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- PDB-7s0s: M. tuberculosis ribosomal RNA methyltransferase TlyA bound to M. ... -

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Basic information

Entry
Database: PDB / ID: 7s0s
TitleM. tuberculosis ribosomal RNA methyltransferase TlyA bound to M. smegmatis 50S ribosomal subunit
Components
  • (50S ribosomal protein ...) x 31
  • 16S/23S rRNA (Cytidine-2'-O)-methyltransferase TlyA
  • 23S rRNA23S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • ribosomal protein bL37
KeywordsRIBOSOME / Methyltransferase / rRNA modification / 50S / TRANSFERASE
Function / homology
Function and homology information


23S rRNA (cytidine1920-2'-O)-methyltransferase / methyltransferase activity / large ribosomal subunit / methylation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / RNA binding / cytoplasm
Similarity search - Function
Haemolysin A /rRNA methyltransferase TlyA / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / 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 L36 signature. / Ribosomal protein L9, N-terminal domain superfamily ...Haemolysin A /rRNA methyltransferase TlyA / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / 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 L36 signature. / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L13, bacterial-type / Ribosomal protein L15, bacterial-type / Ribosomal protein L15, conserved site / Ribosomal protein L15 signature. / Ribosomal protein L22/L17, conserved site / S4 RNA-binding domain / RNA-binding S4 domain / RNA-binding S4 domain superfamily / S4 domain / Ribosomal protein L15 / Ribosomal protein L22 signature. / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal protein L22/L17 / Ribosomal protein L22/L17 superfamily / Ribosomal protein L13 / Ribosomal protein L13 / Ribosomal protein L13 superfamily / Ribosomal protein L22p/L17e / Ribosomal protein L18e/L15P / Ribosomal L18e/L15P superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 16S/23S rRNA (Cytidine-2'-O)-methyltransferase TlyA / : / : / : ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 16S/23S rRNA (Cytidine-2'-O)-methyltransferase TlyA / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / 50S ribosomal protein L9 / 50S ribosomal protein L13 / 50S ribosomal protein L15 / Large ribosomal subunit protein bL36 / Uncharacterized protein / 50S ribosomal protein L22 / 50S ribosomal protein L34
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Mycolicibacterium smegmatis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsLaughlin, Z.T. / Dunham, C.M. / Conn, G.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI088025 United States
Citation
Journal: Proc Natl Acad Sci U S A / Year: 2022
Title: 50S subunit recognition and modification by the ribosomal RNA methyltransferase TlyA.
Authors: Zane T Laughlin / Suparno Nandi / Debayan Dey / Natalia Zelinskaya / Marta A Witek / Pooja Srinivas / Ha An Nguyen / Emily G Kuiper / Lindsay R Comstock / Christine M Dunham / Graeme L Conn /
Abstract: Changes in bacterial ribosomal RNA (rRNA) methylation status can alter the activity of diverse groups of ribosome-targeting antibiotics. These modifications are typically incorporated by a single ...Changes in bacterial ribosomal RNA (rRNA) methylation status can alter the activity of diverse groups of ribosome-targeting antibiotics. These modifications are typically incorporated by a single methyltransferase that acts on one nucleotide target and rRNA methylation directly prevents drug binding, thereby conferring drug resistance. Loss of intrinsic methylation can also result in antibiotic resistance. For example, Mycobacterium tuberculosis becomes sensitized to tuberactinomycin antibiotics, such as capreomycin and viomycin, due to the action of the intrinsic methyltransferase TlyA. TlyA is unique among antibiotic resistance-associated methyltransferases as it has dual 16S and 23S rRNA substrate specificity and can incorporate cytidine-2′-O-methylations within two structurally distinct contexts. Here, we report the structure of a mycobacterial 50S subunit-TlyA complex trapped in a postcatalytic state with a S-adenosyl-L-methionine analog using single-particle cryogenic electron microscopy. Together with complementary functional analyses, this structure reveals critical roles in 23S rRNA substrate recognition for conserved residues across an interaction surface that spans both TlyA domains. These interactions position the TlyA active site over the target nucleotide C2144, which is flipped from 23S Helix 69 in a process stabilized by stacking of TlyA residue Phe157 on the adjacent A2143. Base flipping may thus be a common strategy among rRNA methyltransferase enzymes, even in cases where the target site is accessible without such structural reorganization. Finally, functional studies with 30S subunit suggest that the same TlyA interaction surface is employed to recognize this second substrate, but with distinct dependencies on essential conserved residues.
#1: Journal: Biorxiv / Year: 2022
Title: 50S subunit recognition and modification by the Mycobacterium tuberculosis ribosomal RNA methyltransferase TlyA
Authors: Laughlin, Z.T. / Nandi, S. / Dey, D. / Zelinskaya, N. / Witek, M.A. / Srinivas, P. / Nguyen, H.A. / Kuiper, E.G. / Comstock, L.R. / Dunham, C.M. / Conn, G.L.
History
DepositionAug 31, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2022Group: Data collection / Category: em_imaging / Item: _em_imaging.nominal_defocus_min
Revision 1.2Apr 13, 2022Group: 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 / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
3: ribosomal protein bL37
B: 16S/23S rRNA (Cytidine-2'-O)-methyltransferase TlyA
C: 23S rRNA
D: 50S ribosomal protein L2
E: 50S ribosomal protein L3
F: 50S ribosomal protein L4
G: 50S ribosomal protein L5
H: 50S ribosomal protein L6
I: 50S ribosomal protein L9
J: 50S ribosomal protein L10
K: 50S ribosomal protein L11
L: 50S ribosomal protein L13
M: 50S ribosomal protein L14
N: 50S ribosomal protein L15
O: 50S ribosomal protein L16
P: 50S ribosomal protein L17
Q: 50S ribosomal protein L18
R: 50S ribosomal protein L19
S: 50S ribosomal protein L20
T: 50S ribosomal protein L21
U: 50S ribosomal protein L22
V: 50S ribosomal protein L23
W: 50S ribosomal protein L24
X: 50S ribosomal protein L25
Y: 50S ribosomal protein L27
Z: 50S ribosomal protein L28
a: 50S ribosomal protein L29
b: 50S ribosomal protein L30
c: 50S ribosomal protein L32
d: 50S ribosomal protein L33
e: 50S ribosomal protein L34
f: 50S ribosomal protein L35
g: 50S ribosomal protein L36
h: 50S ribosomal protein L31
i: 5S rRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,494,187441
Polymers1,484,15535
Non-polymers10,032406
Water0
1


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

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Components

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RNA chain , 2 types, 2 molecules Ci

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


Mass: 1012532.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / References: GenBank: CP009494.1
#35: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 38061.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: GenBank: 967054

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50S ribosomal protein ... , 31 types, 31 molecules DEFGHIJKLMNOPQRSTUVWXYZabcdefgh

#4: Protein 50S ribosomal protein L2 /


Mass: 30008.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0A0D6H9F9
#5: Protein 50S ribosomal protein L3 /


Mass: 22621.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0A0D6H852
#6: Protein 50S ribosomal protein L4 /


Mass: 22477.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0A0D6H7R4
#7: Protein 50S ribosomal protein L5 /


Mass: 20588.701 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0A0D6HA71
#8: Protein 50S ribosomal protein L6 /


Mass: 19165.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0A0D6H902
#9: Protein 50S ribosomal protein L9 /


Mass: 15949.253 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0A653F9J9
#10: Protein 50S ribosomal protein L10 /


Mass: 13095.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0A0D6H7F9
#11: Protein 50S ribosomal protein L11 /


Mass: 14109.185 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0A0D6H7I7
#12: Protein 50S ribosomal protein L13 /


Mass: 16015.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0A653FEZ4
#13: Protein 50S ribosomal protein L14 /


Mass: 13400.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0A0D6HA57
#14: Protein 50S ribosomal protein L15 /


Mass: 15383.968 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0A653FF82
#15: Protein 50S ribosomal protein L16 /


Mass: 15498.937 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0A0D6H8A3
#16: Protein 50S ribosomal protein L17 /


Mass: 13210.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0A0D6HA74
#17: Protein 50S ribosomal protein L18 /


Mass: 13580.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0A0D6HAD5
#18: Protein 50S ribosomal protein L19 /


Mass: 12892.806 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0A0D6HUB6
#19: Protein 50S ribosomal protein L20 /


Mass: 14035.175 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0A0D6IFR3
#20: Protein 50S ribosomal protein L21 /


Mass: 10724.440 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0A0D6IQ37
#21: Protein 50S ribosomal protein L22 /


Mass: 12408.192 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: O06115
#22: Protein 50S ribosomal protein L23 /


Mass: 10748.448 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0A0D6H9F4
#23: Protein 50S ribosomal protein L24 /


Mass: 11228.946 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Residues 48-55 are not shown in model. Little to no density seen there.
Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0A0D6HA97
#24: Protein 50S ribosomal protein L25 / / General stress protein CTC


Mass: 20331.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0A0D6IY62
#25: Protein 50S ribosomal protein L27 /


Mass: 8322.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0A0D6IQ33
#26: Protein 50S ribosomal protein L28 /


Mass: 6759.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0A0D6HVA7
#27: Protein 50S ribosomal protein L29 /


Mass: 7590.576 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0A0D6H9R7
#28: Protein 50S ribosomal protein L30 /


Mass: 6761.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0A0D6HAE9
#29: Protein 50S ribosomal protein L32 /


Mass: 6050.149 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0A0D6IYP7
#30: Protein/peptide 50S ribosomal protein L33 /


Mass: 5833.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0A0D6H541
#31: Protein/peptide 50S ribosomal protein L34 /


Mass: 5391.384 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: P0C562
#32: Protein 50S ribosomal protein L35 /


Mass: 7167.310 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0A0D6IFR9
#33: Protein/peptide 50S ribosomal protein L36 /


Mass: 4341.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSL4
#34: Protein/peptide 50S ribosomal protein L31 /


Mass: 5257.952 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0A0D6IUC0

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Protein/peptide / Protein , 2 types, 2 molecules 3B

#1: Protein/peptide ribosomal protein bL37 /


Mass: 2710.179 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0QTP4
#2: Protein 16S/23S rRNA (Cytidine-2'-O)-methyltransferase TlyA / Cytotoxin / haemolysin homologue TlyA / Mutant TlyA


Mass: 29898.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: No density was seen for the His-tag and first three residues (MAR) of TlyA so they were not modeled.
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: tlyA, C0094_09260, DSI38_13410, E5M05_15210, E5M52_14020, E5M78_14045, ERS007663_03298, ERS007720_00106, ERS007741_00698, ERS013471_00042, ERS023446_01647, ERS024276_00313, ERS027646_00010, ...Gene: tlyA, C0094_09260, DSI38_13410, E5M05_15210, E5M52_14020, E5M78_14045, ERS007663_03298, ERS007720_00106, ERS007741_00698, ERS013471_00042, ERS023446_01647, ERS024276_00313, ERS027646_00010, ERS027659_02052, ERS027661_00747, ERS094182_03076, F6W99_00251, GCL30_17265, SAMEA2683035_01391
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A045KH60, 23S rRNA (cytidine1920-2'-O)-methyltransferase

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Non-polymers , 2 types, 406 molecules

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


Mass: 24.305 Da / Num. of mol.: 402 / Source method: obtained synthetically / Formula: Mg
#37: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN

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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

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Mtb TlyA bound to Msg 50S ribosomal subunit modified at C2144 with SAM analog NM6.COMPLEXTlyA occupancy on 50S promoted by covalent modification of NM6 to modification site (C2144).#1-#2, #6, #8-#14, #16-#20, #22-#25, #27-#29, #31-#320MULTIPLE SOURCES
250SCOMPLEX#1, #3-#351NATURAL
3TlyACOMPLEX#21RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
31NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
22Mycolicibacterium smegmatis (bacteria)1772LR222 C101A
33Mycobacterium tuberculosis (bacteria)1773
Source (recombinant)Organism: Escherichia coli BL21 (bacteria)
Buffer solutionpH: 7 / Details: Both components dialyzed into this buffer
Buffer component
IDConc.NameBuffer-ID
120 mMHEPES1
25 mMMagnesium Acetate1
32 mMAmmonium Chloride1
475 mMPotassium Chloride1
53 mMBeta-mercaptoethanol2-Mercaptoethanol1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: 0.5 micromolar 50S, 5 micromolar TlyA, 10 micromolar NM6
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 298 K / Details: 3.0 or 3.3 second blot time allowed for sample

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 81000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 2 sec. / Electron dose: 50.79 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 3364
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
4GctfCTF correction
7Cootmodel fitting
11RELION3classification
12RELION3.13D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1016454
3D reconstructionResolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 129011 / Symmetry type: POINT
Atomic model building
IDPDB-IDPdb chain-ID 3D fitting-ID
15O60

5o60

1
23HP7

3hp7

B1
35KYG

5kyg

B1

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