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- PDB-3iy9: Leishmania Tarentolae Mitochondrial Large Ribosomal Subunit Model -

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Basic information

Entry
Database: PDB / ID: 3iy9
TitleLeishmania Tarentolae Mitochondrial Large Ribosomal Subunit Model
Components
  • (39S ribosomal protein ...) x 9
  • (50S ribosomal protein ...) x 10
  • Leishmania Tarentolae Mitochondrial Large Ribosomal Subunit
KeywordsRIBOSOME / Leishmania tarentolae / Mitochondrial ribosome / CryoEM / Minimal RNA. / Mitochondrion / Ribonucleoprotein / Ribosomal protein / Transit peptide / Methylation / RNA-binding / rRNA-binding
Function / homology
Function and homology information


Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation / mitochondrial large ribosomal subunit / mitochondrial ribosome / mitochondrial translation / mRNA regulatory element binding translation repressor activity / ribosomal large subunit assembly ...Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation / mitochondrial large ribosomal subunit / mitochondrial ribosome / mitochondrial translation / mRNA regulatory element binding translation repressor activity / ribosomal large subunit assembly / mRNA 5'-UTR binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / mitochondrial inner membrane / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / protein domain specific binding / mRNA binding / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L11, bacterial-type / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain ...Ribosomal protein L11, bacterial-type / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11, RNA binding domain / Ribosomal protein L11/L12 / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L20 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L33 superfamily / Ribosomal protein L30, bacterial-type / : / Ribosomal protein L16 / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / 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 protein L24 / Ribosomal protein L13, bacterial-type / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L23/L25, conserved site / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L23 signature. / Ribosomal protein L30, conserved site / Ribosomal protein L30 signature. / Ribosomal protein L29, conserved site / Ribosomal protein L29 signature. / : / Ribosomal protein L15, conserved site / Ribosomal protein L15 signature. / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L16p/L10e / Ribosomal protein L13, conserved site / Ribosomal protein L13 signature. / Ribosomal protein L14P, conserved site / Ribosomal protein L14 signature. / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L25/L23 / Ribosomal L29 protein / Ribosomal protein L29/L35 / Ribosomal protein L29/L35 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L30p/L7e / Ribosomal protein L23 / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L24 signature. / Ribosomal Proteins L2, RNA binding domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L24/L26, conserved site / Ribosomal Proteins L2, RNA binding domain / KOW (Kyprides, Ouzounis, Woese) motif. / Ribosomal protein L22/L17 / Ribosomal protein L22/L17 superfamily / Ribosomal protein L2 / Ribosomal protein L13 / Ribosomal protein L13 / Ribosomal protein L13 superfamily / Ribosomal protein L15 / Ribosomal protein L22p/L17e / Ribosomal protein L4/L1e / Ribosomal protein L4 domain superfamily / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal protein L4/L1 family / Ribosomal protein L14p/L23e / Ribosomal protein L14P / Ribosomal protein L14 superfamily / Ribosomal protein L14p/L23e / Ribosomal protein L26/L24, KOW domain / Ribosomal protein L3, conserved site / Ribosomal protein L3 signature. / Ribosomal protein L3
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL33m / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein uL13 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL33m / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL2m / Large ribosomal subunit protein uL11m / Large ribosomal subunit protein uL24m / Large ribosomal subunit protein uL22m / Large ribosomal subunit protein bL17m / Large ribosomal subunit protein uL2m / Large ribosomal subunit protein uL24m / Large ribosomal subunit protein uL4m / Large ribosomal subunit protein bL17m / Large ribosomal subunit protein uL22m / Large ribosomal subunit protein uL16m / Large ribosomal subunit protein bL27m / Large ribosomal subunit protein uL11m
Similarity search - Component
Biological speciesLeishmania Tarentolae (eukaryote)
Homo sapiens (human)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 14.1 Å
AuthorsSharma, M.R. / Booth, T.M. / Simpson, L. / Maslov, D.A. / Agrawal, R.K.
Citation
Journal: Proc Natl Acad Sci U S A / Year: 2009
Title: Structure of a mitochondrial ribosome with minimal RNA.
Authors: Manjuli R Sharma / Timothy M Booth / Larry Simpson / Dmitri A Maslov / Rajendra K Agrawal /
Abstract: The Leishmania tarentolae mitochondrial ribosome (Lmr) is a minimal ribosomal RNA (rRNA)-containing ribosome. We have obtained a cryo-EM map of the Lmr. The map reveals several features that have not ...The Leishmania tarentolae mitochondrial ribosome (Lmr) is a minimal ribosomal RNA (rRNA)-containing ribosome. We have obtained a cryo-EM map of the Lmr. The map reveals several features that have not been seen in previously-determined structures of eubacterial or eukaryotic (cytoplasmic or organellar) ribosomes to our knowledge. Comparisons of the Lmr map with X-ray crystallographic and cryo-EM maps of the eubacterial ribosomes and a cryo-EM map of the mammalian mitochondrial ribosome show that (i) the overall structure of the Lmr is considerably more porous, (ii) the topology of the intersubunit space is significantly different, with fewer intersubunit bridges, but more tunnels, and (iii) several of the functionally-important rRNA regions, including the alpha-sarcin-ricin loop, have different relative positions within the structure. Furthermore, the major portions of the mRNA channel, the tRNA passage, and the nascent polypeptide exit tunnel contain Lmr-specific proteins, suggesting that the mechanisms for mRNA recruitment, tRNA interaction, and exiting of the nascent polypeptide in Lmr must differ markedly from the mechanisms deduced for ribosomes in other organisms. Our study identifies certain structural features that are characteristic solely of mitochondrial ribosomes and other features that are characteristic of both mitochondrial and chloroplast ribosomes (i.e., organellar ribosomes).
#1: Journal: Science / Year: 2005
Title: Structures of the bacterial ribosome at 3.5 A resolution.
Authors: Barbara S Schuwirth / Maria A Borovinskaya / Cathy W Hau / Wen Zhang / Antón Vila-Sanjurjo / James M Holton / Jamie H Doudna Cate /
Abstract: We describe two structures of the intact bacterial ribosome from Escherichia coli determined to a resolution of 3.5 angstroms by x-ray crystallography. These structures provide a detailed view of the ...We describe two structures of the intact bacterial ribosome from Escherichia coli determined to a resolution of 3.5 angstroms by x-ray crystallography. These structures provide a detailed view of the interface between the small and large ribosomal subunits and the conformation of the peptidyl transferase center in the context of the intact ribosome. Differences between the two ribosomes reveal a high degree of flexibility between the head and the rest of the small subunit. Swiveling of the head of the small subunit observed in the present structures, coupled to the ratchet-like motion of the two subunits observed previously, suggests a mechanism for the final movements of messenger RNA (mRNA) and transfer RNAs (tRNAs) during translocation.
#2: Journal: J Mol Biol / Year: 2006
Title: A structural model for the large subunit of the mammalian mitochondrial ribosome.
Authors: Jason A Mears / Manjuli R Sharma / Robin R Gutell / Amanda S McCook / Paul E Richardson / Thomas R Caulfield / Rajendra K Agrawal / Stephen C Harvey /
Abstract: Protein translation is essential for all forms of life and is conducted by a macromolecular complex, the ribosome. Evolutionary changes in protein and RNA sequences can affect the 3D organization of ...Protein translation is essential for all forms of life and is conducted by a macromolecular complex, the ribosome. Evolutionary changes in protein and RNA sequences can affect the 3D organization of structural features in ribosomes in different species. The most dramatic changes occur in animal mitochondria, whose genomes have been reduced and altered significantly. The RNA component of the mitochondrial ribosome (mitoribosome) is reduced in size, with a compensatory increase in protein content. Until recently, it was unclear how these changes affect the 3D structure of the mitoribosome. Here, we present a structural model of the large subunit of the mammalian mitoribosome developed by combining molecular modeling techniques with cryo-electron microscopic data at 12.1A resolution. The model contains 93% of the mitochondrial rRNA sequence and 16 mitochondrial ribosomal proteins in the large subunit of the mitoribosome. Despite the smaller mitochondrial rRNA, the spatial positions of RNA domains known to be involved directly in protein synthesis are essentially the same as in bacterial and archaeal ribosomes. However, the dramatic reduction in rRNA content necessitates evolution of unique structural features to maintain connectivity between RNA domains. The smaller rRNA sequence also limits the likelihood of tRNA binding at the E-site of the mitoribosome, and correlates with the reduced size of D-loops and T-loops in some animal mitochondrial tRNAs, suggesting co-evolution of mitochondrial rRNA and tRNA structures.
History
DepositionApr 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.3Feb 21, 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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Assembly

Deposited unit
A: Leishmania Tarentolae Mitochondrial Large Ribosomal Subunit
B: 39S ribosomal protein L2, mitochondrial
C: 50S ribosomal protein L3
D: 39S ribosomal protein L4, mitochondrial
H: 50S ribosomal protein L9
G: 39S ribosomal protein L11, mitochondrial
J: 50S ribosomal protein L13
K: 50S ribosomal protein L14
L: 50S ribosomal protein L15
I: 39S ribosomal protein L16, mitochondrial
S: 39S ribosomal protein L17, mitochondrial
Q: 50S ribosomal protein L20
R: 50S ribosomal protein L21
M: 39S ribosomal protein L22, mitochondrial
T: 50S ribosomal protein L23
N: 39S ribosomal protein L24, mitochondrial
O: 39S ribosomal protein L27, mitochondrial
X: 50S ribosomal protein L29
Y: 50S ribosomal protein L30
P: 39S ribosomal protein L33, mitochondrial


Theoretical massNumber of molelcules
Total (without water)564,86520
Polymers564,86520
Non-polymers00
Water0
1


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

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Components

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RNA chain , 1 types, 1 molecules A

#1: RNA chain Leishmania Tarentolae Mitochondrial Large Ribosomal Subunit / Coordinate model: P atoms only


Mass: 327983.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania Tarentolae (eukaryote)

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39S ribosomal protein ... , 9 types, 9 molecules BDGISMNOP

#2: Protein 39S ribosomal protein L2, mitochondrial / Ribosome / Coordinate model: Cα atoms only


Mass: 14442.636 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q5T653, UniProt: Q2TA12*PLUS
#4: Protein 39S ribosomal protein L4, mitochondrial / Ribosome / Coordinate model: Cα atoms only


Mass: 19707.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BYD3
#6: Protein 39S ribosomal protein L11, mitochondrial / Ribosome / Coordinate model: Cα atoms only


Mass: 15606.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3B7, UniProt: Q2YDI0*PLUS
#10: Protein 39S ribosomal protein L16, mitochondrial / Ribosome / Coordinate model: Cα atoms only


Mass: 13107.179 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NX20
#11: Protein 39S ribosomal protein L17, mitochondrial / Ribosome / Coordinate model: Cα atoms only


Mass: 13682.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NRX2, UniProt: Q3T0L3*PLUS
#14: Protein 39S ribosomal protein L22, mitochondrial / Ribosome / Coordinate model: Cα atoms only


Mass: 12914.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NWU5, UniProt: Q3SZX5*PLUS
#16: Protein 39S ribosomal protein L24, mitochondrial / Ribosome / Coordinate model: Cα atoms only


Mass: 11010.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96A35, UniProt: Q3SYS0*PLUS
#17: Protein 39S ribosomal protein L27, mitochondrial / Ribosome / Coordinate model: Cα atoms only


Mass: 7520.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P0M9
#20: Protein 39S ribosomal protein L33, mitochondrial / Ribosome / Coordinate model: Cα atoms only


Mass: 6092.276 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75394

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50S ribosomal protein ... , 10 types, 10 molecules CHJKLQRTXY

#3: Protein 50S ribosomal protein L3 / / Coordinate model: Cα atoms only


Mass: 22277.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60438
#5: Protein 50S ribosomal protein L9 / / Coordinate model: Cα atoms only


Mass: 6580.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7R1
#7: Protein 50S ribosomal protein L13 / / Coordinate model: Cα atoms only


Mass: 15822.360 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AA10
#8: Protein 50S ribosomal protein L14 / / Coordinate model: Cα atoms only


Mass: 13320.714 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADY3
#9: Protein 50S ribosomal protein L15 / / Coordinate model: Cα atoms only


Mass: 15008.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02413
#12: Protein 50S ribosomal protein L20 / / Coordinate model: Cα atoms only


Mass: 13396.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7L3
#13: Protein 50S ribosomal protein L21 / / Coordinate model: Cα atoms only


Mass: 11586.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG48
#15: Protein 50S ribosomal protein L23 / / Coordinate model: Cα atoms only


Mass: 11093.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADZ0
#18: Protein 50S ribosomal protein L29 / / Coordinate model: Cα atoms only


Mass: 7286.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7M6
#19: Protein 50S ribosomal protein L30 / / Coordinate model: Cα atoms only


Mass: 6423.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG51

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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: Leishmania Mitochondrial 50S Ribosome / Type: RIBOSOME / Details: Monomer
Molecular weightValue: 2.1 MDa / Experimental value: YES
Buffer solutionName: 50 mM Tris HCL, pH 7.5, 100mM KCL, 10mM MgCl2, 3mM DTT, 0.1mM EDTA, 0.05% dodecyl maltoside
pH: 7.5
Details: 50 mM Tris HCL, pH 7.5, 100mM KCL, 10mM MgCl2, 3mM DTT, 0.1mM EDTA, 0.05% dodecyl maltoside
SpecimenConc.: 0.067 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: 50 mM Tris-HCl, pH 7.5, 100 mM KCl, 10 mM MgCl2, 3 mM DTT, 0.1 mM EDTA and 0.05% dodecyl maltoside
Specimen supportDetails: Thin film carbon
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 90 %

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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 / Nominal magnification: 50000 X / Calibrated magnification: 50760 X / Nominal defocus max: 4500 nm / Nominal defocus min: 1600 nm / Camera length: 0 mm
Specimen holderSpecimen holder model: OTHER / Specimen holder type: eucentric / Temperature: 80 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingFilm or detector model: KODAK SO-163 FILM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM softwareName: SPIDER / Category: 3D reconstruction
CTF correctionDetails: Each Micrograph
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: Projection Matching / Resolution: 14.1 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 53475 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms2131 1027 0 0 3158

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