trophoblast cell migration / RNA secondary structure unwinding / RISC-loading complex / miRNA metabolic process / mRNA cap binding / RISC complex assembly / mRNA 3'-UTR AU-rich region binding / regulatory ncRNA-mediated post-transcriptional gene silencing / miRNA-mediated gene silencing by inhibition of translation / miRNA processing / RNA 7-methylguanosine cap binding / siRNA binding / pre-miRNA processing / M-decay: degradation of maternal mRNAs by maternally stored factors / regulatory ncRNA-mediated gene silencing / siRNA processing / 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 / negative regulation of translational initiation / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / 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 / single-stranded RNA binding / translation / dendrite / positive regulation of transcription by RNA polymerase II / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / metal ion binding / cytoplasm / cytosol
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'-MONOPHOSPHATE / Protein argonaute-2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.59 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)46,3476
Polymers45,3743
Non-polymers9733
Water8,539474
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.608, 46.339, 64.920
Angle α, β, γ (deg.)87.58, 74.68, 85.87
Int Tables number1
Space group name H-MP1
Symmetry operation#1: x,y,z

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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: 15124.774 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-U / URIDINE-5'-MONOPHOSPHATE


Type: RNA linking / Mass: 324.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H13N2O9P / Source: (synth.) synthetic construct (others) / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 474 / 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: 2.53 Å3/Da / Density % sol: 51.29 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: Drop was 1:1 15 mg/ml MID-UMP and 1.4M sodium citrate tribasic dihydrate, 0.1M HEPES pH7.5

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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: Jan 6, 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: 1.59→21.58 Å / Num. obs: 118253 / % possible obs: 99.17 % / Redundancy: 7.2 % / Biso Wilson estimate: 13.01 Å2 / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 15.2
Reflection shellResolution: 1.59→1.652 Å / Mean I/σ(I) obs: 1.98 / Num. unique obs: 11241 / CC1/2: 0.587

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.59→21.58 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1869 5665 4.83 %
Rwork0.1633 --
obs0.1645 117363 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.59→21.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3061 0 63 474 3598
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153197
X-RAY DIFFRACTIONf_angle_d1.2884335
X-RAY DIFFRACTIONf_dihedral_angle_d14.8291215
X-RAY DIFFRACTIONf_chiral_restr0.093506
X-RAY DIFFRACTIONf_plane_restr0.009543
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.610.24711320.27543120X-RAY DIFFRACTION84
1.61-1.630.29321880.25563813X-RAY DIFFRACTION100
1.63-1.650.28131890.24713793X-RAY DIFFRACTION100
1.65-1.670.27351840.24623701X-RAY DIFFRACTION100
1.67-1.690.26921850.23233726X-RAY DIFFRACTION100
1.69-1.720.24542200.22533779X-RAY DIFFRACTION100
1.72-1.740.23561660.22073665X-RAY DIFFRACTION100
1.74-1.770.22861960.20943746X-RAY DIFFRACTION100
1.77-1.80.24651620.19823879X-RAY DIFFRACTION100
1.8-1.830.22551800.19843620X-RAY DIFFRACTION100
1.83-1.860.22051720.19363849X-RAY DIFFRACTION100
1.86-1.890.1991700.18823806X-RAY DIFFRACTION100
1.89-1.930.26322100.18943644X-RAY DIFFRACTION99
1.93-1.970.20392020.17433787X-RAY DIFFRACTION100
1.97-2.010.18821900.16193716X-RAY DIFFRACTION100
2.01-2.060.19132160.16433679X-RAY DIFFRACTION100
2.06-2.110.19861870.15563773X-RAY DIFFRACTION99
2.11-2.160.16921960.14573713X-RAY DIFFRACTION100
2.16-2.230.17191800.14433727X-RAY DIFFRACTION100
2.23-2.30.19871910.1563732X-RAY DIFFRACTION99
2.3-2.380.16171640.14973763X-RAY DIFFRACTION100
2.38-2.480.19662200.1563736X-RAY DIFFRACTION100
2.48-2.590.16151940.1593755X-RAY DIFFRACTION100
2.59-2.730.18362060.16313720X-RAY DIFFRACTION100
2.73-2.90.23491820.1613808X-RAY DIFFRACTION100
2.9-3.120.14812080.15373700X-RAY DIFFRACTION100
3.12-3.430.17451740.14543741X-RAY DIFFRACTION100
3.43-3.920.1531930.13123792X-RAY DIFFRACTION100
3.93-4.940.12991940.12193740X-RAY DIFFRACTION100
4.94-21.580.16832140.15433675X-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)
11.4516-0.5174-0.18240.94180.00481.05660.01550.0087-0.017-0.0592-0.03210.04380.0087-0.11520.01830.05870.00660.00550.0718-0.01140.0736-23.54990.5615-14.3213
20.77170.13570.19181.60490.45770.9062-0.06840.02980.0072-0.12590.0957-0.0517-0.01740.0704-0.02620.0837-0.01470.01070.05450.00390.071-4.895819.4057-32.065
30.83120.01640.3531.0503-0.06811.75040.0781-0.0295-0.0420.09750.01210.0897-0.0297-0.3536-0.04920.0593-0.0070.00630.12970.01030.0853-20.0483-4.1114-50.1941
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 442:573

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