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- PDB-7c6b: Crystal structure of Ago2 MID domain in complex with 6-(3-(2-carb... -

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Basic information

Entry
Database: PDB / ID: 7c6b
TitleCrystal structure of Ago2 MID domain in complex with 6-(3-(2-carboxyethyl)phenyl)purine riboside monophosphate
ComponentsProtein argonaute-2
KeywordsRNA BINDING PROTEIN / ARGONAUTE / 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 / RISC-loading complex / miRNA metabolic process / mRNA cap binding / RISC complex assembly / mRNA 3'-UTR AU-rich region binding / miRNA-mediated gene silencing by inhibition of translation / regulatory ncRNA-mediated post-transcriptional gene silencing / 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 / Regulation of RUNX1 Expression and Activity / RISC complex / 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
Chem-K2R / PHOSPHATE ION / Protein argonaute-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsSuzuki, M. / Takahashi, Y. / Saito, J. / Miyagi, H. / Shinohara, F.
CitationJournal: Rna / Year: 2021
Title: siRNA potency enhancement via chemical modifications of nucleotide bases at the 5'-end of the siRNA guide strand.
Authors: Shinohara, F. / Oashi, T. / Harumoto, T. / Nishikawa, T. / Takayama, Y. / Miyagi, H. / Takahashi, Y. / Nakajima, T. / Sawada, T. / Koda, Y. / Makino, A. / Sato, A. / Hamaguchi, K. / Suzuki, ...Authors: Shinohara, F. / Oashi, T. / Harumoto, T. / Nishikawa, T. / Takayama, Y. / Miyagi, H. / Takahashi, Y. / Nakajima, T. / Sawada, T. / Koda, Y. / Makino, A. / Sato, A. / Hamaguchi, K. / Suzuki, M. / Yamamoto, J. / Tomari, Y. / Saito, J.I.
History
DepositionMay 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)48,0278
Polymers46,3963
Non-polymers1,6315
Water5,098283
1
A: Protein argonaute-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9462
Polymers15,4651
Non-polymers4801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7210 Å2
MethodPISA
2
B: Protein argonaute-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9462
Polymers15,4651
Non-polymers4801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7000 Å2
MethodPISA
3
C: Protein argonaute-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1364
Polymers15,4651
Non-polymers6703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-4 kcal/mol
Surface area7420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.280, 66.460, 40.420
Angle α, β, γ (deg.)107.060, 95.630, 86.400
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Protein argonaute-2 / hAgo2 / Argonaute RISC catalytic component 2 / Eukaryotic translation initiation factor 2C 2 / ...hAgo2 / Argonaute RISC catalytic component 2 / Eukaryotic translation initiation factor 2C 2 / eIF2C 2 / PAZ Piwi domain protein / PPD / Protein slicer


Mass: 15465.193 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-K2R / 3-[3-[9-[(2R,3R,4S,5R)-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]purin-6-yl]phenyl]propanoic acid


Mass: 480.365 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C19H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.6 Å3/Da / Density % sol: 52.74 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M imidazole pH8.0, 0.2M NaCl, 0.46M NaH2PO4, 1.84M K2HPO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→38.51 Å / Num. obs: 51572 / % possible obs: 99.8 % / Redundancy: 4.429 % / Biso Wilson estimate: 37.512 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.191 / Rrim(I) all: 0.215 / Χ2: 1.143 / Net I/σ(I): 5.44 / Num. measured all: 228418 / Scaling rejects: 456
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.7-1.83.3511.11.4427052811180730.6011.30799.5
1.8-1.934.0980.6642.9433629823382070.8320.76399.7
1.93-2.084.6410.4144.9332942710970980.9270.46899.8
2.08-2.284.8140.3136.2232811682468160.9390.35299.9
2.28-2.554.7930.2597.0129262611461050.9460.29199.9
2.55-2.944.7660.2257.6525292530753070.9580.253100
2.94-3.614.7890.2078.2621964459245860.9560.23399.9
3.61-5.14.7890.168.5916656349034780.970.1899.7
5.1-38.514.6320.1268.488810192019020.9860.14399.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.05 Å38.51 Å
Translation3.05 Å38.51 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASER2.8.2phasing
REFMAC5.8.0232refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6L45

6l45
PDB Unreleased entry


Resolution: 1.7→38.51 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 8.614 / SU ML: 0.13 / SU R Cruickshank DPI: 0.1072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2286 2589 5 %RANDOM
Rwork0.1944 ---
obs0.1962 48783 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 102.25 Å2 / Biso mean: 42.944 Å2 / Biso min: 23.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20.14 Å2-0.49 Å2
2---0.57 Å20.57 Å2
3----0.15 Å2
Refinement stepCycle: final / Resolution: 1.7→38.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3103 0 109 283 3495
Biso mean--62.62 51.16 -
Num. residues----400
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133304
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173131
X-RAY DIFFRACTIONr_angle_refined_deg1.7171.6964485
X-RAY DIFFRACTIONr_angle_other_deg1.3771.5967282
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7165404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.78822.329146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.17315584
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2851519
X-RAY DIFFRACTIONr_chiral_restr0.0870.2437
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023575
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02644
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 205 -
Rwork0.363 3583 -
all-3788 -
obs--99.27 %
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)
11.8147-0.25730.79533.54020.12933.7279-0.0709-0.0488-0.0272-0.01350.0860.1568-0.03150.0587-0.0150.1514-0.0101-0.08640.01090.02040.07586.4337-10.7326-23.8075
24.58921.36670.64442.86930.34891.62910.2503-0.12190.10690.2069-0.073-0.0220.0341-0.1775-0.17730.25890.0485-0.15490.0372-0.00770.1728-13.84251.0475-2.7079
31.7634-0.1389-0.62743.55541.52213.74310.02760.223-0.0639-0.71540.0562-0.2679-0.25220.2501-0.08380.43920.022-0.0540.08010.03680.274611.08622.3642-10.1524
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A441 - 601
2X-RAY DIFFRACTION2B441 - 601
3X-RAY DIFFRACTION3C441 - 601

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