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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mdz
TitleHuman Argonaute2-miR-122 bound to a target RNA with two central mismatches (bu2)
Components
  • Protein argonaute-2
  • RNA (5'-R(P*AP*AP*AP*CP*AP*CP*CP*AP*UP*UP*UP*CP*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 / 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 / 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 / RNA 7-methylguanosine cap binding / siRNA processing / siRNA binding / regulation of synapse maturation / M-decay: degradation of maternal mRNAs by maternally stored factors / mRNA 3'-UTR AU-rich region binding / Regulation of MITF-M-dependent genes involved in apoptosis / RISC complex / TGFBR3 expression / regulatory ncRNA-mediated gene silencing / Regulation of RUNX1 Expression and Activity / miRNA binding / P-body assembly / 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 / 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 / translation initiation factor activity / negative regulation of translational initiation / RNA endonuclease activity / positive regulation of translation / post-embryonic development / TP53 Regulates Metabolic Genes / P-body / Transcriptional regulation by small RNAs / 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 / postsynapse / translation / dendrite / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / RNA binding / extracellular exosome / nucleoplasm / metal ion binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Protein argonaute-2 / paz domain / paz domain / 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 ...Protein argonaute-2 / paz domain / paz domain / 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 profile. / Piwi domain / Piwi domain / Piwi / PAZ domain superfamily / PAZ / PAZ domain / PAZ domain profile. / PAZ domain / Response regulator / Ribonuclease H-like superfamily/Ribonuclease H / Beta Complex / 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 / RNA / RNA (> 10) / Protein argonaute-2
Similarity search - Component
Biological speciesHomo sapiens (human)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 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 5, 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*CP*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*CP*CP*AP*CP*AP*CP*UP*CP*CP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,10610
Polymers222,7296
Non-polymers3764
Water00
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*CP*CP*AP*CP*AP*CP*UP*CP*CP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,5535
Polymers111,3653
Non-polymers1882
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7110 Å2
ΔGint-56 kcal/mol
Surface area41840 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*CP*CP*AP*CP*AP*CP*UP*CP*CP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,5535
Polymers111,3653
Non-polymers1882
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-50 kcal/mol
Surface area40120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.615, 138.289, 152.610
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: S387D, D669A, D824A, 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*CP*CP*AP*CP*AP*CP*UP*CP*CP*AP*AP*A)-3')


Mass: 7218.399 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#4: Chemical
ChemComp-IPH / PHENOL


Mass: 94.111 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H6O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.75 %
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: Mar 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.4→39.5 Å / Num. obs: 31940 / % possible obs: 99.5 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.08 / Net I/σ(I): 8.4
Reflection shellResolution: 3.4→3.58 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 3 / Num. unique obs: 4579 / Rpim(I) all: 0.268 / % possible all: 99

-
Processing

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

4w5o


Resolution: 3.4→38.293 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.23
RfactorNum. reflection% reflection
Rfree0.2643 1588 4.99 %
Rwork0.2197 --
obs0.2219 31825 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.4→38.293 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12834 1520 28 0 14382
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214856
X-RAY DIFFRACTIONf_angle_d0.57120439
X-RAY DIFFRACTIONf_dihedral_angle_d13.1265797
X-RAY DIFFRACTIONf_chiral_restr0.0232334
X-RAY DIFFRACTIONf_plane_restr0.0032367
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3973-3.50690.33131390.29522692X-RAY DIFFRACTION99
3.5069-3.63210.3561360.2752741X-RAY DIFFRACTION100
3.6321-3.77740.29171450.25882670X-RAY DIFFRACTION100
3.7774-3.94920.29091560.24472747X-RAY DIFFRACTION100
3.9492-4.15720.27041440.22652711X-RAY DIFFRACTION99
4.1572-4.41730.25431410.21442726X-RAY DIFFRACTION100
4.4173-4.75770.24821520.19192744X-RAY DIFFRACTION99
4.7577-5.23550.2231330.19542766X-RAY DIFFRACTION100
5.2355-5.99050.26221490.20492768X-RAY DIFFRACTION99
5.9905-7.5380.25051550.2212772X-RAY DIFFRACTION99
7.538-38.29590.22871380.19162900X-RAY DIFFRACTION98

+
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