[English] 日本語
Yorodumi
- EMDB-25023: tRNA-like Structure from Brome Mosaic Virus Bound to Tyrosyl-tRNA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-25023
TitletRNA-like Structure from Brome Mosaic Virus Bound to Tyrosyl-tRNA Synthetase from Phaseolus vulgaris. Conformation: Bound State 1.
Map data
SampleRNA-protein complex: tyrosyl-tRNA synthetase from Phaseolus vulgaris bound to tRNA-like structure from brome mosaic virus RNA 3.:
Tyrosine--tRNA ligase / nucleic-acidNucleic acid
Function / homologyTyrosine-tRNA ligase, archaeal/eukaryotic-type / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / tRNA aminoacylation for protein translation / Rossmann-like alpha/beta/alpha sandwich fold / ATP binding / Tyrosine--tRNA ligase
Function and homology information
Biological speciesPhaseolus vulgaris (French bean) / Brome mosaic virus
Methodsingle particle reconstruction / cryo EM / Resolution: 5.51 Å
AuthorsKieft JS / Bonilla SL
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118070 United States
National Science Foundation (NSF, United States)F32GM139385 United States
Howard Hughes Medical Institute (HHMI)Hanna H. Gray Fellowship United States
CitationJournal: Science / Year: 2021
Title: A viral RNA hijacks host machinery using dynamic conformational changes of a tRNA-like structure.
Authors: Steve L Bonilla / Madeline E Sherlock / Andrea MacFadden / Jeffrey S Kieft /
Abstract: Viruses require multifunctional structured RNAs to hijack their host’s biochemistry, but their mechanisms can be obscured by the difficulty of solving conformationally dynamic RNA structures. Using ...Viruses require multifunctional structured RNAs to hijack their host’s biochemistry, but their mechanisms can be obscured by the difficulty of solving conformationally dynamic RNA structures. Using cryo–electron microscopy (cryo-EM), we visualized the structure of the mysterious viral transfer RNA (tRNA)–like structure (TLS) from the brome mosaic virus, which affects replication, translation, and genome encapsidation. Structures in isolation and those bound to tyrosyl-tRNA synthetase (TyrRS) show that this ~55-kilodalton purported tRNA mimic undergoes large conformational rearrangements to bind TyrRS in a form that differs substantially from that of tRNA. Our study reveals how viral RNAs can use a combination of static and dynamic RNA structures to bind host machinery through highly noncanonical interactions, and we highlight the utility of cryo-EM for visualizing small, conformationally dynamic structured RNAs.
History
DepositionSep 27, 2021-
Header (metadata) releaseDec 1, 2021-
Map releaseDec 1, 2021-
UpdateDec 1, 2021-
Current statusDec 1, 2021Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0336
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0336
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7sc6
  • Surface level: 0.0336
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_25023.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 432 pix.
= 358.56 Å
0.83 Å/pix.
x 432 pix.
= 358.56 Å
0.83 Å/pix.
x 432 pix.
= 358.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 0.0336 / Movie #1: 0.0336
Minimum - Maximum-0.03478344 - 0.1662234
Average (Standard dev.)-0.00012665533 (±0.0039383667)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 358.56 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.830.830.83
M x/y/z432432432
origin x/y/z0.0000.0000.000
length x/y/z358.560358.560358.560
α/β/γ90.00090.00090.000
start NX/NY/NZ-140-140-140
NX/NY/NZ280280280
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS432432432
D min/max/mean-0.0350.166-0.000

-
Supplemental data

-
Additional map: Sharpened (B factor: 341.8) cryo-EM map of tyrosyl-t RNA...

Fileemd_25023_additional_1.map
AnnotationSharpened (B factor: 341.8) cryo-EM map of tyrosyl-tRNA synthetase (TyrRS) from Phaseolus vulgaris bound to tRNA-like structure (TLS) from brome mosaic virus (BMV). Complex in 'bound state 1'.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Half map: Half-map A of tyrosyl-t RNA synthetase (Tyr RS) from Phaseolus...

Fileemd_25023_half_map_1.map
AnnotationHalf-map A of tyrosyl-tRNA synthetase (TyrRS) from Phaseolus vulgaris bound to tRNA-like structure (TLS) from brome mosaic virus (BMV). Complex in 'bound state 1'.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Half map: Half-map B of tyrosyl-t RNA synthetase (Tyr RS) from Phaseolus...

Fileemd_25023_half_map_2.map
AnnotationHalf-map B of tyrosyl-tRNA synthetase (TyrRS) from Phaseolus vulgaris bound to tRNA-like structure (TLS) from brome mosaic virus (BMV).Complex in 'bound state 1'.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Sample components

-
Entire RNA-protein complex: tyrosyl-tRNA synthetase from Phaseolus vulga...

EntireName: RNA-protein complex: tyrosyl-tRNA synthetase from Phaseolus vulgaris bound to tRNA-like structure from brome mosaic virus RNA 3.
Number of Components: 3

-
Component #1: protein, RNA-protein complex: tyrosyl-tRNA synthetase from Phaseo...

ProteinName: RNA-protein complex: tyrosyl-tRNA synthetase from Phaseolus vulgaris bound to tRNA-like structure from brome mosaic virus RNA 3.
Recombinant expression: No
SourceSpecies: Phaseolus vulgaris (French bean)
Source (engineered)Expression System: Escherichia coli (E. coli)

-
Component #2: protein, Tyrosine--tRNA ligase

ProteinName: Tyrosine--tRNA ligase / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 45.482191 kDa
SourceSpecies: Phaseolus vulgaris (French bean)
Source (engineered)Expression System: Escherichia coli (E. coli)

-
Component #3: nucleic-acid, tRNA-like structure from brome mosaic virus RNA 3

nucleic acidName: tRNA-like structure from brome mosaic virus RNA 3 / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GGCGUGGUUG ACACGCAGAC CUCUUACAAG AGUGUCUAGG UGCCUUUGAG AGUUACUCUU UGCUCUCUUC GGAAGAACCC UUAGGGGUUC GUGCAUGGGC UUGCAUAGCA AGUCUUAGAA UGCGGGUACC GUACAGUGUU GAAAAACACU GUAAAUCUCU AAAAGAGACC A
MassTheoretical: 55.044559 kDa
SourceSpecies: Brome mosaic virus

-
Experimental details

-
Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionpH: 7
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen Name: ETHANE / Temperature: 277 K / Humidity: 100 % / Details: Blot for 2.5 seconds before plunging..

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 60 e/Å2 / Illumination Mode: OTHER
LensCs: 2.7 mm / Imaging Mode: BRIGHT FIELD / Energy Filter: GIF Bioquantum
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Number of Projections: 129643
3D reconstructionResolution: 5.51 Å / Resolution Method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
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