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

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Basic information

Entry
Database: PDB / ID: 9lmz
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
: / (4S)-4-amino-5-hydroxypentanamide / Protein argonaute-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYao, Y.Q. / Ma, J.B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971130 China
CitationJournal: To Be Published
Title: hAGO2-MID in complex with a chemical modified uridine monophosphate
Authors: Yao, Y.Q. / Ma, J.B.
History
DepositionJan 20, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)47,0747
Polymers45,8013
Non-polymers1,2734
Water5,999333
1
A: Protein argonaute-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6472
Polymers15,2671
Non-polymers3801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein argonaute-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7793
Polymers15,2671
Non-polymers5122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein argonaute-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6472
Polymers15,2671
Non-polymers3801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.561, 46.536, 66.277
Angle α, β, γ (deg.)86.95, 73.95, 85.04
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: 15266.931 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-A1EY1 / [(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)thieno[2,3-d]pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate


Type: RNA linking / Mass: 380.268 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H13N2O9PS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ECC / (4S)-4-amino-5-hydroxypentanamide


Type: L-peptide linking / Mass: 132.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.61 Å3/Da / Density % sol: 52.94 %
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: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.8→46.34 Å / Num. obs: 40082 / % possible obs: 93 % / Redundancy: 1.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.034 / Rrim(I) all: 0.049 / Χ2: 0.29 / Net I/σ(I): 6.9
Reflection shellResolution: 1.8→1.9 Å / Num. unique obs: 5883 / CC1/2: 0.902

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→46.34 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 2.03 / Phase error: 20.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2061 1973 4.92 %
Rwork0.1745 --
obs0.176 40080 92.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→46.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3159 0 81 333 3573
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083302
X-RAY DIFFRACTIONf_angle_d1.1014473
X-RAY DIFFRACTIONf_dihedral_angle_d23.381488
X-RAY DIFFRACTIONf_chiral_restr0.062516
X-RAY DIFFRACTIONf_plane_restr0.007602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.26851210.23412781X-RAY DIFFRACTION93
1.84-1.890.26521210.21422733X-RAY DIFFRACTION94
1.89-1.950.22531350.19532778X-RAY DIFFRACTION94
1.95-2.010.24711460.17952760X-RAY DIFFRACTION94
2.01-2.080.20331350.18522712X-RAY DIFFRACTION94
2.08-2.170.21721410.1812749X-RAY DIFFRACTION93
2.17-2.270.21611500.17192733X-RAY DIFFRACTION93
2.27-2.390.22121340.17782728X-RAY DIFFRACTION93
2.39-2.530.21531320.1772713X-RAY DIFFRACTION93
2.53-2.730.23251590.18222704X-RAY DIFFRACTION93
2.73-30.21481630.17822674X-RAY DIFFRACTION92
3-3.440.19091520.17392672X-RAY DIFFRACTION91
3.44-4.330.17781530.14812654X-RAY DIFFRACTION91
4.33-46.340.18181310.16692716X-RAY DIFFRACTION92

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