[English] 日本語
Yorodumi
- PDB-6mfr: Human Argonaute2-miR-122 bound to a target RNA with three central... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mfr
TitleHuman Argonaute2-miR-122 bound to a target RNA with three central mismatches (bu3)
Components
  • Protein argonaute-2
  • RNA (5'-R(P*AP*AP*AP*CP*AP*CP*CP*AP*UP*UP*UP*UP*CP*AP*CP*AP*CP*UP*CP*CP*AP*AP*A)-3')
  • RNA (5'-R(P*UP*GP*GP*AP*GP*UP*GP*UP*GP*AP*CP*AP*AP*UP*GP*GP*UP*GP*UP*U)-3')
Keywordshydrolase/rna / RNA-binding protein / microRNA / target directed microRNA decay / HYDROLASE / hydrolase-rna complex
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 / paz domain / Protein argonaute, Mid domain / Argonaute-like, PIWI domain / Mid domain of argonaute / paz domain / Argonaute linker 2 domain / Protein argonaute, N-terminal / N-terminal domain of argonaute / Argonaute linker 2 domain ...Protein argonaute-2 / paz domain / Protein argonaute, Mid domain / Argonaute-like, PIWI domain / Mid domain of argonaute / paz domain / 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 / Beta Complex / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHENOL / PHOSPHATE ION / RNA / RNA (> 10) / Protein argonaute-2
Similarity search - Component
Biological speciesHomo sapiens (human)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsSheu-Gruttadauria, J. / MacRae, I.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM104475 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115649 United States
CitationJournal: Mol.Cell / Year: 2019
Title: Structural Basis for Target-Directed MicroRNA Degradation.
Authors: Sheu-Gruttadauria, J. / Pawlica, P. / Klum, S.M. / Wang, S. / Yario, T.A. / Schirle Oakdale, N.T. / Steitz, J.A. / MacRae, I.J.
History
DepositionSep 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein argonaute-2
B: Protein argonaute-2
C: RNA (5'-R(P*UP*GP*GP*AP*GP*UP*GP*UP*GP*AP*CP*AP*AP*UP*GP*GP*UP*GP*UP*U)-3')
D: RNA (5'-R(P*UP*GP*GP*AP*GP*UP*GP*UP*GP*AP*CP*AP*AP*UP*GP*GP*UP*GP*UP*U)-3')
E: RNA (5'-R(P*AP*AP*AP*CP*AP*CP*CP*AP*UP*UP*UP*UP*CP*AP*CP*AP*CP*UP*CP*CP*AP*AP*A)-3')
F: RNA (5'-R(P*AP*AP*AP*CP*AP*CP*CP*AP*UP*UP*UP*UP*CP*AP*CP*AP*CP*UP*CP*CP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,24911
Polymers222,7776
Non-polymers4715
Water0
1
A: Protein argonaute-2
C: RNA (5'-R(P*UP*GP*GP*AP*GP*UP*GP*UP*GP*AP*CP*AP*AP*UP*GP*GP*UP*GP*UP*U)-3')
E: RNA (5'-R(P*AP*AP*AP*CP*AP*CP*CP*AP*UP*UP*UP*UP*CP*AP*CP*AP*CP*UP*CP*CP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,5775
Polymers111,3893
Non-polymers1882
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-55 kcal/mol
Surface area41790 Å2
MethodPISA
2
B: Protein argonaute-2
D: RNA (5'-R(P*UP*GP*GP*AP*GP*UP*GP*UP*GP*AP*CP*AP*AP*UP*GP*GP*UP*GP*UP*U)-3')
F: RNA (5'-R(P*AP*AP*AP*CP*AP*CP*CP*AP*UP*UP*UP*UP*CP*AP*CP*AP*CP*UP*CP*CP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,6726
Polymers111,3893
Non-polymers2833
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-50 kcal/mol
Surface area40130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.174, 137.960, 153.122
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
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: 97358.188 Da / Num. of mol.: 2 / Mutation: D669A, S387D, S824A, S828D, s831D, S834A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGO2, EIF2C2 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9UKV8, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#2: RNA chain RNA (5'-R(P*UP*GP*GP*AP*GP*UP*GP*UP*GP*AP*CP*AP*AP*UP*GP*GP*UP*GP*UP*U)-3')


Mass: 6788.021 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: RNA chain RNA (5'-R(P*AP*AP*AP*CP*AP*CP*CP*AP*UP*UP*UP*UP*CP*AP*CP*AP*CP*UP*CP*CP*AP*AP*A)-3')


Mass: 7242.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#4: Chemical
ChemComp-IPH / PHENOL / Phenol


Mass: 94.111 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H6O
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10% PEG3350, 50mM Tris pH8, 20mM MgCl2, 75mM Phenol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.59→39.57 Å / Num. obs: 27731 / % possible obs: 98.7 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.193 / Rpim(I) all: 0.076 / Net I/σ(I): 8.5
Reflection shellResolution: 3.59→3.81 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 4136 / Rpim(I) all: 0.311 / % possible all: 92.6

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4W5O

4w5o


Resolution: 3.6→39.422 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.1
RfactorNum. reflection% reflection
Rfree0.2827 1386 5.01 %
Rwork0.2392 --
obs0.2413 27646 98.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.6→39.422 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12797 1479 33 0 14309
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314776
X-RAY DIFFRACTIONf_angle_d0.85120321
X-RAY DIFFRACTIONf_dihedral_angle_d13.425756
X-RAY DIFFRACTIONf_chiral_restr0.0352315
X-RAY DIFFRACTIONf_plane_restr0.0052361
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5706-3.69810.33311170.32442264X-RAY DIFFRACTION86
3.6981-3.84610.28311400.28132628X-RAY DIFFRACTION100
3.8461-4.02090.30281490.26972633X-RAY DIFFRACTION100
4.0209-4.23270.25161500.25322602X-RAY DIFFRACTION100
4.2327-4.49750.30171250.23622647X-RAY DIFFRACTION99
4.4975-4.84420.27381530.2272638X-RAY DIFFRACTION100
4.8442-5.33070.26681310.23312669X-RAY DIFFRACTION100
5.3307-6.09960.31721410.2362664X-RAY DIFFRACTION100
6.0996-7.67550.29861450.24172712X-RAY DIFFRACTION100
7.6755-39.42420.25461350.19862803X-RAY DIFFRACTION99
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)
14.6256-3.02172.00974.7881-2.34392.6161-0.5079-0.1070.52440.1290.32890.6947-0.6595-0.68630.18420.85170.0427-0.08670.63-0.16730.7819124.4112137.9328180.5532
24.2901-1.4014-0.63810.86641.41366.5892-0.10680.06970.0828-0.0212-0.16550.6705-0.7366-0.48280.1950.8105-0.028-0.03390.46630.03660.9447127.5836139.1199177.0941
30.5107-1.0452.08732.5804-2.33725.06740.50180.0835-0.2746-0.0569-0.15540.07590.36390.2988-0.38550.7348-0.0705-0.05491.05130.07240.5231138.1798146.0437145.9507
43.5599-0.5162-0.81453.56550.50713.3153-0.00960.5554-0.5684-0.372-0.10590.16470.15180.21860.12720.40840.0409-0.08820.4965-0.02320.3981149.1936107.4792174.9841
55.3077-1.35861.63915.5295-1.08762.2382-0.1913-0.39340.8927-0.06520.44381.0311-0.2008-0.6829-0.24390.57290.06670.10720.60810.02130.7802128.0363204.8919179.3569
65.4037-1.635-0.93612.18350.71046.82420.3630.1166-0.0879-0.30370.00761.314-0.6387-1.0253-0.2440.70970.0674-0.12270.63750.08271.2109121.6736211.1703174.1683
7-0.9341-0.6562.14881.1951-3.21239.63410.08060.1261-0.1608-0.1430.0950.16630.17240.0317-0.3210.61440.034-0.05380.78190.04680.5659138.5678214.0162147.5321
83.0719-0.2836-0.26832.4070.30332.67210.04640.6185-0.787-0.1331-0.06820.24580.52760.15890.00230.46440.0522-0.15370.5483-0.18460.5309148.9795177.8059170.3677
93.73663.9173-0.12385.6269-1.6811.52940.10241.5089-0.118-2.6919-0.2272-0.851-1.3489-0.81290.2921.06020.16210.07571.07880.00420.4275153.7099118.4092167.494
103.57780.75084.18530.19120.7564.74910.51.3926-3.5484-0.6675-0.2079-0.17471.17181.5078-0.38361.5080.3209-0.32821.82850.05612.4321123.5571126.4246157.9003
112.79592.9088-0.40745.32051.22799.0354-0.15321.40650.2662-1.39050.0659-0.1601-0.9770.23630.05380.56720.0867-0.03960.8603-0.13340.4304153.6459189.1221163.5236
126.1452.23032.9382.73721.20644.2925-0.706-0.02891.741-0.89240.63171.80070.79310.9860.21651.5652-0.19860.02731.6439-0.04622.787128.2658194.8843155.6172
138.7601-3.3573-3.06864.3671.0171.1135-0.8865-0.2872-1.0638-0.11060.8111-0.8218-1.41331.6185-0.53882.03130.2959-0.04231.9891-0.37111.5028126.5086125.3084160.4965
149.45452.57556.48784.85952.76834.649-1.0349-0.0131-0.7533-0.8310.15610.2299-0.56280.26691.07540.9262-0.19480.00071.1020.08880.6606160.8173122.4177165.3815
155.94056.6153-0.51697.8894-0.99955.21790.50630.7227-3.65860.2091-0.98463.4368-1.3391.07940.61211.5226-0.22410.20791.9956-0.91852.8262131.1617193.4017161.6291
166.3879-1.08344.08115.54480.8515.22050.07621.96180.0605-0.775-0.58340.46920.13620.87030.29750.99760.10670.05760.97030.02360.6943160.9194193.0459161.5919
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 102 )
2X-RAY DIFFRACTION2chain 'A' and (resid 103 through 225 )
3X-RAY DIFFRACTION3chain 'A' and (resid 226 through 386 )
4X-RAY DIFFRACTION4chain 'A' and (resid 387 through 859 )
5X-RAY DIFFRACTION5chain 'B' and (resid 22 through 80 )
6X-RAY DIFFRACTION6chain 'B' and (resid 81 through 195 )
7X-RAY DIFFRACTION7chain 'B' and (resid 196 through 386 )
8X-RAY DIFFRACTION8chain 'B' and (resid 387 through 859 )
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 8 )
10X-RAY DIFFRACTION10chain 'C' and (resid 9 through 20 )
11X-RAY DIFFRACTION11chain 'D' and (resid 1 through 8 )
12X-RAY DIFFRACTION12chain 'D' and (resid 9 through 16 )
13X-RAY DIFFRACTION13chain 'E' and (resid 2 through 13 )
14X-RAY DIFFRACTION14chain 'E' and (resid 14 through 23 )
15X-RAY DIFFRACTION15chain 'F' and (resid 6 through 13 )
16X-RAY DIFFRACTION16chain 'F' and (resid 14 through 23 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more