[English] 日本語
Yorodumi
- EMDB-25472: Cryo-EM structure of Arabidopsis Ago10-guide-target RNA complex i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-25472
TitleCryo-EM structure of Arabidopsis Ago10-guide-target RNA complex in a central duplex conformation
Map data
Sample
  • Complex: AtAgo10-guide-target RNA complex
    • Protein or peptide: Protein argonaute 10
    • RNA: RNA (5'-R(P*UP*GP*GP*AP*GP*UP*GP*UP*GP*AP*CP*AP*AP*UP*GP*GP*U)-3')
    • RNA: RNA (5'-R(P*CP*CP*AP*UP*UP*GP*UP*CP*AP*CP*AP*CP*UP*CP*CP*AP*A)-3')
  • Ligand: MAGNESIUM ION
KeywordsmiRNA / siRNA / RNA silencing / Argonaute / plant / GENE REGULATION
Function / homology
Function and homology information


regulation of shoot apical meristem development / primary shoot apical meristem specification / regulation of meristem structural organization / miRNA metabolic process / regulatory ncRNA-mediated gene silencing / miRNA binding / plastid / somatic stem cell population maintenance / regulation of translation / defense response to virus ...regulation of shoot apical meristem development / primary shoot apical meristem specification / regulation of meristem structural organization / miRNA metabolic process / regulatory ncRNA-mediated gene silencing / miRNA binding / plastid / somatic stem cell population maintenance / regulation of translation / defense response to virus / ribonucleoprotein complex / cytoplasm
Similarity search - Function
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 ...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 / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
Protein argonaute 10
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress) / unidentified (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.79 Å
AuthorsXiao Y / MacRae IJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM127090 United States
CitationJournal: Nucleic Acids Res / Year: 2022
Title: The molecular mechanism of microRNA duplex selectivity of Arabidopsis ARGONAUTE10.
Authors: Yao Xiao / Ian J MacRae /
Abstract: Small RNAs (sRNAs), including microRNAs (miRNAs) and small interfering RNAs (siRNAs), are essential gene regulators for plant and animal development. The loading of sRNA duplexes into the proper ...Small RNAs (sRNAs), including microRNAs (miRNAs) and small interfering RNAs (siRNAs), are essential gene regulators for plant and animal development. The loading of sRNA duplexes into the proper ARGONAUTE (AGO) protein is a key step to forming a functional silencing complex. In Arabidopsis thaliana, the specific loading of miR166/165 into AGO10 (AtAGO10) is critical for the maintenance of the shoot apical meristem, the source of all shoot organs, but the mechanism by which AtAGO10 distinguishes miR166/165 from other cellular miRNAs is not known. Here, we show purified AtAGO10 alone lacks loading selectivity towards miR166/165 duplexes. However, phosphate and HSP chaperone systems reshape the selectivity of AtAGO10 to its physiological substrates. A loop in the AtAGO10 central cleft is essential for recognizing specific mismatches opposite the guide strand 3' region in miR166/165 duplexes. Replacing this loop with the equivalent loop from Homo sapiens AGO2 (HsAGO2) changes AtAGO10 miRNA loading behavior such that 3' region mismatches are ignored and mismatches opposite the guide 5' end instead drive loading, as in HsAGO2. Thus, this study uncovers the molecular mechanism underlying the miR166/165 selectivity of AtAGO10, essential for plant development, and provides new insights into how miRNA duplex structures are recognized for sRNA sorting.
History
DepositionNov 19, 2021-
Header (metadata) releaseAug 3, 2022-
Map releaseAug 3, 2022-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_25472.png

Downloads & links

-
Map

FileDownload / File: emd_25472.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.91 Å/pix.
x 200 pix.
= 182. Å		0.91 Å/pix.
x 200 pix.
= 182. Å		0.91 Å/pix.
x 200 pix.
= 182. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.91 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.008
Minimum - Maximum-0.03761009 - 0.06994262
Average (Standard dev.)0.00007741307 (±0.002742027)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 182.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: #1

Fileemd_25472_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_25472_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_25472_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : AtAgo10-guide-target RNA complex

EntireName: AtAgo10-guide-target RNA complex
Components
  • Complex: AtAgo10-guide-target RNA complex
    • Protein or peptide: Protein argonaute 10
    • RNA: RNA (5'-R(P*UP*GP*GP*AP*GP*UP*GP*UP*GP*AP*CP*AP*AP*UP*GP*GP*U)-3')
    • RNA: RNA (5'-R(P*CP*CP*AP*UP*UP*GP*UP*CP*AP*CP*AP*CP*UP*CP*CP*AP*A)-3')
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: AtAgo10-guide-target RNA complex

SupramoleculeName: AtAgo10-guide-target RNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: The complex of Arabidopsis Argonaute10 with a synthetic guide RNA and a target pairing to 2-16nt of guide guide
Source (natural)Organism: Arabidopsis thaliana (thale cress)

-
Macromolecule #1: Protein argonaute 10

MacromoleculeName: Protein argonaute 10 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 110.981633 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MPIRQMKDSS ETHLVIKTQP LKHHNPKTVQ NGKIPPPSPS PVTVTTPATV TQSQASSPSP PSKNRSRRRN RGGRKSDQGD VCMRPSSRP RKPPPPSQTT SSAVSVATAG EIVAVNHQMQ MGVRKNSNFA PRPGFGTLGT KCIVKANHFL ADLPTKDLNQ Y DVTITPEV ...String:
MPIRQMKDSS ETHLVIKTQP LKHHNPKTVQ NGKIPPPSPS PVTVTTPATV TQSQASSPSP PSKNRSRRRN RGGRKSDQGD VCMRPSSRP RKPPPPSQTT SSAVSVATAG EIVAVNHQMQ MGVRKNSNFA PRPGFGTLGT KCIVKANHFL ADLPTKDLNQ Y DVTITPEV SSKSVNRAII AELVRLYKES DLGRRLPAYD GRKSLYTAGE LPFTWKEFSV KIVDEDDGII NGPKRERSYK VA IKFVARA NMHHLGEFLA GKRADCPQEA VQILDIVLRE LSVKRFCPVG RSFFSPDIKT PQRLGEGLES WCGFYQSIRP TQM GLSLNI DMASAAFIEP LPVIEFVAQL LGKDVLSKPL SDSDRVKIKK GLRGVKVEVT HRANVRRKYR VAGLTTQPTR ELMF PVDEN CTMKSVIEYF QEMYGFTIQH THLPCLQVGN QKKASYLPME ACKIVEGQRY TKRLNEKQIT ALLKVTCQRP RDREN DILR TVQHNAYDQD PYAKEFGMNI SEKLASVEAR ILPAPWLKYH ENGKEKDCLP QVGQWNMMNK KMINGMTVSR WACVNF SRS VQENVARGFC NELGQMCEVS GMEFNPEPVI PIYSARPDQV EKALKHVYHT SMNKTKGKEL ELLLAILPDN NGSLYGD LK RICETELGLI SQCCLTKHVF KISKQYLANV SLKINVKMGG RNTVLVDAIS CRIPLVSDIP TIIFGADVTH PENGEESS P SIAAVVASQD WPEVTKYAGL VCAQAHRQEL IQDLYKTWQD PVRGTVSGGM IRDLLISFRK ATGQKPLRII FYRAGVSEG QFYQVLLYEL DAIRKACASL EPNYQPPVTF IVVQKRHHTR LFANNHRDKN STDRSGNILP GTVVDTKICH PTEFDFYLCS HAGIQGTSR PAHYHVLWDE NNFTADGIQS LTNNLCYTYA RCTRSVSIVP PAYYAHLAAF RARFYLEPEI MQDNGSPGKK N TKTTTVGD VGVKPLPALK ENVKRVMFYC

UniProtKB: Protein argonaute 10

-
Macromolecule #2: RNA (5'-R(P*UP*GP*GP*AP*GP*UP*GP*UP*GP*AP*CP*AP*AP*UP*GP*GP*U)-3')

MacromoleculeName: RNA (5'-R(P*UP*GP*GP*AP*GP*UP*GP*UP*GP*AP*CP*AP*AP*UP*GP*GP*U)-3')
type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: unidentified (others)
Molecular weightTheoretical: 6.788021 KDa
SequenceString:
UGGAGUGUGA CAAUGGUGUU U

-
Macromolecule #3: RNA (5'-R(P*CP*CP*AP*UP*UP*GP*UP*CP*AP*CP*AP*CP*UP*CP*CP*AP*A)-3')

MacromoleculeName: RNA (5'-R(P*CP*CP*AP*UP*UP*GP*UP*CP*AP*CP*AP*CP*UP*CP*CP*AP*A)-3')
type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: unidentified (others)
Molecular weightTheoretical: 5.636419 KDa
SequenceString:
CCAUUGUCAC ACUCCAAA

-
Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.3 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
10.0 mMC4H11NO3Tris
100.0 mMNaClNaCl
0.5 mMC9H15O6PTCEP
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: HOMEMADE PLUNGER

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 2049 / Average electron dose: 66.88 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.7 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 45000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 1935081
CTF correctionSoftware - Name: Gctf / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.79 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1-cuda) / Number images used: 38833
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1-cuda)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1-cuda)
FSC plot (resolution estimation)

+
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