[English] 日本語
Yorodumi
- PDB-9bsl: 45SRbgA particle in complex with RbgA and YphC. Class A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9bsl
Title45SRbgA particle in complex with RbgA and YphC. Class A
Components
  • (Large ribosomal subunit protein ...) x 19
  • 23S rRNA
  • GTPase Der
  • Ribosome biogenesis GTPase A
KeywordsRIBOSOME / ribosome assembly / YphC
Function / homology
Function and homology information


positive regulation of rRNA processing / nucleoid / rRNA processing / regulation of translation / ribosome biogenesis / large ribosomal subunit / transferase activity / ribosome binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding ...positive regulation of rRNA processing / nucleoid / rRNA processing / regulation of translation / ribosome biogenesis / large ribosomal subunit / transferase activity / ribosome binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / GTPase activity / mRNA binding / GTP binding / DNA binding / RNA binding / cytoplasm
Similarity search - Function
EngA-type guanine nucleotide-binding (G) domain / EngA-type guanine nucleotide-binding (G) domain profile. / GTP-binding protein EngA / GTP-binding protein, ribosome biogenesis / GTPase Der, C-terminal KH-domain-like / KH-domain-like of EngA bacterial GTPase enzymes, C-terminal / GTPase, MTG1 / GTP-binding protein, orthogonal bundle domain superfamily / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile. ...EngA-type guanine nucleotide-binding (G) domain / EngA-type guanine nucleotide-binding (G) domain profile. / GTP-binding protein EngA / GTP-binding protein, ribosome biogenesis / GTPase Der, C-terminal KH-domain-like / KH-domain-like of EngA bacterial GTPase enzymes, C-terminal / GTPase, MTG1 / GTP-binding protein, orthogonal bundle domain superfamily / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile. / 50S ribosome-binding GTPase / Ribosomal protein L1, bacterial-type / GTP binding domain / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / : / Ribosomal protein L17 signature. / Ribosomal protein L32p, bacterial type / : / : / Ribosomal protein L6, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L30, bacterial-type / : / Ribosomal protein L20 / Ribosomal L32p protein family / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 superfamily / Ribosomal protein L21 / Ribosomal protein L32p / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L24 / 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 L2 signature. / Ribosomal protein L29, conserved site / Ribosomal protein L29 signature. / Ribosomal protein L2, conserved site / Ribosomal protein L15, conserved site / Ribosomal protein L15 signature. / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L6 / Ribosomal protein L6 / Small GTP-binding protein domain / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L13 signature. / Ribosomal protein L2, domain 3 / Ribosomal protein L13, conserved site / K homology domain-like, alpha/beta / Ribosomal protein L22/L17, conserved site / Ribosomal protein L22 signature. / Ribosomal protein L14P, conserved site / Ribosomal protein L14 signature. / Ribosomal L29 protein / Ribosomal protein L29/L35 / Ribosomal protein L29/L35 superfamily / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, C-terminal domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L24 signature. / Ribosomal protein L2 / Ribosomal protein L24/L26, conserved site / KOW (Kyprides, Ouzounis, Woese) motif. / Ribosomal protein L30, ferredoxin-like fold domain
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL19 / Ribosome biogenesis GTPase A / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL34 ...PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL19 / Ribosome biogenesis GTPase A / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL6 / GTPase Der / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL1
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsArpin, D. / Ortega, J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Nucleic Acids Res / Year: 2025
Title: The binding of RbgA to a critical 50S assembly intermediate facilitates YphC function in bacterial ribosomal assembly.
Authors: Dominic Arpin / Armando Palacios / Kaustuv Basu / Joaquin Ortega /
Abstract: The intricate process of 50S ribosomal subunit assembly in Bacillus subtilis involves multiple parallel pathways converging into a crucial intermediate known as the 45S particle. RbgA and YphC, play ...The intricate process of 50S ribosomal subunit assembly in Bacillus subtilis involves multiple parallel pathways converging into a crucial intermediate known as the 45S particle. RbgA and YphC, play pivotal roles in completing the maturation of the functional sites in the 45S particle. In this work, we found that RbgA and YphC can independently bind the 45S particle with high affinity, but when RbgA binds first to the particle, it significantly increases the binding affinity of YphC. Using cryo-electron microscopy, we determined that the changes exerted by RbgA and YphC when binding independently closely resemble those observed when the two factors bind to the 45S particle simultaneously. However, the structural analysis revealed that RbgA binding causes a conformational change that uncovers the binding site for YphC, thus increasing its binding affinity. We concluded that the functional interplay between RbgA and YphC primarily revolves around one factor promoting the binding of the other, rather than the binding of the two factors inducing entirely new conformational changes compared with those induced by the factors individually. These results highlight the synergic mechanism between two essential assembly factors, underscoring the intricate mechanism bacteria use to maximize the efficiency of the ribosome assembly process.
History
DepositionMay 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release
Revision 1.0Dec 25, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 25, 2024Data content type: Additional map / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Dec 25, 2024Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 25, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 25, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 25, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 25, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Dec 25, 2024Data content type: Additional map / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Dec 25, 2024Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 25, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 25, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 25, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 25, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.year / _em_admin.last_update
Revision 1.2May 28, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 28, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 23S rRNA
C: Large ribosomal subunit protein uL2
D: Large ribosomal subunit protein uL3
E: Large ribosomal subunit protein uL4
F: Large ribosomal subunit protein uL6
G: Large ribosomal subunit protein uL13
H: Large ribosomal subunit protein uL14
I: Large ribosomal subunit protein uL15
J: Large ribosomal subunit protein bL17
K: Large ribosomal subunit protein bL19
L: Large ribosomal subunit protein bL20
M: Large ribosomal subunit protein bL21
N: Large ribosomal subunit protein uL22
O: Large ribosomal subunit protein uL23
P: Large ribosomal subunit protein uL24
R: Large ribosomal subunit protein uL29
S: Large ribosomal subunit protein uL30
T: Large ribosomal subunit protein bL32
U: Large ribosomal subunit protein bL34
V: Ribosome biogenesis GTPase A
W: GTPase Der
Y: Large ribosomal subunit protein uL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,309,82325
Polymers1,308,25622
Non-polymers1,5673
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
Large ribosomal subunit protein ... , 19 types, 19 molecules CDEFGHIJKLMNOPRSTUY

#2: Protein Large ribosomal subunit protein uL2 / 50S ribosomal protein L2 / BL2


Mass: 30335.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: rplB, BSU01190
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42919
#3: Protein Large ribosomal subunit protein uL3 / 50S ribosomal protein L3 / BL3


Mass: 22723.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: rplC, BSU01160
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42920
#4: Protein Large ribosomal subunit protein uL4 / 50S ribosomal protein L4


Mass: 22424.951 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: rplD, BSU01170
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42921
#5: Protein Large ribosomal subunit protein uL6 / 50S ribosomal protein L6 / BL10


Mass: 19543.389 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: rplF, BSU01310
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P46898
#6: Protein Large ribosomal subunit protein uL13 / 50S ribosomal protein L13


Mass: 16407.104 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: rplM, BSU01490
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P70974
#7: Protein Large ribosomal subunit protein uL14 / 50S ribosomal protein L14


Mass: 13175.288 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: rplN, BSU01260
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12875
#8: Protein Large ribosomal subunit protein uL15 / 50S ribosomal protein L15


Mass: 15410.694 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: rplO, BSU01350
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P19946
#9: Protein Large ribosomal subunit protein bL17 / 50S ribosomal protein L17 / BL15 / BL21


Mass: 13774.806 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: rplQ, BSU01440
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P20277
#10: Protein Large ribosomal subunit protein bL19 / 50S ribosomal protein L19


Mass: 13416.853 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: rplS, BSU16040
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: O31742
#11: Protein Large ribosomal subunit protein bL20 / 50S ribosomal protein L20


Mass: 13537.993 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: rplT, BSU28850
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P55873
#12: Protein Large ribosomal subunit protein bL21 / 50S ribosomal protein L21 / BL20


Mass: 11296.081 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: rplU, BSU27960
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P26908
#13: Protein Large ribosomal subunit protein uL22 / 50S ribosomal protein L22


Mass: 12481.608 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: rplV, BSU01210
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42060
#14: Protein Large ribosomal subunit protein uL23 / 50S ribosomal protein L23


Mass: 10978.813 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: rplW, BSU01180
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42924
#15: Protein Large ribosomal subunit protein uL24 / 12 kDa DNA-binding protein / 50S ribosomal protein L24 / BL23 / HPB12


Mass: 11166.120 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: rplX, BSU01270
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P0CI78
#16: Protein Large ribosomal subunit protein uL29 / 50S ribosomal protein L29


Mass: 7728.029 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: rpmC, BSU01240
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12873
#17: Protein Large ribosomal subunit protein uL30 / 50S ribosomal protein L30 / BL27


Mass: 6650.795 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: rpmD, BSU01340
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P19947
#18: Protein Large ribosomal subunit protein bL32 / 50S ribosomal protein L32


Mass: 6745.073 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: rpmF, BSU15080
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: O34687
#19: Protein/peptide Large ribosomal subunit protein bL34 / 50S ribosomal protein L34


Mass: 5271.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: rpmH, BSU41060
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P05647
#22: Protein Large ribosomal subunit protein uL1 / 50S ribosomal protein L1 / BL1


Mass: 25026.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: rplA, BSU01030
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: Q06797

-
Protein , 2 types, 2 molecules VW

#20: Protein Ribosome biogenesis GTPase A


Mass: 32033.236 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: rbgA, ylqF, BSU16050
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: O31743
#21: Protein GTPase Der / GTP-binding protein EngA


Mass: 48828.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: der, engA, yphC, BSU22840
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P50743

-
RNA chain / Non-polymers , 2 types, 4 molecules A

#1: RNA chain 23S rRNA


Mass: 949300.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: GenBank: 467326
#23: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM

-
Details

Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: 50S assembly intermediate 45SYphC Class 1 / Type: RIBOSOME / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Bacillus subtilis (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
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 FIELD / Nominal defocus max: 2750 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40501 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00388164
ELECTRON MICROSCOPYf_angle_d0.627132560
ELECTRON MICROSCOPYf_dihedral_angle_d19.19335696
ELECTRON MICROSCOPYf_chiral_restr0.03617069
ELECTRON MICROSCOPYf_plane_restr0.0056683

+
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