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- PDB-3luh: Crystal structure of MID domain from hAGO2 in complex with GMP -

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Basic information

Entry
Database: PDB / ID: 3luh
TitleCrystal structure of MID domain from hAGO2 in complex with GMP
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 / 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 ...: / 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 / 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 / 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 / pre-miRNA processing / siRNA processing / RNA 7-methylguanosine cap binding / regulation of synapse maturation / siRNA binding / mRNA 3'-UTR AU-rich region binding / Regulation of MITF-M-dependent genes involved in apoptosis / M-decay: degradation of maternal mRNAs by maternally stored factors / P-body assembly / RISC complex / TGFBR3 expression / regulatory ncRNA-mediated gene silencing / Regulation of RUNX1 Expression and Activity / miRNA binding / MicroRNA (miRNA) biogenesis / 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 / core promoter sequence-specific DNA binding / Nuclear events stimulated by ALK signaling in cancer / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / negative regulation of translational initiation / translation initiation factor activity / RNA endonuclease 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 / 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 / Piwi domain profile. / Piwi domain / Piwi / PAZ domain superfamily / PAZ / PAZ domain / PAZ domain profile. / PAZ domain / Response regulator / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-MONOPHOSPHATE / PHOSPHATE ION / Protein argonaute-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.999 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

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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)47,1627
Polymers45,9783
Non-polymers1,1854
Water5,603311
1
A: Protein argonaute-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6892
Polymers15,3261
Non-polymers3631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein argonaute-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0523
Polymers15,3261
Non-polymers7262
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protein argonaute-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4212
Polymers15,3261
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.433, 46.971, 66.352
Angle α, β, γ (deg.)86.06, 72.77, 83.70
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-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14N5O8P
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.6 Å3/Da / Density % sol: 52.69 %
Crystal growTemperature: 277 K / Method: 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, temperature 277K

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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: MicroMax-007 HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.999→30 Å / Num. all: 29127 / Num. obs: 29127 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.999→2.07 Å / % possible all: 76.8

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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: 1.999→23.497 Å / SU ML: 0.28 / σ(F): 0.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1560 5.91 %Random
Rwork0.1846 ---
obs0.1875 26409 84.21 %-
all-26409 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.054 Å2 / ksol: 0.4 e/Å3
Refinement stepCycle: LAST / Resolution: 1.999→23.497 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3108 0 20 311 3439
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073182
X-RAY DIFFRACTIONf_angle_d1.0284301
X-RAY DIFFRACTIONf_dihedral_angle_d16.2161192
X-RAY DIFFRACTIONf_chiral_restr0.069495
X-RAY DIFFRACTIONf_plane_restr0.005544
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.999-2.070.29741340.23921802X-RAY DIFFRACTION62
2.07-2.15280.27191400.2192274X-RAY DIFFRACTION77
2.1528-2.25070.23351670.20032494X-RAY DIFFRACTION84
2.2507-2.36920.27171450.19772521X-RAY DIFFRACTION85
2.3692-2.51750.25251690.2012435X-RAY DIFFRACTION83
2.5175-2.71160.26321580.19682414X-RAY DIFFRACTION82
2.7116-2.9840.24541510.19822398X-RAY DIFFRACTION82
2.984-3.41470.22291590.17832743X-RAY DIFFRACTION92
3.4147-4.29790.21221800.14132861X-RAY DIFFRACTION97
4.2979-23.49830.19011570.17012907X-RAY DIFFRACTION98

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