[English] 日本語
Yorodumi
- EMDB-14704: Structure of human 80S ribosome obtained from ssDNA coated grid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-14704
TitleStructure of human 80S ribosome obtained from ssDNA coated grid
Map dataFinal map
Sample
  • Complex: human 80S ribosomeEukaryotic ribosome
    • RNA: RNA (615-MER)
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsHrebik D / Plevka P
Funding support Czech Republic, 1 items
OrganizationGrant numberCountry
Grant Agency of the Czech Republic Czech Republic
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Polyelectrolyte coating of cryo-EM grids improves lateral distribution and prevents aggregation of macromolecules.
Authors: Dominik Hrebík / Mária Gondová / Lucie Valentová / Tibor Füzik / Antonín Přidal / Jiří Nováček / Pavel Plevka /
Abstract: Cryo-electron microscopy (cryo-EM) is one of the primary methods used to determine the structures of macromolecules and their complexes. With the increased availability of cryo-electron microscopes, ...Cryo-electron microscopy (cryo-EM) is one of the primary methods used to determine the structures of macromolecules and their complexes. With the increased availability of cryo-electron microscopes, the preparation of high-quality samples has become a bottleneck in the cryo-EM structure-determination pipeline. Macromolecules can be damaged during the purification or preparation of vitrified samples for cryo-EM, making them prone to binding to the grid support, to aggregation or to the adoption of preferential orientations at the air-water interface. Here, it is shown that coating cryo-EM grids with a negatively charged polyelectrolyte, such as single-stranded DNA, before applying the sample reduces the aggregation of macromolecules and improves their distribution. The single-stranded DNA-coated grids enabled the determination of high-resolution structures from samples that aggregated on conventional grids. The polyelectrolyte coating reduces the diffusion of macromolecules and thus may limit the negative effects of the contact of macromolecules with the grid support and blotting paper, as well as of the shear forces on macromolecules during grid blotting. Coating grids with polyelectrolytes can readily be employed in any laboratory dealing with cryo-EM sample preparation, since it is fast, simple, inexpensive and does not require specialized equipment.
History
DepositionApr 1, 2022-
Header (metadata) releaseNov 23, 2022-
Map releaseNov 23, 2022-
UpdateNov 23, 2022-
Current statusNov 23, 2022Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_14704.png

Downloads & links

-
Map

FileDownload / File: emd_14704.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 300 pix.
= 321. Å		1.07 Å/pix.
x 300 pix.
= 321. Å		1.07 Å/pix.
x 300 pix.
= 321. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.0282865 - 0.08902308
Average (Standard dev.)0.0019046045 (±0.011653392)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 321.00003 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half Map 1

Fileemd_14704_half_map_1.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map 2

Fileemd_14704_half_map_2.map
AnnotationHalf Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : human 80S ribosome

EntireName: human 80S ribosomeEukaryotic ribosome
Components
  • Complex: human 80S ribosomeEukaryotic ribosome
    • RNA: RNA (615-MER)

-
Supramolecule #1: human 80S ribosome

SupramoleculeName: human 80S ribosome / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4.3 MDa

-
Macromolecule #1: RNA (615-MER)

MacromoleculeName: RNA (615-MER) / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.22354775 MDa
SequenceString: CGCGACCUCA GAUCAGACGU GGCGACCCGC UGAAUUUAAG CAUAUUAGUC AGCGGAGGAG AAGAAACUAA CCAGGAUUCC CUCAGUAAC GGCGAGUGAA CAGGGAAGAG CCCAGCGCCG AAUCCCCGCC CCGCGGCGGG GCGCGGGACA UGUGGCGUAC G GAAGACCC ...String:
CGCGACCUCA GAUCAGACGU GGCGACCCGC UGAAUUUAAG CAUAUUAGUC AGCGGAGGAG AAGAAACUAA CCAGGAUUCC CUCAGUAAC GGCGAGUGAA CAGGGAAGAG CCCAGCGCCG AAUCCCCGCC CCGCGGCGGG GCGCGGGACA UGUGGCGUAC G GAAGACCC GCUCCCCGGC GCCGCUCGUG GGGGGCCCAA GUCCUUCUGA UCGAGGCCCA GCCCGUGGAC GGUGUGAGGC CG GUAGCGG CCCCCGGCGC GCCGGGCCCG GGUCUUCCCG GAGUCGGGUU GCUUGGGAAU GCAGCCCAAA GCGGGUGGUA AAC UCCAUC UAAGGCUAAA UACCGGCACG AGACCGAUAG UCAACAAGUA CCGUAA(OMG)GGG AAAGUUGAAA AGAACUUUGA AG(A2M)AGAGAG UUCAAGAGGG CGUGAAACCG UUAAGAGGUA AACGGGUGGG GUCCGCGCAG UCCGCCCGGA GGAUUCA AC CCGGCGGCGG GUCCGGCCGU GUCGGCGGCC CGGCGGAUCU UUCCCGCGCG GGGGACCGUC CCCCGACCGG CGACCGGC C GCCGCCGGGC GCAUUUCCAC CGCGGCGGUG CGCCGCGACC GGCUCCGGGA CGGCU(2MG)GGGA AGGCCCGGCG GGGAA GGUG GCUCGGGGGC CCCCGAGUGU UACAGCCCCC CCGGCAGCAG CACUCGCCGA AUCCCGGGGC CGAGGGAGCG AGACCC GUC GCCGCGCUCU CCCCCCUCCC GGCGCGCCGG GGGGGGCCGG GCCACCCCUC CCACGGCGCG ACCGCUCGGG GCGGACU GU CCCCAGUGCG CCCCGGGCGG GUCGCGCCGU CGGGCCCGGG GGAGGCCACG CGCGCGUCCC CCGAAGAGGG GGACGGCG G AGCGAGCGCA CGGGGUCGGC GGCGACGUCG GCUACCCACC CGACCCGUCU UGAAACACGG ACCAAGGAGU CUAACACGU GCGCGAGUCG GGGGCUCGCA CGAAAGCCGC CGUGGCGCAA UGAAGGUGAA GGCCGGCGCG CUCGCCGGCC GAGGUGGGAU CCCGAGGCC UCUCCAGUCC GCCGAGGGCG CACCACCGGC CCGUCUCGCC CGCCGCGCCG GGGAGGUGGA GCACGAGCGC A CGUGUUAG GACCCGAAAG AUGGUGAACU AUGCCUGGGC AGGGCGAAGC CAGAGGAAAC UCUGGUGGAG GUCCGUAGCG GU CCUGACG UGCAAAUCGG UCGUCCGACC UGGGUAUAGG GGCGAAAGAC UAAUCGAACC AUCUAGUAGC UGGUUCCCUC CGA AGUUUC CCUCAGGAUA GCUGGCGCUC UCGCAGACCC GACGCCCGCC ACGCAGUUUU AUCCGGUAAA GCGAAUGAUU AGAG GUCUU GGGGCCGAAA CGAUCUCAAC CUAUUCUCAA ACUUUAAAUG GGUAAGAAGC CCGGCUCGCU GGCGUGGAGC CGGGC GUGG AAUGCGAGUG CCUAGUGGGC CACUUUUGGU AAGCAGAACU GGCGCUGCGG GAUGAACCGA ACGCCGGGUU AAGGCG CCC GAUGCCGACG CUCAUCAGAC CCCAGAAAAG GUGUUGGUUG AUAUAGACAG CAGGACGGUG GCCAUGGAAG UCGGAAU CC GCUAAGGAGU GUGUAACAAC UCACCUGCCG AAUCAACUAG CCCUGAAAAU GGAUGGCGCU GGAGCGUCGG GCCCAUAC C CGGCCGUCGC CGGCAGUCGA GAGUGGACGG GAGCGGCGGG CCGGAGCCCC GCGGACGCUA CGCCGCGACG AGUAGGAGG GCCGCUGCGG UGAGCCUUGA AGCCUAGGGC GCGGGCCCGG GUGGAGCCGC CGCAGGUGCA GAUCUUGGUG GUAGUAGCAA AUAUUCAAA CGAGAACUUU GAAGGCCGAA GUGGAGAAGG GUUCCAUGUG AACAGCAGUU GAACAUGGGU CAGUCGGUCC U GAGAGAUG GGCGAGCGCC GUUCCGAAGG GACGGGCGAU GGCCUCCGUU GCCCUCGGCC GAUCGAAAGG GAGUCGGGUU CA GAUCCCC GAAUCCGGAG UGGCGGAGAU GGGCGCCGCG AGGCGUCCAG UGCGGUAACG CGACCGAUCC CGGAGAAGCC GGC GGGAGC CCCGGGGAGA GUUCUCUUUU CUUUGUGAAG GGCAGGGCGC CCUGGAAUGG GUUCGCCCCG AGAGAGGGGC CCGU GCCUU GGAAAGCGUC GCGGUUCCGG CGGCGUCCGG UGAGCUCUCG CUGGCCCUUG AAAAUCCGGG GGAGAGGGUG UAAAU CUCG CGCCGGGCCG UACCCAUAUC CGCAGCAGGU CUCCAAGGUG AACAGCCUCU GGCAUGUUGG AACAAUGUAG GUAAGG GAA GUCGGCAAGC CGGAUCCGUA ACUUCGGGAU AAGGAUUGGC UCUAAGGGCU GGGUCGGUCG CGGCCGGCGC CUAGCAG CC GACUUAGAAC UGGUGCGGAC CAGGGGAAUC CGACUGUUUA AUUAAAACAA AGCAUCGCGA AGGCCCGCGG CGGGUGUU G ACGCGAUGUG AUUUCUGCCC AGUGCUCUGA AUGUCAAAGU GAAGAAAUUC AAUGAAGCGC GGGUAAACGG CGGGAGUAA CUAUGACUCU CUUAAGGUAG CCAAAUGCCU CGUCAUCUAA UUAGUGACGC GCAUGAAUGG AUGAACGAGA UUCCCACUGU CCCUACCUA CUAUCCAGCG AAACCACAGC CAAGGGAACG GGCUUGGCGG AAUCAGCGGG GAAAGAAGAC CCUGUUGAGC U UGACUCUA GUCUGGCACG GUGAAGAGAC AUGAGAGGUG UAGAAUAAGU GGGAGGCCCC CGGCGCCCCC CCGGUGUCCC CG CGAGGGG CCCGGGGCGG GGUCCGCCGG CCCUGCGGGC CGCCGGUGAA AUACCACUAC UCUGAUCGUU UUUUCACUGA CCC GGUGAG GCGGGGGGGC GAGCCCCGAG GGGCUCUCGC UUCUGGCGCC AAGCGCCCGG CCGCGCGCCG GCCGGGCGCG ACCC GCUCC GGGGACAGUG CCAGGUGGGG AGUUUGACUG GGGCGGUACA CCUGUCAAAC GGUAACGCAG GUGUCCUAAG GCGAG CUCA GGGAGGACAG AAACCUCCCG UGGAGCAGAA GGGCAAAAGC UCGCUUGAUC UUGAUUUUCA GUACGAAUAC AGACCG UGA AAGCGGGGCC UCACGAUCCU UCUGACCUUU UGGGUUUUAA GCAGGAGGUG UCAGAAAAGU UACCACAGGG AUAACUG GC UUGUGGCGGC CAAGCGUUCA UAGCGACGUC GCUUUUUGAU CCUUCGAUGU CGGCUCUUCC UAUCAUUGUG AAGCAGAA U UCACCAAGCG UUGGAUUGUU CACCCACUAA UAGGGAACGU GAGCUGGGUU UAGACCGUCG UGAGACAGGU UAGUUUUAC CCUACUGAUG AUGUGUUGUU GCCAUGGUAA UCCUGCUCAG UACGAGAGGA ACCGCAGGUU CAGACAUUUG GUGUAUGUGC UUGGCUGAG GAGCCAAUGG GGCGAAGCUA CCAUCUGUGG GAUUAUGACU GAACGCCUCU AAGUCAGAAU CCCGCCCAGG C GGAACGAU ACGGCAGCGC CGCGGAGCCU CGGUUGGCCU CGGAUAGCCG GUCCCCCGCC GGGGUCCGGU GCGGAGUGCC CU UCGUCCU GGGAAACGGG GCGCGGCCGG AGAGGCGGCC GCCCCCUCGC CCGUCACGCA CCGCACGUUC GUGGGGAACC UGG CGCUAA ACCAUUCGUA GACGACCUGC UUCUGGGUCG GGGUUUCGUA CGUAGCAGAG CAGCUCCCUC GCUGCGAUCU AUUG AAAGU CAGCCCUCGA CACAAGGGUU UGU

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.2 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
25.0 mMHEPES
125.0 mMpotassium chlorideKCl
5.0 mMMg(AOC)2
1.0 mMdithiothreitol
0.01 %DDM
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 5.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: NITROGEN
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details: 3 s blot time,30 s waiting time, ssDNA covered grid.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Number grids imaged: 1 / Number real images: 4527 / Average exposure time: 1.0 sec. / Average electron dose: 64.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 133524
CTF correctionSoftware - Name: Gctf
Startup modelType of model: EMDB MAP
EMDB ID:

2938

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 5 / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 66372
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

6qzp

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 177 / Target criteria: correlation coefficient
Output model

PDB-7zfw:
Structure of human 80S ribosome obtained from ssDNA coated grid

+
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