[English] 日本語
Yorodumi
- PDB-8r6f: CryoEM structure of wheat 40S ribosomal subunit, body domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8r6f
TitleCryoEM structure of wheat 40S ribosomal subunit, body domain
Components
  • (30S ribosomal protein ...) x 2
  • (40S ribosomal protein ...) x 10
  • (Small ribosomal subunit protein ...) x 5
  • Genome assembly, chromosome: II
  • Large ribosomal subunit protein eL41z/eL41y/eL41x/eL41w/eL41v
  • RNA (1177-MER)
  • S5 DRBM domain-containing protein
KeywordsRIBOSOME / small ribosomal subunit / wheat / eukaryotes / 40S
Function / homology
Function and homology information


plastid / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small-subunit processome / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / rRNA processing / cytosolic small ribosomal subunit / cytoplasmic translation / rRNA binding ...plastid / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small-subunit processome / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / rRNA processing / cytosolic small ribosomal subunit / cytoplasmic translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / nucleolus / RNA binding / metal ion binding / cytosol
Similarity search - Function
Ribosomal protein L41 / Ribosomal protein L41 / : / Ribosomal protein S21e, conserved site / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S26e signature. / : / Ribosomal protein S2, eukaryotic ...Ribosomal protein L41 / Ribosomal protein L41 / : / Ribosomal protein S21e, conserved site / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S26e signature. / : / Ribosomal protein S2, eukaryotic / Ribosomal protein S30 / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S21e signature. / Ribosomal protein S3Ae, conserved site / Ribosomal protein S30 / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S5, eukaryotic/archaeal / 40S ribosomal protein S11, N-terminal / Ribosomal protein S8e, conserved site / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S6, eukaryotic / Ribosomal protein S7e / Ribosomal protein S4e, N-terminal, conserved site / 40S ribosomal protein S4, C-terminal domain / Ribosomal S17 / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S27 / Ribosomal protein S6/S6e/A/B/2, conserved site / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal protein S7e / Ribosomal protein S8e / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S6e / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S6e / Ribosomal protein S4/S9, eukaryotic/archaeal / RS4NT (NUC023) domain / Ribosomal protein S27 / Ribosomal S3Ae family / Ribosomal family S4e / Ribosomal protein S7e signature. / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S6e / Ribosomal protein S3Ae signature. / Ribosomal protein S27e signature. / Ribosomal protein S4e signature. / Ribosomal protein S8e signature. / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein S24e / Ribosomal protein S24e / Ribosomal protein S6e signature. / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S8e / Ribosomal protein S2 signature 2. / : / Ribosomal protein S17, conserved site / Ribosomal protein S2, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S4, conserved site / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9 / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S5 / Ribosomal protein S5, N-terminal / Ribosomal S11, conserved site / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, C-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S8 / Ribosomal protein S17 signature. / Ribosomal protein S5, C-terminal domain / S4 RNA-binding domain / Ribosomal protein S11 / RNA-binding S4 domain / RNA-binding S4 domain superfamily / Ribosomal protein S8 signature. / Ribosomal protein S11
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S4 / 40S ribosomal protein S8 / 40S ribosomal protein S27 / 40S ribosomal protein S17 / Small ribosomal subunit protein eS1 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S4 / 40S ribosomal protein S8 / 40S ribosomal protein S27 / 40S ribosomal protein S17 / Small ribosomal subunit protein eS1 / 40S ribosomal protein S26 / S5 DRBM domain-containing protein / 40S ribosomal protein S24 / 40S ribosomal protein S30 / 30S ribosomal protein S11, chloroplastic / Genome assembly, chromosome: II / Small ribosomal subunit protein uS8c / Large ribosomal subunit protein eL41z/eL41y/eL41x/eL41w/eL41v / 40S ribosomal protein S7 / Small ribosomal subunit protein uS17 N-terminal domain-containing protein / 40S ribosomal protein S6 / Small ribosomal subunit protein uS2 / 30S ribosomal protein S4, chloroplastic / 40S ribosomal protein S23 / Small ribosomal subunit protein uS15 N-terminal domain-containing protein
Similarity search - Component
Biological speciesTriticum aestivum (bread wheat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.34 Å
AuthorsKravchenko, O.V. / Baymukhametov, T.N. / Afonina, Z.A. / Vasilenko, K.S.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation19-74-20186 Russian Federation
CitationJournal: Int J Mol Sci / Year: 2023
Title: High-Resolution Structure and Internal Mobility of a Plant 40S Ribosomal Subunit.
Authors: Olesya V Kravchenko / Timur N Baymukhametov / Zhanna A Afonina / Konstantin S Vassilenko /
Abstract: Ribosome is a major part of the protein synthesis machinery, and analysis of its structure is of paramount importance. However, the structure of ribosomes from only a limited number of organisms has ...Ribosome is a major part of the protein synthesis machinery, and analysis of its structure is of paramount importance. However, the structure of ribosomes from only a limited number of organisms has been resolved to date; it especially concerns plant ribosomes and ribosomal subunits. Here, we report a high-resolution cryo-electron microscopy reconstruction of the small subunit of the (common wheat) cytoplasmic ribosome. A detailed atomic model was built that includes the majority of the rRNA and some of the protein modifications. The analysis of the obtained data revealed structural peculiarities of the 40S subunit in the monocot plant ribosome. We applied the 3D Flexible Refinement approach to analyze the internal mobility of the 40S subunit and succeeded in decomposing it into four major motions, describing rotations of the head domain and a shift in the massive rRNA expansion segment. It was shown that these motions are almost uncorrelated and that the 40S subunit is flexible enough to spontaneously adopt any conformation it takes as a part of a translating ribosome or ribosomal complex. Here, we introduce the first high-resolution structure of an isolated plant 40S subunit and the first quantitative analysis of the flexibility of small ribosomal subunits, hoping that it will help in studying various aspects of ribosome functioning.
History
DepositionNov 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 24, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
Y: 40S ribosomal protein S24
X: 40S ribosomal protein S23
E: 40S ribosomal protein S4
O: 30S ribosomal protein S11, chloroplastic
W: Small ribosomal subunit protein uS8c
b: 40S ribosomal protein S27
e: 40S ribosomal protein S30
k: Small ribosomal subunit protein uS2
B: Small ribosomal subunit protein eS1
V: Genome assembly, chromosome: II
a: 40S ribosomal protein S26
J: 30S ribosomal protein S4, chloroplastic
C: S5 DRBM domain-containing protein
G: 40S ribosomal protein S6
H: 40S ribosomal protein S7
h: 40S ribosomal protein S17
L: Small ribosomal subunit protein uS17 N-terminal domain-containing protein
N: Small ribosomal subunit protein uS15 N-terminal domain-containing protein
n: Large ribosomal subunit protein eL41z/eL41y/eL41x/eL41w/eL41v
I: 40S ribosomal protein S8
A: RNA (1177-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)966,15468
Polymers964,76321
Non-polymers1,39147
Water19,2221067
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
40S ribosomal protein ... , 10 types, 10 molecules YXEbeaGHhI

#1: Protein 40S ribosomal protein S24 /


Mass: 15769.710 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6RHV8
#2: Protein 40S ribosomal protein S23 /


Mass: 15696.476 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5FV77
#3: Protein 40S ribosomal protein S4 /


Mass: 30008.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A1D5SLI4
#6: Protein 40S ribosomal protein S27 /


Mass: 9583.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A341UET3
#7: Protein 40S ribosomal protein S30 /


Mass: 6934.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6S9M7
#11: Protein 40S ribosomal protein S26 /


Mass: 15319.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6KQB8
#14: Protein 40S ribosomal protein S6 /


Mass: 28522.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5C8N6
#15: Protein 40S ribosomal protein S7 /


Mass: 22297.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q5I7K2
#16: Protein 40S ribosomal protein S17 /


Mass: 16479.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B5XY60
#20: Protein 40S ribosomal protein S8 /


Mass: 25183.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A1D5UKZ4

-
30S ribosomal protein ... , 2 types, 2 molecules OJ

#4: Protein 30S ribosomal protein S11, chloroplastic / Ribosome


Mass: 16398.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: IAS - BETA-L-ASPARTIC ACID post-translational modification in the protein
Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6SS17
#12: Protein 30S ribosomal protein S4, chloroplastic / Ribosome


Mass: 22534.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5FPA7

-
Small ribosomal subunit protein ... , 5 types, 5 molecules WkBLN

#5: Protein Small ribosomal subunit protein uS8c


Mass: 14815.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: E2F3W4
#8: Protein Small ribosomal subunit protein uS2


Mass: 33300.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5E2W7
#9: Protein Small ribosomal subunit protein eS1


Mass: 30043.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6IU74
#17: Protein Small ribosomal subunit protein uS17 N-terminal domain-containing protein


Mass: 17841.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5BFB7
#18: Protein Small ribosomal subunit protein uS15 N-terminal domain-containing protein


Mass: 17132.303 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5I035

-
Protein , 2 types, 2 molecules VC

#10: Protein Genome assembly, chromosome: II


Mass: 8993.040 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: AME -N-ACETYLMETHIONINE post translational modification
Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A7H4LCS1
#13: Protein S5 DRBM domain-containing protein


Mass: 30081.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6KRQ3

-
Protein/peptide / RNA chain , 2 types, 2 molecules nA

#19: Protein/peptide Large ribosomal subunit protein eL41z/eL41y/eL41x/eL41w/eL41v


Mass: 3445.437 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: P62120
#21: RNA chain RNA (1177-MER)


Mass: 584382.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)

-
Non-polymers , 4 types, 1114 molecules

#22: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#23: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: Mg
#24: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: K
#25: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1067 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: small ribosomal subunit from Triticum aestivum (common wheat)
Type: RIBOSOME / Entity ID: #1-#21 / Source: NATURAL
Source (natural)Organism: Triticum aestivum (bread wheat)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 75000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 600 nm / Cs: 0.1 mm / C2 aperture diameter: 100 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.6 sec. / Electron dose: 84 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6201
Image scansWidth: 4096 / Height: 4096 / Movie frames/image: 32 / Used frames/image: 0-32

-
Processing

EM software
IDNameVersionCategory
7UCSF Chimera1.14model fitting
9cryoSPARC4.2.1initial Euler assignment
10cryoSPARC4.2.1final Euler assignment
13PHENIX1.21model refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 982063
3D reconstructionResolution: 2.34 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 256000 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingPDB-ID: 7qix

7qix


Accession code: 7qix / Source name: PDB / Type: experimental model

+
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