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- PDB-6ppk: RbgA+45SRbgA complex -

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Basic information

Entry
Database: PDB / ID: 6ppk
TitleRbgA+45SRbgA complex
Components
  • (50S ribosomal protein ...) x 21
  • 23S rRNA23S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • Ribosome biogenesis GTPase A
KeywordsRIBOSOME / Ribosome assembly / 50S subunit / RbgA / YlqF
Function / homology
Function and homology information


positive regulation of rRNA processing / nucleoid / rRNA processing / large ribosomal subunit rRNA binding / large ribosomal subunit / ribosome biogenesis / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity ...positive regulation of rRNA processing / nucleoid / rRNA processing / large ribosomal subunit rRNA binding / large ribosomal subunit / ribosome biogenesis / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / GTPase activity / GTP binding / DNA binding / RNA binding / cytoplasm
Similarity search - Function
GTPase, MTG1 / GTP-binding protein, ribosome biogenesis / 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 / GTP binding domain / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / : ...GTPase, MTG1 / GTP-binding protein, ribosome biogenesis / 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 / GTP binding domain / 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 L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / 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 L30, bacterial-type / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / 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 L23/L25, conserved site / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L23 signature. / Ribosomal protein L30, conserved site / Ribosomal protein L5, conserved site / Ribosomal protein L29, conserved site / Ribosomal protein L30 signature. / Ribosomal protein L5, N-terminal / Ribosomal protein L5 signature. / Ribosomal protein L15, conserved site / Ribosomal protein L5, C-terminal / Ribosomal protein L5 / Ribosomal protein L5 domain superfamily / Ribosomal protein L2, conserved site / Ribosomal protein L2 signature. / Ribosomal protein L29 signature. / Ribosomal protein L5 / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L6 / ribosomal L5P family C-terminus / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L6 / Ribosomal protein L2, domain 3 / Ribosomal protein L14P, conserved site / Ribosomal protein L15 signature. / Ribosomal protein L22/L17, conserved site / Ribosomal protein L29/L35 / Ribosomal protein L29/L35 superfamily / Ribosomal L29 protein / Ribosomal protein L13, conserved site / Ribosomal protein L13 signature. / Ribosomal protein L24/L26, conserved site / KOW (Kyprides, Ouzounis, Woese) motif. / 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 protein L2 / Ribosomal protein L14 signature. / Ribosomal protein L22 signature. / Ribosomal protein L15 / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L25/L23
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL14 / 50S ribosomal protein L6 ...PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL14 / 50S ribosomal protein L6 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL21 / Ribosome biogenesis GTPase A / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL19 / Ribosome biogenesis GTPase A / 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 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 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein uL13
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsOrtega, J.
Funding support Canada, United States, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-153044 Canada
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01GM110248 United States
CitationJournal: Nucleic Acids Res / Year: 2019
Title: Structural consequences of the interaction of RbgA with a 50S ribosomal subunit assembly intermediate.
Authors: Amal Seffouh / Nikhil Jain / Dushyant Jahagirdar / Kaustuv Basu / Aida Razi / Xiaodan Ni / Alba Guarné / Robert A Britton / Joaquin Ortega /
Abstract: Bacteria harbor a number GTPases that function in the assembly of the ribosome and are essential for growth. RbgA is one of these GTPases and is required for the assembly of the 50S subunit in most ...Bacteria harbor a number GTPases that function in the assembly of the ribosome and are essential for growth. RbgA is one of these GTPases and is required for the assembly of the 50S subunit in most bacteria. Homologs of this protein are also implicated in the assembly of the large subunit of the mitochondrial and eukaryotic ribosome. We present here the cryo-electron microscopy structure of RbgA bound to a Bacillus subtilis 50S subunit assembly intermediate (45SRbgA particle) that accumulates in cells upon RbgA depletion. Binding of RbgA at the P site of the immature particle stabilizes functionally important rRNA helices in the A and P-sites, prior to the completion of the maturation process of the subunit. The structure also reveals the location of the highly conserved N-terminal end of RbgA containing the catalytic residue Histidine 9. The derived model supports a mechanism of GTP hydrolysis, and it shows that upon interaction of RbgA with the 45SRbgA particle, Histidine 9 positions itself near the nucleotide potentially acting as the catalytic residue with minimal rearrangements. This structure represents the first visualization of the conformational changes induced by an assembly factor in a bacterial subunit intermediate.
History
DepositionJul 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Feb 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: 23S rRNA
B: 5S rRNA
C: 50S ribosomal protein L2
D: 50S ribosomal protein L3
E: 50S ribosomal protein L4
F: 50S ribosomal protein L5
G: 50S ribosomal protein L6
J: 50S ribosomal protein L13
K: 50S ribosomal protein L14
L: 50S ribosomal protein L15
N: 50S ribosomal protein L17
O: 50S ribosomal protein L18
P: 50S ribosomal protein L19
Q: 50S ribosomal protein L20
R: 50S ribosomal protein L21
S: 50S ribosomal protein L22
T: 50S ribosomal protein L23
U: 50S ribosomal protein L24
V: 50S ribosomal protein L27
Z: 50S ribosomal protein L30
b: 50S ribosomal protein L32
Y: 50S ribosomal protein L29
d: 50S ribosomal protein L34
W: Ribosome biogenesis GTPase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,316,95025
Polymers1,316,42824
Non-polymers5221
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 2 types, 2 molecules AB

#1: RNA chain 23S rRNA / 23S ribosomal RNA


Mass: 949340.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: GenBank: 723796434
#2: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 38423.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: GenBank: 1012899741

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50S ribosomal protein ... , 21 types, 21 molecules CDEFGJKLNOPQRSTUVZbYd

#3: Protein 50S ribosomal protein L2 /


Mass: 30335.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063XCB6, UniProt: P42919*PLUS
#4: Protein 50S ribosomal protein L3 /


Mass: 22723.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063X745, UniProt: P42920*PLUS
#5: Protein 50S ribosomal protein L4 /


Mass: 22424.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063X8U6, UniProt: P42921*PLUS
#6: Protein 50S ribosomal protein L5 /


Mass: 20177.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063XB64, UniProt: P12877*PLUS
#7: Protein 50S ribosomal protein L6 /


Mass: 19543.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063X781, UniProt: P46898*PLUS
#8: Protein 50S ribosomal protein L13 /


Mass: 16407.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063XCH0, UniProt: P70974*PLUS
#9: Protein 50S ribosomal protein L14 /


Mass: 13175.288 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063X754, UniProt: P12875*PLUS
#10: Protein 50S ribosomal protein L15 /


Mass: 15410.694 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063XCP1, UniProt: P19946*PLUS
#11: Protein 50S ribosomal protein L17 /


Mass: 13774.806 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063XCG5, UniProt: P20277*PLUS
#12: Protein 50S ribosomal protein L18 /


Mass: 12993.829 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: F5HRS9, UniProt: P46899*PLUS
#13: Protein 50S ribosomal protein L19 /


Mass: 13416.853 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063XHU6, UniProt: O31742*PLUS
#14: Protein 50S ribosomal protein L20 /


Mass: 13537.993 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063XFC1, UniProt: P55873*PLUS
#15: Protein 50S ribosomal protein L21 /


Mass: 11296.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063XIS2, UniProt: P26908*PLUS
#16: Protein 50S ribosomal protein L22 /


Mass: 12481.608 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: F5HRT3, UniProt: P42060*PLUS
#17: Protein 50S ribosomal protein L23 /


Mass: 10978.813 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063XB36, UniProt: P42924*PLUS
#18: Protein 50S ribosomal protein L24 /


Mass: 11166.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: F5HRS7, UniProt: P0CI78*PLUS
#19: Protein 50S ribosomal protein L27 /


Mass: 10391.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063XF22, UniProt: P05657*PLUS
#20: Protein 50S ribosomal protein L30 /


Mass: 6650.795 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: F5HRU6, UniProt: P19947*PLUS
#21: Protein 50S ribosomal protein L32 /


Mass: 6745.073 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A3A5I502, UniProt: O34687*PLUS
#22: Protein 50S ribosomal protein L29 /


Mass: 7728.029 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: F5HRV8, UniProt: P12873*PLUS
#23: 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 (bacteria) / References: UniProt: A0A063XCT1, UniProt: P05647*PLUS

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Protein / Non-polymers , 2 types, 2 molecules W

#24: 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 (bacteria) / Gene: B4417_3550 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A164SGC3, UniProt: O31743*PLUS
#25: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: RbgA + 45SRbgA ribosomal assembly intermediate complex
Type: RIBOSOME
Details: 50S subunit assembly intermediate generated by RbgA depletion in cells in complex with RbgA protein
Entity ID: #1-#23 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Bacillus subtilis (bacteria) / Strain: JH642
Buffer solutionpH: 7.5
Details: 20mM Tris-HCl pH 7.5, 10mM MgCl2, 50mM NH4Cl, 1mM DTT
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %
Details: Cryo-EM grids were prepared by applying a 3.6 microliters volume of the diluted samples to holey carbon grids (c-flat CF-2/2-2C-T) with a freshly applied additional layer of continuous thin ...Details: Cryo-EM grids were prepared by applying a 3.6 microliters volume of the diluted samples to holey carbon grids (c-flat CF-2/2-2C-T) with a freshly applied additional layer of continuous thin carbon (5-10nm). Grids were blotted for 3 seconds and with a blot force +1

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Specimen holderCryogen: NITROGEN
Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Image recordingAverage exposure time: 15 sec. / Electron dose: 43 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 1228

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Processing

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
EM software
IDNameCategory
2EPUimage acquisition
4GctfCTF correction
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 169095
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 81392 / Symmetry type: POINT

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