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- PDB-3lug: Crystal structure of MID domain from hAGO2 in complex with CMP -

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Basic information

Entry
Database: PDB / ID: 3lug
TitleCrystal structure of MID domain from hAGO2 in complex with CMP
ComponentsProtein argonaute-2
KeywordsRNA BINDING PROTEIN / MID domain / Ribonucleoprotein / RNA-binding / RNA-mediated gene silencing / Translation regulation
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 / miRNA-mediated gene silencing by mRNA destabilization / 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 ...: / endoribonuclease activity, cleaving miRNA-paired mRNA / endoribonuclease activity, cleaving siRNA-paired mRNA / siRNA-mediated gene silencing by mRNA destabilization / miRNA-mediated gene silencing by mRNA destabilization / 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 / 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 / miRNA metabolic process / RISC-loading complex / mRNA cap binding / regulatory ncRNA-mediated post-transcriptional gene silencing / : / RISC complex assembly / mRNA 3'-UTR AU-rich region binding / miRNA processing / pre-miRNA processing / miRNA-mediated gene silencing by inhibition of translation / siRNA processing / RNA 7-methylguanosine cap binding / siRNA binding / M-decay: degradation of maternal mRNAs by maternally stored factors / regulatory ncRNA-mediated gene silencing / RISC complex / miRNA binding / Regulation of RUNX1 Expression and Activity / 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 / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / negative regulation of translational initiation / core promoter sequence-specific DNA binding / RNA endonuclease activity / translation initiation factor activity / post-embryonic development / positive regulation of translation / P-body / TP53 Regulates Metabolic Genes / Transcriptional regulation by small RNAs / MAPK6/MAPK4 signaling / cytoplasmic ribonucleoprotein granule / Pre-NOTCH Transcription and Translation / 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 / metal ion binding / nucleus / 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 / PAZ domain profile. / Response regulator / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CYTIDINE-5'-MONOPHOSPHATE / PHOSPHATE ION / Protein argonaute-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.849 Å
AuthorsFrank, F. / Sonenberg, N. / Nagar, B.
CitationJournal: Nature / Year: 2010
Title: Structural basis for 5'-nucleotide base-specific recognition of guide RNA by human AGO2.
Authors: Frank, F. / Sonenberg, N. / Nagar, B.
History
DepositionFeb 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)47,42211
Polymers45,9783
Non-polymers1,4448
Water6,972387
1
A: Protein argonaute-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7443
Polymers15,3261
Non-polymers4182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein argonaute-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8394
Polymers15,3261
Non-polymers5133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protein argonaute-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8394
Polymers15,3261
Non-polymers5133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.503, 47.306, 66.403
Angle α, β, γ (deg.)86.06, 72.80, 83.18
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 15325.955 Da / Num. of mol.: 3 / Fragment: MID domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2C2, AGO2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UKV8
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE / Cytidine monophosphate


Mass: 323.197 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H14N3O8P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 387 / 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: 2.62 Å3/Da / Density % sol: 53.11 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M imidazole, 0.2 M NaCl, 0.46 M NaH2PO4, 1.84 M K2HPO4. Protein: 15 mg/mL, pH 8.0, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 6, 2009
RadiationMonochromator: VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.849→30 Å / Num. obs: 30819 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.849→2.07 Å / % possible all: 83

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.5_2)refinement
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.849→24.208 Å / SU ML: 0.27 / σ(F): 0.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2248 1850 6 %
Rwork0.1824 --
obs0.1848 30819 77.17 %
all-30819 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.955 Å2 / ksol: 0.4 e/Å3
Refinement stepCycle: LAST / Resolution: 1.849→24.208 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3116 0 40 387 3543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083208
X-RAY DIFFRACTIONf_angle_d1.084340
X-RAY DIFFRACTIONf_dihedral_angle_d16.8841197
X-RAY DIFFRACTIONf_chiral_restr0.072496
X-RAY DIFFRACTIONf_plane_restr0.005548
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.849-1.91520.2822690.2677875X-RAY DIFFRACTION24
1.9152-1.99190.29611060.22981555X-RAY DIFFRACTION42
1.9919-2.08250.29571660.2192758X-RAY DIFFRACTION73
2.0825-2.19220.25442210.1993091X-RAY DIFFRACTION83
2.1922-2.32950.24962130.19123281X-RAY DIFFRACTION87
2.3295-2.50920.22281910.19023312X-RAY DIFFRACTION88
2.5092-2.76130.27692260.19763312X-RAY DIFFRACTION89
2.7613-3.16020.23022170.18713457X-RAY DIFFRACTION91
3.1602-3.97860.18162310.15423622X-RAY DIFFRACTION97
3.9786-24.21050.18282100.16573706X-RAY DIFFRACTION98

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