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- PDB-9vlc: hAGO2-MID in complex with a chemical modified uridine monophosphate -

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Basic information

Entry
Database: PDB / ID: 9vlc
TitlehAGO2-MID in complex with a chemical modified uridine monophosphate
ComponentsProtein argonaute-2
KeywordsRNA BINDING PROTEIN / Argonaute / chemical modification
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 / 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 / miRNA-mediated gene silencing by mRNA destabilization ...: / endoribonuclease activity, cleaving miRNA-paired mRNA / endoribonuclease activity, cleaving siRNA-paired mRNA / siRNA-mediated gene silencing by mRNA destabilization / 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 / miRNA-mediated gene silencing by mRNA destabilization / negative regulation of amyloid precursor protein biosynthetic process / Small interfering RNA (siRNA) biogenesis / Regulation of CDH1 mRNA translation by microRNAs / positive regulation of trophoblast cell migration / Transcriptional Regulation by MECP2 / Regulation of PD-L1(CD274) translation / RISC-loading complex / mRNA cap binding / miRNA processing / RISC complex assembly / regulatory ncRNA-mediated post-transcriptional gene silencing / miRNA-mediated gene silencing by inhibition of translation / RNA 7-methylguanosine cap binding / pre-miRNA processing / regulation of synapse maturation / siRNA binding / mRNA 3'-UTR AU-rich region binding / M-decay: degradation of maternal mRNAs by maternally stored factors / Regulation of MITF-M-dependent genes involved in apoptosis / RISC complex / TGFBR3 expression / regulatory ncRNA-mediated gene silencing / Regulation of RUNX1 Expression and Activity / P-body assembly / miRNA binding / 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 / core promoter sequence-specific DNA binding / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / Nuclear events stimulated by ALK signaling in cancer / RNA endonuclease activity / translation initiation factor activity / negative regulation of translational initiation / 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 / dendrite / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / DNA-templated transcription / RNA binding / extracellular exosome / nucleoplasm / membrane / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Protein argonaute-2 / 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 ...Protein argonaute-2 / 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 / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
: / Protein argonaute-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsYao, Y.Q. / Ma, J.B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: hAGO2-MID in complex with a chemical modified uridine monophosphate
Authors: Yao, Y.Q. / Ma, J.B.
History
DepositionJun 25, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 1, 2026Provider: 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)46,4496
Polymers45,0323
Non-polymers1,4173
Water1,54986
1
A: Protein argonaute-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4832
Polymers15,0111
Non-polymers4721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein argonaute-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4832
Polymers15,0111
Non-polymers4721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein argonaute-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4832
Polymers15,0111
Non-polymers4721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.404, 46.763, 66.240
Angle α, β, γ (deg.)86.70, 73.76, 84.53
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: 15010.672 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 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9UKV8, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#2: Chemical ChemComp-A1ESK / 3-[3-[1-[(2R,3R,4S,5R)-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-2,4-bis(oxidanylidene)pyrimidin-5-yl]phenyl]propanoic acid


Mass: 472.340 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H21N2O11P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.65 Å3/Da / Density % sol: 53.67 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 0.25M Ammonium sulfate 0.1M Sodium cacodylate trihydrate pH 6.5 30% w/v Polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.09→63.56 Å / Num. obs: 26547 / % possible obs: 96.1 % / Redundancy: 2.4 % / CC1/2: 0.991 / Net I/σ(I): 5.1
Reflection shellResolution: 2.09→2.2 Å / Num. unique obs: 3852 / CC1/2: 0.861

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→63.56 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.887 / SU B: 7.301 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.238 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27864 1277 4.8 %RANDOM
Rwork0.21076 ---
obs0.214 25269 96.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.173 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å21.03 Å2-0.38 Å2
2--1.11 Å22.13 Å2
3----1.32 Å2
Refinement stepCycle: 1 / Resolution: 2.09→63.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3162 0 64 86 3312
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133300
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153246
X-RAY DIFFRACTIONr_angle_refined_deg1.6181.6444470
X-RAY DIFFRACTIONr_angle_other_deg1.3081.6027476
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4865402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.26222.5144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.20415591
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0591518
X-RAY DIFFRACTIONr_chiral_restr0.0780.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023744
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02732
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9293.1261617
X-RAY DIFFRACTIONr_mcbond_other2.9283.1221616
X-RAY DIFFRACTIONr_mcangle_it4.4264.6652016
X-RAY DIFFRACTIONr_mcangle_other4.4254.672017
X-RAY DIFFRACTIONr_scbond_it3.4163.6141683
X-RAY DIFFRACTIONr_scbond_other3.43.6121682
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2475.2362455
X-RAY DIFFRACTIONr_long_range_B_refined7.3837.1933497
X-RAY DIFFRACTIONr_long_range_B_other7.38637.1983493
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.09→2.14 Å
RfactorNum. reflection% reflection
Rfree0.35 101 -
Rwork0.3 1885 -
obs--95.48 %

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