[English] 日本語
Yorodumi
- PDB-9nta: Methanosarcina acetivorans 50S subunit obtained from methanol-gro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9nta
TitleMethanosarcina acetivorans 50S subunit obtained from methanol-grown cells
Components
  • (Large ribosomal subunit protein ...) x 30
  • 23S rRNA
  • 5S rRNA
KeywordsRIBOSOME / Archaea / Methanosarcina acetivorans / Large subunit / 50S subunit / growth conditions / methanol
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / ribosome biogenesis / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation ...ribonuclease P activity / tRNA 5'-leader removal / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / ribosome biogenesis / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Ribosomal protein L40e, archaeal / Ribosomal protein L19e, domain 2 / Ribosomal protein L19e, domain 3 / Ribosomal protein L15e, archaeal / Ribosomal protein L19e, archaeal / Ribosomal protein L30, archaeal / Ribosomal protein L6P, archaea / Ribosomal protein L14P, archaeal / Ribosomal protein L21e, archaeal / Ribosomal protein L18e, archaea ...Ribosomal protein L40e, archaeal / Ribosomal protein L19e, domain 2 / Ribosomal protein L19e, domain 3 / Ribosomal protein L15e, archaeal / Ribosomal protein L19e, archaeal / Ribosomal protein L30, archaeal / Ribosomal protein L6P, archaea / Ribosomal protein L14P, archaeal / Ribosomal protein L21e, archaeal / Ribosomal protein L18e, archaea / Ribosomal protein L10e, archaea / Ribosomal protein L3, archaeal / Ribosomal protein L4, archaea / Ribosomal protein L5, archaeal / Ribosomal protein L32e, archaeal / : / Ribosomal protein L7Ae, archaea / Ribosomal protein L30e / Ribosomal L15/L27a, N-terminal / Ribosomal protein L23 / : / Ribosomal protein L2, archaeal-type / metallochaperone-like domain / TRASH domain / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / : / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal L40e family / Ribosomal protein L18e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein 60S L18 and 50S L18e / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein L30e signature 2. / Ribosomal protein L39e, conserved site / Ribosomal protein L30e, conserved site / Ribosomal protein L39e signature. / 60S ribosomal protein L19 / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L30/YlxQ / Ribosomal protein L31e, conserved site / Ribosomal protein L31e signature. / Ribosomal protein L18e / Ribosomal protein L19e, C-terminal domain / Ribosomal_L19e / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e, N-terminal domain / Ribosomal protein L37ae / Ribosomal L37ae protein family / Ribosomal protein L32e, conserved site / Ribosomal protein L32e signature. / Ribosomal protein L6, conserved site-2 / Ribosomal protein L6 signature 2. / Ribosomal protein L39e / Ribosomal protein L39e domain superfamily / Ribosomal L39 protein / Ribosomal protein L5 eukaryotic/L18 archaeal / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal protein L15e, conserved site / Ribosomal protein L15e signature. / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L1e signature. / Ribosomal protein L31e / Ribosomal protein L31e domain superfamily / Ribosomal protein L31e / Ribosomal_L31e / Ribosomal protein L21e / Ribosomal protein L21e, conserved site / Ribosomal protein L21 superfamily / Ribosomal protein L21e / Ribosomal protein L21e signature. / Ribosomal protein L24e-related / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L24e / Ribosomal protein L37e, conserved site / Ribosomal protein L37e signature. / Ribosomal protein L22/L17, eukaryotic/archaeal / Ribosomal protein L37e / Ribosomal protein L37e / Ribosomal_L15e / Ribosomal protein L4, eukaryotic and archaeal type / Ribosomal protein L15e / Ribosomal protein L15e core domain superfamily / Ribosomal L15 / Ribosomal protein L3, domain 3, archaeal type superfamily / Ribosomal protein L3, archaeal/eukaryotic type / Ribosomal protein L32e / Ribosomal protein L37ae/L37e / Ribosomal protein L32e superfamily
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein eL42 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein eL40 / Large ribosomal subunit protein eL37 / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein eL18 / Large ribosomal subunit protein uL16
Similarity search - Component
Biological speciesMethanosarcina acetivorans (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.38 Å
AuthorsGhosh, A. / Fordjour, G.N.R. / Armache, J.-P. / Ferry, J.G. / Murakami, K.S. / Bevilacqua, P.C.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM156623 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM127064 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM149417 United States
CitationJournal: J Biol Chem / Year: 2025
Title: Cryo-EM study and in vivo chemical mapping of the Methanosarcina acetivorans ribosome and its dimerization via a repurposed enzyme and translation factor.
Authors: George N R Fordjour / Anwesha Ghosh / James G Ferry / Jean-Paul Armache / Philip C Bevilacqua / Katsuhiko S Murakami /
Abstract: Despite the overall conservation of ribosomes across all domains of life, differences in their 3D architecture, rRNA sequences, ribosomal protein composition, and translation factor requirements ...Despite the overall conservation of ribosomes across all domains of life, differences in their 3D architecture, rRNA sequences, ribosomal protein composition, and translation factor requirements reflect lineage-specific adaptations to environmental niches. In the domain Archaea, structural studies have primarily focused on nonmethanogenic thermophiles and halophiles, leaving it unclear whether these represent the broader Archaea domain. Here, we report the cryo-electron microscopy (cryo-EM) structure of the ribosome from Methanosarcina acetivorans, a previously unreported high-resolution structure from a model mesophilic methanogenic archaeon. Compared to ribosomes from extremophiles, the M. acetivorans ribosome has a simplified architecture, lacking paralogous duplications and containing a reduced complement of ribosomal proteins. Structures of the large subunit (50S) from cells grown with either methanol or acetate show conserved rRNA folding and protein composition. High-resolution structures of the 50S subunit from the two growth substrates enabled us to investigate structural properties that may influence in vivo dimethyl sulfate reactivity, an orthogonal chemical approach used to probe RNA structure. We observed good agreement between in vivo dimethyl sulfate reactivity and ribosome structure. Finally, we identify a previously uncharacterized ribosome dimerization mode involving only 50S subunits and mediated by a heterotetrameric complex of PurH and aEF2-proteins with alternative metabolic and translational roles. This macromolecular assembly, which we term the methanogen ribosome dimerization factor, likely mediates ribosome hibernation, revealing an alternative regulatory mechanism in translation.
History
DepositionMar 18, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.title / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
BA: 23S rRNA
BB: 5S rRNA
BC: Large ribosomal subunit protein uL2
BD: Large ribosomal subunit protein uL3
BE: Large ribosomal subunit protein uL4
BF: Large ribosomal subunit protein uL5
BG: Large ribosomal subunit protein uL6
BH: Large ribosomal subunit protein eL8
BI: Large ribosomal subunit protein uL16
BJ: Large ribosomal subunit protein uL13
BK: Large ribosomal subunit protein uL14
BL: Large ribosomal subunit protein uL15
BM: Large ribosomal subunit protein eL15
BN: Large ribosomal subunit protein uL18
BO: Large ribosomal subunit protein eL18
BP: Large ribosomal subunit protein eL19
BQ: Large ribosomal subunit protein eL20
BR: Large ribosomal subunit protein eL21
BS: Large ribosomal subunit protein uL22
BT: Large ribosomal subunit protein uL23
BU: Large ribosomal subunit protein uL24
BV: Large ribosomal subunit protein eL24
BW: Large ribosomal subunit protein uL29
BX: Large ribosomal subunit protein uL30
BY: Large ribosomal subunit protein eL30
BZ: Large ribosomal subunit protein eL31
Ba: Large ribosomal subunit protein eL32
Bb: Large ribosomal subunit protein eL43
Bc: Large ribosomal subunit protein eL37
Bd: Large ribosomal subunit protein eL39
Be: Large ribosomal subunit protein eL40
Bf: Large ribosomal subunit protein eL42
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,427,87391
Polymers1,426,07132
Non-polymers1,80259
Water00
1


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

-
Components

-
RNA chain , 2 types, 2 molecules BABB

#1: RNA chain 23S rRNA


Mass: 937739.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Contains an rRNA modifications: G7M2251, OMG2260, OMU2563, OMG2564, G7M2615
Source: (natural) Methanosarcina acetivorans (archaea) / References: GenBank: 19918815
#2: RNA chain 5S rRNA


Mass: 41399.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: GenBank: 19918815

+
Large ribosomal subunit protein ... , 30 types, 30 molecules BCBDBEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBTBUBVBWBXBYBZBaBbBcBdBeBf

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


Mass: 25738.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRU4
#4: Protein Large ribosomal subunit protein uL3 / 50S ribosomal protein L3


Mass: 36949.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRU7
#5: Protein Large ribosomal subunit protein uL4 / 50S ribosomal protein L4


Mass: 27516.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRU6
#6: Protein Large ribosomal subunit protein uL5 / 50S ribosomal protein L5


Mass: 18398.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRT4
#7: Protein Large ribosomal subunit protein uL6 / 50S ribosomal protein L6


Mass: 19530.715 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRT1
#8: Protein Large ribosomal subunit protein eL8 / 50S ribosomal protein L7Ae / Ribosomal protein L8e


Mass: 12741.726 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TQL9
#9: Protein Large ribosomal subunit protein uL16 / 50S ribosomal protein L10e


Mass: 19409.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TU90
#10: Protein Large ribosomal subunit protein uL13 / 50S ribosomal protein L13


Mass: 16085.799 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TT43
#11: Protein Large ribosomal subunit protein uL14 / 50S ribosomal protein L14


Mass: 14356.907 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRT7
#12: Protein Large ribosomal subunit protein uL15 / 50S ribosomal protein L15


Mass: 15129.009 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRS5
#13: Protein Large ribosomal subunit protein eL15 / 50S ribosomal protein L15e


Mass: 22650.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TPX0
#14: Protein Large ribosomal subunit protein uL18 / 50S ribosomal protein L18


Mass: 19233.713 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRS8
#15: Protein Large ribosomal subunit protein eL18 / 50S ribosomal protein L18e


Mass: 13714.989 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TT44
#16: Protein Large ribosomal subunit protein eL19


Mass: 17061.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: A0A832W9G6
#17: Protein Large ribosomal subunit protein eL20 / 50S ribosomal protein L18Ae / 50S ribosomal protein L20e / 50S ribosomal protein LX


Mass: 6972.045 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TIN5
#18: Protein Large ribosomal subunit protein eL21 / 50S ribosomal protein L21e


Mass: 11063.720 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TQU3
#19: Protein Large ribosomal subunit protein uL22 / 50S ribosomal protein L22


Mass: 16764.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRU2
#20: Protein Large ribosomal subunit protein uL23 / 50S ribosomal protein L23


Mass: 9447.194 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRU5
#21: Protein Large ribosomal subunit protein uL24 / 50S ribosomal protein L24


Mass: 13075.341 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRT6
#22: Protein Large ribosomal subunit protein eL24 / 50S ribosomal protein L24e


Mass: 7204.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TQL7
#23: Protein Large ribosomal subunit protein uL29 / 50S ribosomal protein L29


Mass: 7622.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRU0
#24: Protein Large ribosomal subunit protein uL30 / 50S ribosomal protein L30


Mass: 17627.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRS6
#25: Protein Large ribosomal subunit protein eL30 / 50S ribosomal protein L30e


Mass: 10316.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRB9
#26: Protein Large ribosomal subunit protein eL31 / 50S ribosomal protein L31e


Mass: 10331.096 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TIN3
#27: Protein Large ribosomal subunit protein eL32


Mass: 17880.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: A0A832W8Z7
#28: Protein Large ribosomal subunit protein eL43


Mass: 10557.483 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: A0A832SMV9
#29: Protein Large ribosomal subunit protein eL37 / 50S ribosomal protein L37e


Mass: 6456.628 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TL48
#30: Protein Large ribosomal subunit protein eL39 / 50S ribosomal protein L39e


Mass: 6257.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TIN2
#31: Protein Large ribosomal subunit protein eL40 / 50S ribosomal protein L40e


Mass: 5964.202 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TJ19
#32: Protein Large ribosomal subunit protein eL42


Mass: 10872.954 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: A0A832W9V9

-
Non-polymers , 3 types, 59 molecules

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


Mass: 24.305 Da / Num. of mol.: 43 / Source method: obtained synthetically / Formula: Mg
#34: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: K
#35: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn

-
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: Methanosarcina acetivorans 50S subunit obtained from methanol-grown cells
Type: RIBOSOME / Entity ID: #1-#32 / Source: NATURAL
Source (natural)Organism: Methanosarcina acetivorans (archaea)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris acetate1
260 mMAmmonium chlorideNH4Cl1
37.5 mMMagnessium acetateMg(CH3COO)21
46 mMbeta-mercaptoethanol1
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

-
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 / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

-
Processing

EM software
IDNameVersionCategory
1cryoSPARCv4.6.2particle selection
2EPUimage acquisition
4cryoSPARCv4.6.2CTF correction
7UCSF ChimeraXv1.7model fitting
8ISOLDEmodel fitting
10Cootv0.9.8.95model refinement
11PHENIXv1.20.1model refinement
12cryoSPARCv4.6.2initial Euler assignment
13cryoSPARCv4.6.2final Euler assignment
15cryoSPARCv4.6.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.38 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 197922 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 41.02 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0055103325
ELECTRON MICROSCOPYf_angle_d0.7052154325
ELECTRON MICROSCOPYf_chiral_restr0.04219648
ELECTRON MICROSCOPYf_plane_restr0.00618425
ELECTRON MICROSCOPYf_dihedral_angle_d13.991940462

+
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