[English] 日本語
Yorodumi
- EMDB-27831: Wild-type HsDis3L2 in complex with 50% GC hairpin E-U7 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-27831
TitleWild-type HsDis3L2 in complex with 50% GC hairpin E-U7
Map data
Sample
  • Complex: Wild-type HsDis3L2 in complex with hairpinD-U7
    • Protein or peptide: Wild-type HS Dis3L2
    • RNA: Hairpin E-U7
Keywords3'-5' exonuclease / ds-RNA bound exonuclease / human exonuclease / RNA BINDING PROTEIN-RNA complex
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.9 Å
AuthorsMeze K / Thomas DR / Joshua-Tor L
Funding support United States, 2 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM114147 United States
CitationJournal: Nat Struct Mol Biol / Year: 2023
Title: A shape-shifting nuclease unravels structured RNA.
Authors: Katarina Meze / Armend Axhemi / Dennis R Thomas / Ahmet Doymaz / Leemor Joshua-Tor /
Abstract: RNA turnover pathways ensure appropriate gene expression levels by eliminating unwanted transcripts. Dis3-like 2 (Dis3L2) is a 3'-5' exoribonuclease that plays a critical role in human development. ...RNA turnover pathways ensure appropriate gene expression levels by eliminating unwanted transcripts. Dis3-like 2 (Dis3L2) is a 3'-5' exoribonuclease that plays a critical role in human development. Dis3L2 independently degrades structured substrates, including coding and noncoding 3' uridylated RNAs. While the basis for Dis3L2's substrate recognition has been well characterized, the mechanism of structured RNA degradation by this family of enzymes is unknown. We characterized the discrete steps of the degradation cycle by determining cryogenic electron microscopy structures representing snapshots along the RNA turnover pathway and measuring kinetic parameters for RNA processing. We discovered a dramatic conformational change that is triggered by double-stranded RNA (dsRNA), repositioning two cold shock domains by 70 Å. This movement exposes a trihelix linker region, which acts as a wedge to separate the two RNA strands. Furthermore, we show that the trihelix linker is critical for dsRNA, but not single-stranded RNA, degradation. These findings reveal the conformational plasticity of Dis3L2 and detail a mechanism of structured RNA degradation.
History
DepositionAug 14, 2022-
Header (metadata) releaseMar 1, 2023-
Map releaseMar 1, 2023-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_27831.png

Downloads & links

-
Map

FileDownload / File: emd_27831.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.67 Å/pix.
x 300 pix.
= 201. Å		0.67 Å/pix.
x 300 pix.
= 201. Å		0.67 Å/pix.
x 300 pix.
= 201. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.67 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0311
Minimum - Maximum-0.06407455 - 0.13802864
Average (Standard dev.)-0.00003884468 (±0.0065183523)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 201.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_27831_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_27831_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Wild-type HsDis3L2 in complex with hairpinD-U7

EntireName: Wild-type HsDis3L2 in complex with hairpinD-U7
Components
  • Complex: Wild-type HsDis3L2 in complex with hairpinD-U7
    • Protein or peptide: Wild-type HS Dis3L2
    • RNA: Hairpin E-U7

-
Supramolecule #1: Wild-type HsDis3L2 in complex with hairpinD-U7

SupramoleculeName: Wild-type HsDis3L2 in complex with hairpinD-U7 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 100 KDa

-
Macromolecule #1: Wild-type HS Dis3L2

MacromoleculeName: Wild-type HS Dis3L2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSHPDYRMNL RPLGTPRGVS AVAGPHDIGA SPGDKKSKNR STRGKKKSIF ETYMSKEDVS EGLKRGTLIQ GVLRINPKKF HEAFIPSPDG DRDIFIDGVV ARNRALNGDL VVVKLLPEEH WKVVKPESND KETEAAYESD IPEELCGHHL PQQSLKSYND SPDVIVEAQF ...String:
MSHPDYRMNL RPLGTPRGVS AVAGPHDIGA SPGDKKSKNR STRGKKKSIF ETYMSKEDVS EGLKRGTLIQ GVLRINPKKF HEAFIPSPDG DRDIFIDGVV ARNRALNGDL VVVKLLPEEH WKVVKPESND KETEAAYESD IPEELCGHHL PQQSLKSYND SPDVIVEAQF DGSDSEDGHG ITQNVLVDGV KKLSVCVSEK GREDGDAPVT KDETTCISQD TRALSEKSLQ RSAKVVYILE KKHSRAATGF LKLLADKNSE LFRKYALFSP SDHRVPRIYV PLKDCPQDFV ARPKDYANTL FICRIVDWKE DCNFALGQLA KSLGQAGEIE PETEGILTEY GVDFSDFSSE VLECLPQGLP WTIPPEEFSK RRDLRKDCIF TIDPSTARDL DDALSCKPLA DGNFKVGVHI ADVSYFVPEG SDLDKVAAER ATSVYLVQKV VPMLPRLLCE ELCSLNPMSD KLTFSVIWTL TPEGKILDEW FGRTIIRSCT KLSYEHAQSM IESPTEKIPA KELPPISPEH SSEEVHQAVL NLHGIAKQLR QQRFVDGALR LDQLKLAFTL DHETGLPQGC HIYEYRESNK LVEEFMLLAN MAVAHKIHRA FPEQALLRRH PPPQTRMLSD LVEFCDQMGL PVDFSSAGAL NKSLTQTFGD DKYSLARKEV LTNMCSRPMQ MALYFCSGLL QDPAQFRHYA LNVPLYTHFT SPIRRFADVL VHRLLAAALG YRERLDMAPD TLQKQADHCN DRRMASKRVQ ELSTSLFFAV LVKESGPLES EAMVMGILKQ AFDVLVLRYG VQKRIYCNAL ALRSHHFQKV GKKPELTLVW EPEDMEQEPA QQVITIFSLV EVVLQAESTA LKYSAILKRP GTQGHLGPEK EEEESDGEPE DSSTS

-
Macromolecule #2: Hairpin E-U7

MacromoleculeName: Hairpin E-U7 / type: rna / ID: 2
Source (natural)Organism: synthetic construct (others)
SequenceString:
UGAGACUUUC GAGUCUUUUU UUUU

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.3 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
150.0 mMNaClSodium Chloride
5.0 mMDTTDithiothreitol
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.042 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 80.0 K / Max: 80.0 K
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Digitization - Frames/image: 1-30 / Number grids imaged: 1 / Average electron dose: 62.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 2.8000000000000003 µm / Calibrated defocus min: 0.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 1102688
Startup modelType of model: OTHER / Details: Ab initio in cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.1.0) / Number images used: 226117
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.1.0) / Details: stochastic gradient descent
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.1.0)
Final 3D classificationNumber classes: 5 / Software - Name: cryoSPARC (ver. 3.1.0)

+
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