[English] 日本語
Yorodumi
- PDB-6tpq: RNase M5 bound to 50S ribosome with precursor 5S rRNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tpq
TitleRNase M5 bound to 50S ribosome with precursor 5S rRNA
Components
  • (50S ribosomal protein ...) x 27
  • Ribonuclease M5
  • pre-23S rRNA
  • pre-5S rRNA
KeywordsRIBOSOMAL PROTEIN / RNase M5 / M5 / complex / ribosome / 50S / RNA maturation / RNA processing / precursor 5S rRNA / pre-5S rRNA / 5S rRNA / L18 / Toprim domain / RNase
Function / homology
Function and homology information


ribonuclease M5 / ribonuclease M5 activity / positive regulation of rRNA processing / nucleoid / rRNA processing / large ribosomal subunit / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit ...ribonuclease M5 / ribonuclease M5 activity / positive regulation of rRNA processing / nucleoid / rRNA processing / large ribosomal subunit / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / DNA binding / RNA binding / metal ion binding / cytoplasm
Similarity search - Function
Ribonuclease M5 / Ribonuclease M5, C-terminal domain / Domain of unknown function (DUF4093) / Ribonuclease M5-like, TOPRIM domain / Toprim domain / TOPRIM / Toprim domain / Toprim domain profile. / TOPRIM domain / Ribosomal protein L10, eubacterial, conserved site ...Ribonuclease M5 / Ribonuclease M5, C-terminal domain / Domain of unknown function (DUF4093) / Ribonuclease M5-like, TOPRIM domain / Toprim domain / TOPRIM / Toprim domain / Toprim domain profile. / TOPRIM domain / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 / : / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10 / Ribosomal protein L16 signature 1. / Ribosomal protein L10P / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L17 signature. / Ribosomal protein L36 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L32p, bacterial type / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L20 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / Ribosomal protein L30, bacterial-type / : / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L16 / L28p-like / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal L32p protein family / Ribosomal protein L24 / Ribosomal protein L32p / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L13, bacterial-type / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal protein L30, conserved site / Ribosomal protein L30 signature. / Ribosomal protein L5, conserved site / Ribosomal protein L5 signature. / Ribosomal protein L2 signature. / Ribosomal protein L29, conserved site / Ribosomal protein L29 signature. / : / Ribosomal protein L2, conserved site
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ribonuclease M5 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL34 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ribonuclease M5 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL33A / Large ribosomal subunit protein uL13
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
Bacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / Resolution: 3.07 Å
AuthorsOerum, S. / Dendooven, T. / Gilet, L. / Catala, M. / Degut, C. / Trinquier, A. / Barraud, P. / Luisi, B. / Condon, C. / Tisne, C.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research Agency France
CitationJournal: Mol Cell / Year: 2020
Title: Structures of B. subtilis Maturation RNases Captured on 50S Ribosome with Pre-rRNAs.
Authors: Stephanie Oerum / Tom Dendooven / Marjorie Catala / Laetitia Gilet / Clément Dégut / Aude Trinquier / Maxime Bourguet / Pierre Barraud / Sarah Cianferani / Ben F Luisi / Ciarán Condon / Carine Tisné /
Abstract: The pathways for ribosomal RNA (rRNA) maturation diverge greatly among the domains of life. In the Gram-positive model bacterium, Bacillus subtilis, the final maturation steps of the two large ...The pathways for ribosomal RNA (rRNA) maturation diverge greatly among the domains of life. In the Gram-positive model bacterium, Bacillus subtilis, the final maturation steps of the two large ribosomal subunit (50S) rRNAs, 23S and 5S pre-rRNAs, are catalyzed by the double-strand specific ribonucleases (RNases) Mini-RNase III and RNase M5, respectively. Here we present a protocol that allowed us to solve the 3.0 and 3.1 Å resolution cryoelectron microscopy structures of these RNases poised to cleave their pre-rRNA substrates within the B. subtilis 50S particle. These data provide the first structural insights into rRNA maturation in bacteria by revealing how these RNases recognize and process double-stranded pre-rRNA. Our structures further uncover how specific ribosomal proteins act as chaperones to correctly fold the pre-rRNA substrates and, for Mini-III, anchor the RNase to the ribosome. These r-proteins thereby serve a quality-control function in the process from accurate ribosome assembly to rRNA processing.
History
DepositionDec 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 28, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3May 22, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-10543
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Ribonuclease M5
V: pre-5S rRNA
A: Ribonuclease M5
b: 50S ribosomal protein L10
U: pre-23S rRNA
W: 50S ribosomal protein L2
X: 50S ribosomal protein L3
Y: 50S ribosomal protein L4
Z: 50S ribosomal protein L5
a: 50S ribosomal protein L6
c: 50S ribosomal protein L13
d: 50S ribosomal protein L14
e: 50S ribosomal protein L15
f: 50S ribosomal protein L16
g: 50S ribosomal protein L17
h: 50S ribosomal protein L18
i: 50S ribosomal protein L19
j: 50S ribosomal protein L20
k: 50S ribosomal protein L21
l: 50S ribosomal protein L22
m: 50S ribosomal protein L23
n: 50S ribosomal protein L24
o: 50S ribosomal protein L27
p: 50S ribosomal protein L32
q: 50S ribosomal protein L33 1
r: 50S ribosomal protein L34
s: 50S ribosomal protein L35
t: 50S ribosomal protein L36
u: 50S ribosomal protein L28
v: 50S ribosomal protein L29
w: 50S ribosomal protein L30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,390,813253
Polymers1,385,29431
Non-polymers5,519222
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry, Components of the 50S particle were determined by electrophoresis followed by band digestion and mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Protein , 1 types, 2 molecules BA

#1: Protein Ribonuclease M5 / RNase M5 / Ribosomal RNA terminal maturase M5


Mass: 20778.699 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: rnmV, B4109_0079, B4114_0027, D9548_05595, GT94_11730, TGS27_1231
Production host: Escherichia coli (E. coli) / References: UniProt: A0A087LGV4, ribonuclease M5

-
RNA chain , 2 types, 2 molecules VU

#2: RNA chain pre-5S rRNA


Mass: 39687.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: GenBank: 1150402534
#4: RNA chain pre-23S rRNA


Mass: 948320.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: GenBank: 467326

+
50S ribosomal protein ... , 27 types, 27 molecules bWXYZacdefghijklmnopqrstuvw

#3: Protein 50S ribosomal protein L10 / BL5 / Cold acclimatization protein / CAP / Vegetative protein 300 / VEG300


Mass: 18101.748 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42923
#5: Protein 50S ribosomal protein L2 / BL2


Mass: 30335.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42919
#6: Protein 50S ribosomal protein L3 / BL3


Mass: 22723.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42920
#7: Protein 50S ribosomal protein L4


Mass: 22424.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42921
#8: Protein 50S ribosomal protein L5 / BL6


Mass: 20177.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12877
#9: Protein 50S ribosomal protein L6 / BL10


Mass: 19543.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P46898
#10: Protein 50S ribosomal protein L13


Mass: 16407.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P70974
#11: Protein 50S ribosomal protein L14


Mass: 13175.288 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12875
#12: Protein 50S ribosomal protein L15


Mass: 15410.694 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P19946
#13: Protein 50S ribosomal protein L16


Mass: 16223.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P14577
#14: Protein 50S ribosomal protein L17 / BL15 / BL21


Mass: 13774.806 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P20277
#15: Protein 50S ribosomal protein L18 / BL16


Mass: 12993.829 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P46899
#16: Protein 50S ribosomal protein L19


Mass: 13416.853 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: O31742
#17: Protein 50S ribosomal protein L20


Mass: 13669.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P55873
#18: Protein 50S ribosomal protein L21 / BL20


Mass: 11296.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P26908
#19: Protein 50S ribosomal protein L22


Mass: 12481.608 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42060
#20: Protein 50S ribosomal protein L23


Mass: 10978.813 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42924
#21: Protein 50S ribosomal protein L24 / 12 kDa DNA-binding protein / BL23 / HPB12


Mass: 11166.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P0CI78
#22: Protein 50S ribosomal protein L27 / BL24 / BL30


Mass: 10391.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P05657
#23: Protein 50S ribosomal protein L32


Mass: 6745.073 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: O34687
#24: Protein/peptide 50S ribosomal protein L33 1


Mass: 5915.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P56849
#25: Protein/peptide 50S ribosomal protein L34


Mass: 5271.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P05647
#26: Protein 50S ribosomal protein L35


Mass: 7581.128 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P55874
#27: Protein/peptide 50S ribosomal protein L36 / BL38 / Ribosomal protein B / Ribosomal protein II


Mass: 4318.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P20278
#28: Protein 50S ribosomal protein L28


Mass: 6826.144 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P37807
#29: Protein 50S ribosomal protein L29


Mass: 7728.029 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12873
#30: Protein 50S ribosomal protein L30 / BL27


Mass: 6650.795 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P19947

-
Non-polymers , 2 types, 222 molecules

#31: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 219 / Source method: obtained synthetically / Formula: Mg
#32: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1RNase M5 bound to 50S ribosome with precursor 5S rRNARIBOSOME#1-#300MULTIPLE SOURCES
2Ribonuclease M5COMPLEX#11RECOMBINANT
350S ribosome with precursor 5S rRNACOMPLEX#2-#301NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
13Bacillus subtilis subsp. subtilis str. 168 (bacteria)224308
22Geobacillus stearothermophilus (bacteria)1422
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO

-
Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 23.94 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

-
Processing

EM software
IDNameVersionCategory
7UCSF Chimera1.11.2model fitting
9PHENIX1.16model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 92799 / Symmetry type: POINT
Atomic model buildingPDB-ID: 3J3V

3j3v


Accession code: 3J3V / 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://pdbjlvh1.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