[English] 日本語
Yorodumi
- PDB-4v7h: Structure of the 80S rRNA and proteins and P/E tRNA for eukaryoti... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4v7h
TitleStructure of the 80S rRNA and proteins and P/E tRNA for eukaryotic ribosome based on cryo-EM map of Thermomyces lanuginosus ribosome at 8.9A resolution
Components
  • (40S ribosomal protein ...) x 15
  • (60S ribosomal protein ...) x 31
  • 18S rRNA18S ribosomal RNA
  • 26S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • P/E tRNA
  • RACK1 proteinReceptor for activated C kinase 1
  • s19e protein
KeywordsRIBOSOME / eukaryotic ribosome / 80S / RACK1 protein / flexible fitting
Function / homologyRNA / RNA (> 10) / RNA (> 100) / RNA (> 1000)
Function and homology information
Biological speciesThermomyces lanuginosus (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.9 Å
AuthorsTaylor, D.J. / Devkota, B. / Huang, A.D. / Topf, M. / Narayanan, E. / Sali, A. / Harvey, S.C. / Frank, J.
CitationJournal: Structure / Year: 2009
Title: Comprehensive molecular structure of the eukaryotic ribosome.
Authors: Derek J Taylor / Batsal Devkota / Andrew D Huang / Maya Topf / Eswar Narayanan / Andrej Sali / Stephen C Harvey / Joachim Frank /
Abstract: Despite the emergence of a large number of X-ray crystallographic models of the bacterial 70S ribosome over the past decade, an accurate atomic model of the eukaryotic 80S ribosome is still not ...Despite the emergence of a large number of X-ray crystallographic models of the bacterial 70S ribosome over the past decade, an accurate atomic model of the eukaryotic 80S ribosome is still not available. Eukaryotic ribosomes possess more ribosomal proteins and ribosomal RNA than do bacterial ribosomes, which are implicated in extraribosomal functions in the eukaryotic cells. By combining cryo-EM with RNA and protein homology modeling, we obtained an atomic model of the yeast 80S ribosome complete with all ribosomal RNA expansion segments and all ribosomal proteins for which a structural homolog can be identified. Mutation or deletion of 80S ribosomal proteins can abrogate maturation of the ribosome, leading to several human diseases. We have localized one such protein unique to eukaryotes, rpS19e, whose mutations are associated with Diamond-Blackfan anemia in humans. Additionally, we characterize crucial interactions between the dynamic stalk base of the ribosome with eukaryotic elongation factor 2.
History
DepositionSep 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 3JYV, 3JYW, 3JYX
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Apr 22, 2015Group: Other
Revision 1.3Nov 22, 2017Group: Data collection / Category: em_image_scans
Revision 1.4Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id
Revision 1.5Dec 18, 2019Group: Derived calculations / Other / Category: atom_sites / struct_conn
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _struct_conn.pdbx_leaving_atom_flag
Revision 1.6Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-1345
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AA: 18S rRNA
AB: 40S ribosomal protein S0(A)
AC: 40S ribosomal protein S3
AD: 40S ribosomal protein S9(A)
AE: 40S ribosomal protein S2
AG: 40S ribosomal protein S5
AH: 40S ribosomal protein S22(A)
AI: 40S ribosomal protein S16(A)
AJ: 40S ribosomal protein S20
AK: 40S ribosomal protein S14(A)
AL: 40S ribosomal protein S23(A)
AM: 40S ribosomal protein S18
AN: 40S ribosomal protein S29(A)
AO: 40S ribosomal protein S13
AQ: 40S ribosomal protein S11
AS: 40S ribosomal protein S15
AR: RACK1 protein
AT: s19e protein
A7: P/E tRNA
B0: 60S ribosomal protein L32
B1: 60S ribosomal protein L39
B2: 60S ribosomal protein L30e
B8: 60S ribosomal protein LP0
B9: 60S ribosomal protein L43
BA: 60S ribosomal protein L1
BB: 60S ribosomal protein L2
BC: 60S ribosomal protein L3
BD: 60S ribosomal protein L4(B)
BE: 60S ribosomal protein L5
BF: 60S ribosomal protein L7(A)
BG: 60S ribosomal protein L8(A)
BH: 60S ribosomal protein L9(A)
BI: 60S ribosomal protein L10
BJ: 60S ribosomal protein L11(B)
BK: 60S ribosomal protein L12
BL: 60S ribosomal protein L15(A)
BM: 60S ribosomal protein L16(A)
BN: 60S ribosomal protein L17(A)
BO: 60S ribosomal protein L18(A)
BP: 60S ribosomal protein L19
BQ: 60S ribosomal protein L21(A)
BR: 60S ribosomal protein L23
BS: 60S ribosomal protein L24(A)
BT: 60S ribosomal protein L25
BU: 60S ribosomal protein L26(A)
BV: 60S ribosomal protein L28
BW: 60S ribosomal protein L31(A)
BX: 60S ribosomal protein L35
BY: 60S ribosomal protein L37(A)
BZ: 60S ribosomal protein L42
B3: 5S ribosomal RNA
B4: 5.8S ribosomal RNA
B5: 26S ribosomal RNA


Theoretical massNumber of molelcules
Total (without water)2,462,33253
Polymers2,462,33253
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
RNA chain , 5 types, 5 molecules AAA7B3B4B5

#1: RNA chain 18S rRNA / 18S ribosomal RNA


Mass: 567333.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#19: RNA chain P/E tRNA


Mass: 24890.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#51: RNA chain 5S ribosomal RNA /


Mass: 36339.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#52: RNA chain 5.8S ribosomal RNA /


Mass: 50369.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#53: RNA chain 26S ribosomal RNA /


Mass: 1024354.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)

-
40S ribosomal protein ... , 15 types, 15 molecules ABACADAEAGAHAIAJAKALAMANAOAQAS

#2: Protein 40S ribosomal protein S0(A) / Ribosome


Mass: 21236.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#3: Protein 40S ribosomal protein S3 /


Mass: 20925.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#4: Protein 40S ribosomal protein S9(A) / Ribosome


Mass: 18415.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#5: Protein 40S ribosomal protein S2 /


Mass: 17146.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#6: Protein 40S ribosomal protein S5 /


Mass: 20728.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#7: Protein 40S ribosomal protein S22(A) / Ribosome


Mass: 14100.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#8: Protein 40S ribosomal protein S16(A) / Ribosome


Mass: 15391.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#9: Protein 40S ribosomal protein S20 /


Mass: 10980.823 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#10: Protein 40S ribosomal protein S14(A) / Ribosome


Mass: 13191.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#11: Protein 40S ribosomal protein S23(A) / Ribosome


Mass: 12879.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#12: Protein 40S ribosomal protein S18 /


Mass: 15301.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#13: Protein/peptide 40S ribosomal protein S29(A) / Ribosome


Mass: 5953.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#14: Protein 40S ribosomal protein S13 /


Mass: 9842.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#15: Protein 40S ribosomal protein S11 /


Mass: 9133.838 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#16: Protein 40S ribosomal protein S15 /


Mass: 7863.368 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)

-
Protein , 2 types, 2 molecules ARAT

#17: Protein RACK1 protein / Receptor for activated C kinase 1


Mass: 34209.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#18: Protein s19e protein


Mass: 15656.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)

+
60S ribosomal protein ... , 31 types, 31 molecules B0B1B2B8B9BABBBCBDBEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBTBUBVBWBXBYBZ

#20: Protein 60S ribosomal protein L32 /


Mass: 12495.563 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#21: Protein/peptide 60S ribosomal protein L39 /


Mass: 6043.208 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#22: Protein 60S ribosomal protein L30e / Ribosome


Mass: 10687.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#23: Protein 60S ribosomal protein LP0 /


Mass: 13436.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#24: Protein 60S ribosomal protein L43 /


Mass: 7737.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#25: Protein 60S ribosomal protein L1 /


Mass: 24014.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#26: Protein 60S ribosomal protein L2 /


Mass: 26203.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#27: Protein 60S ribosomal protein L3 /


Mass: 40945.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#28: Protein 60S ribosomal protein L4(B) / Ribosome


Mass: 27670.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#29: Protein 60S ribosomal protein L5 /


Mass: 27062.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#30: Protein 60S ribosomal protein L7(A) / Ribosome


Mass: 22063.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#31: Protein 60S ribosomal protein L8(A) / Ribosome


Mass: 12028.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#32: Protein 60S ribosomal protein L9(A) / Ribosome


Mass: 20164.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#33: Protein 60S ribosomal protein L10 /


Mass: 18890.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#34: Protein 60S ribosomal protein L11(B) / Ribosome


Mass: 17021.576 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#35: Protein 60S ribosomal protein L12 /


Mass: 14800.197 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#36: Protein 60S ribosomal protein L15(A) / Ribosome


Mass: 22901.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#37: Protein 60S ribosomal protein L16(A) / Ribosome


Mass: 18659.998 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#38: Protein 60S ribosomal protein L17(A) / Ribosome


Mass: 16833.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#39: Protein 60S ribosomal protein L18(A) / Ribosome


Mass: 13216.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#40: Protein 60S ribosomal protein L19 /


Mass: 18692.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#41: Protein 60S ribosomal protein L21(A) / Ribosome


Mass: 12686.745 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#42: Protein 60S ribosomal protein L23 /


Mass: 13976.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#43: Protein/peptide 60S ribosomal protein L24(A) / Ribosome


Mass: 5230.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#44: Protein 60S ribosomal protein L25 /


Mass: 9146.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#45: Protein 60S ribosomal protein L26(A) / Ribosome


Mass: 13020.296 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#46: Protein 60S ribosomal protein L28 /


Mass: 15914.622 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#47: Protein 60S ribosomal protein L31(A) / Ribosome


Mass: 9421.024 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#48: Protein 60S ribosomal protein L35 /


Mass: 8638.103 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#49: Protein 60S ribosomal protein L37(A) / Ribosome


Mass: 5772.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)
#50: Protein 60S ribosomal protein L42 /


Mass: 10711.857 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus)

-
Details

Sequence detailsTHE RIBOSOME ORIGINATES FROM THERMOMYCES LANUGINOSUS HOWEVER THE MODEL WAS BUILT BASED ON THE ...THE RIBOSOME ORIGINATES FROM THERMOMYCES LANUGINOSUS HOWEVER THE MODEL WAS BUILT BASED ON THE SEQUENCE OF SACCHAROMYCES CEREVISIAE.

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY / Number of used crystals: 1
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Thermomyces lanuginosus ribosome / Type: RIBOSOME
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE
Details: Apply sample, wait 30s, blot for 6s, plunge in liquid ethane

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30 / Date: Jul 7, 2005
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 39000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1400 nm
Specimen holderTemperature: 84 K
Image recordingElectron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM

-
Processing

SoftwareName: OTHER / Classification: refinement
EM software
IDNameCategory
1Yup.scxmodel fitting
2SPIDER3D reconstruction
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 8.9 Å / Num. of particles: 102689
Details: SPIDER package. Residue H LYS 32 and Residue H VAL 33 are not properly linked. Distance of C-N bond is 2.59 Angstrom. Residue T LYS 78 and Residue T LEU 79 are not properly linked. Distance ...Details: SPIDER package. Residue H LYS 32 and Residue H VAL 33 are not properly linked. Distance of C-N bond is 2.59 Angstrom. Residue T LYS 78 and Residue T LEU 79 are not properly linked. Distance of C-N bond is 2.49 Angstrom.
Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation / Details: METHOD--Flexible fitting
RefinementHighest resolution: 8.9 Å / Occupancy max: 1 / Occupancy min: 0
Displacement parametersBiso max: 362.94 Å2 / Biso mean: 4.424 Å2 / Biso min: 0 Å2
Refinement stepCycle: LAST / Highest resolution: 8.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18221 39106 0 0 57327

+
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