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- PDB-7d7u: Crystal structure of Ago2 MID domain in complex with 8-Br-adenosi... -

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Basic information

Entry
Database: PDB / ID: 7d7u
TitleCrystal structure of Ago2 MID domain in complex with 8-Br-adenosin-5'-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 / 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 / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
8-BROMO-ADENOSINE-5'-MONOPHOSPHATE / Protein argonaute-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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
DepositionOct 6, 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)47,6746
Polymers46,3963
Non-polymers1,2783
Water3,783210
1
A: Protein argonaute-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8912
Polymers15,4651
Non-polymers4261
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint-4 kcal/mol
Surface area7040 Å2
MethodPISA
2
B: Protein argonaute-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8912
Polymers15,4651
Non-polymers4261
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint-4 kcal/mol
Surface area6970 Å2
MethodPISA
3
C: Protein argonaute-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8912
Polymers15,4651
Non-polymers4261
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint-4 kcal/mol
Surface area7380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.170, 65.770, 40.790
Angle α, β, γ (deg.)105.830, 96.460, 87.560
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 / Fragment: MID domain
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-8BR / 8-BROMO-ADENOSINE-5'-MONOPHOSPHATE


Mass: 426.117 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H13BrN5O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.61 Å3/Da / Density % sol: 52.82 %
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: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→31.31 Å / Num. obs: 29976 / % possible obs: 94.6 % / Redundancy: 2 % / CC1/2: 0.989 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.107 / Rrim(I) all: 0.151 / Net I/σ(I): 4.2 / Num. measured all: 58839
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.0520.758442922520.450.7581.0720.893.9
8.94-31.311.90.0226013110.9980.0220.03116.688.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.7.2data scaling
MOLREPphasing
REFMAC5.8.0232refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3lud

3lud


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.927 / SU B: 8.917 / SU ML: 0.216 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.202 / ESU R Free: 0.177
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1495 5 %RANDOM
Rwork0.2043 ---
obs0.2067 28480 94.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 94.56 Å2 / Biso mean: 29.892 Å2 / Biso min: 6.43 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20.19 Å2-2.07 Å2
2---1.83 Å20.65 Å2
3---0.77 Å2
Refinement stepCycle: final / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3119 0 72 210 3401
Biso mean--34.64 29.87 -
Num. residues----401
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133254
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173099
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.6524410
X-RAY DIFFRACTIONr_angle_other_deg1.2651.5747218
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7095398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.35722.5144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.13915589
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8811518
X-RAY DIFFRACTIONr_chiral_restr0.070.2436
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023518
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02617
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 111 -
Rwork0.338 2128 -
all-2239 -
obs--93.88 %

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