[English] 日本語
Yorodumi
- PDB-4adv: Structure of the E. coli methyltransferase KsgA bound to the E. c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4adv
TitleStructure of the E. coli methyltransferase KsgA bound to the E. coli 30S ribosomal subunit
Components
  • (30S RIBOSOMAL PROTEIN ...) x 20
  • 16S RIBOSOMAL RNA
  • RIBOSOMAL RNA SMALL SUBUNIT METHYLTRANSFERASE A
KeywordsTRANSLATION / RIBOSOME BIOGENESIS / SMALL RIBOSOMAL SUBUNIT
Function / homology
Function and homology information


16S rRNA (adenine1518-N6/adenine1519-N6)-dimethyltransferase / 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase activity / rRNA (adenine-N6,N6-)-dimethyltransferase activity / rRNA base methylation / rRNA methylation / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / ribosomal small subunit binding / misfolded RNA binding / transcription antitermination factor activity, RNA binding ...16S rRNA (adenine1518-N6/adenine1519-N6)-dimethyltransferase / 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase activity / rRNA (adenine-N6,N6-)-dimethyltransferase activity / rRNA base methylation / rRNA methylation / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / ribosomal small subunit binding / misfolded RNA binding / transcription antitermination factor activity, RNA binding / Group I intron splicing / RNA folding / maturation of SSU-rRNA / four-way junction DNA binding / negative regulation of translational initiation / regulation of mRNA stability / mRNA regulatory element binding translation repressor activity / transcription elongation factor complex / positive regulation of RNA splicing / DNA endonuclease activity / regulation of DNA-templated transcription elongation / transcription antitermination / maintenance of translational fidelity / DNA-templated transcription termination / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / rRNA processing / cytosolic small ribosomal subunit / ribosome biogenesis / regulation of translation / small ribosomal subunit / cytoplasmic translation / double-stranded DNA binding / tRNA binding / negative regulation of translation / rRNA binding / molecular adaptor activity / ribosome / structural constituent of ribosome / translation / response to antibiotic / mRNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
rRNA adenine dimethylase-like, C-terminal / Ribosomal RNA adenine dimethylase / Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal RNA adenine methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases signature. / Ribosomal RNA adenine dimethylases / Ribosomal RNA adenine methyltransferase KsgA/Erm / Ribosomal RNA adenine dimethylase / rRNA adenine N(6)-methyltransferase family profile. / Ribosomal protein S21, conserved site ...rRNA adenine dimethylase-like, C-terminal / Ribosomal RNA adenine dimethylase / Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal RNA adenine methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases signature. / Ribosomal RNA adenine dimethylases / Ribosomal RNA adenine methyltransferase KsgA/Erm / Ribosomal RNA adenine dimethylase / rRNA adenine N(6)-methyltransferase family profile. / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S15, bacterial-type / Ribosomal protein S2 signature 2. / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / K Homology domain / K homology RNA-binding domain / Ribosomal protein S3, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S10, conserved site / : / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / KH domain / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S10 / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3 signature. / Ribosomal protein S10 signature. / Ribosomal protein S14 signature. / Ribosomal protein S7, conserved site / K homology domain superfamily, prokaryotic type / Ribosomal protein S17, conserved site / Ribosomal protein S19 / Ribosomal protein S2 signature 1. / Ribosomal protein S2, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S2 / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S14 / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S4, conserved site / Type-2 KH domain profile. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S13/S18 / Ribosomal protein S4/S9 / Ribosomal protein S19 signature. / K homology domain-like, alpha/beta / Ribosomal protein S14p/S29e / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S5 / Ribosomal protein S5, N-terminal / Ribosomal protein S7 signature. / Ribosomal protein S10p/S20e / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, C-terminal / Ribosomal protein S9, conserved site
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / 30S ribosomal protein S14 / 30S ribosomal protein S15 / 30S ribosomal protein S17 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / 30S ribosomal protein S14 / 30S ribosomal protein S15 / 30S ribosomal protein S17 / Ribosomal RNA small subunit methyltransferase A / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein bS21
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 13.5 Å
AuthorsBoehringer, D. / O'Farrell, H.C. / Rife, J.P. / Ban, N.
CitationJournal: J Biol Chem / Year: 2012
Title: Structural insights into methyltransferase KsgA function in 30S ribosomal subunit biogenesis.
Authors: Daniel Boehringer / Heather C O'Farrell / Jason P Rife / Nenad Ban /
Abstract: The assembly of the ribosomal subunits is facilitated by ribosome biogenesis factors. The universally conserved methyltransferase KsgA modifies two adjacent adenosine residues in the 3'-terminal ...The assembly of the ribosomal subunits is facilitated by ribosome biogenesis factors. The universally conserved methyltransferase KsgA modifies two adjacent adenosine residues in the 3'-terminal helix 45 of the 16 S ribosomal RNA (rRNA). KsgA recognizes its substrate adenosine residues only in the context of a near mature 30S subunit and is required for the efficient processing of the rRNA termini during ribosome biogenesis. Here, we present the cryo-EM structure of KsgA bound to a nonmethylated 30S ribosomal subunit. The structure reveals that KsgA binds to the 30S platform with the catalytic N-terminal domain interacting with substrate adenosine residues in helix 45 and the C-terminal domain making extensive contacts to helix 27 and helix 24. KsgA excludes the penultimate rRNA helix 44 from adopting its position in the mature 30S subunit, blocking the formation of the decoding site and subunit joining. We suggest that the activation of methyltransferase activity and subsequent dissociation of KsgA control conformational changes in helix 44 required for final rRNA processing and translation initiation.
History
DepositionJan 3, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2012Group: Other
Revision 1.2Sep 25, 2013Group: Other
Revision 1.3Aug 23, 2017Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Structure summary
Category: em_3d_fitting / em_image_scans ...em_3d_fitting / em_image_scans / em_software / entity / struct_conn
Item: _em_3d_fitting.target_criteria / _em_software.fitting_id ..._em_3d_fitting.target_criteria / _em_software.fitting_id / _em_software.image_processing_id / _entity.src_method
Revision 1.4Apr 4, 2018Group: Data collection / Database references / Category: citation / Item: _citation.page_last
Revision 1.5Apr 11, 2018Group: Data collection / Source and taxonomy / Category: entity_src_nat

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-2017
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 16S RIBOSOMAL RNA
B: 30S RIBOSOMAL PROTEIN S2
C: 30S RIBOSOMAL PROTEIN S3
D: 30S RIBOSOMAL PROTEIN S4
E: 30S RIBOSOMAL PROTEIN S5
F: 30S RIBOSOMAL PROTEIN S6
G: 30S RIBOSOMAL PROTEIN S7
H: 30S RIBOSOMAL PROTEIN S8
I: 30S RIBOSOMAL PROTEIN S9
J: 30S RIBOSOMAL PROTEIN S10
K: 30S RIBOSOMAL PROTEIN S11
L: 30S RIBOSOMAL PROTEIN S12
M: 30S RIBOSOMAL PROTEIN S13
N: 30S RIBOSOMAL PROTEIN S14
O: 30S RIBOSOMAL PROTEIN S15
P: 30S RIBOSOMAL PROTEIN S16
Q: 30S RIBOSOMAL PROTEIN S17
R: 30S RIBOSOMAL PROTEIN S18
S: 30S RIBOSOMAL PROTEIN S19
T: 30S RIBOSOMAL PROTEIN S20
U: 30S RIBOSOMAL PROTEIN S21
V: RIBOSOMAL RNA SMALL SUBUNIT METHYLTRANSFERASE A


Theoretical massNumber of molelcules
Total (without water)815,55722
Polymers815,55722
Non-polymers00
Water2,504139
1


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

-
Components

-
30S RIBOSOMAL PROTEIN ... , 20 types, 20 molecules BCDEFGHIJKLMNOPQRSTU

#2: Protein 30S RIBOSOMAL PROTEIN S2 /


Mass: 26650.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: KASUGAMYCIN RESISTANT / Strain: MRE600 / References: UniProt: P0A7V0
#3: Protein 30S RIBOSOMAL PROTEIN S3 /


Mass: 25900.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: KASUGAMYCIN RESISTANT / Strain: MRE600 / References: UniProt: P0A7V3
#4: Protein 30S RIBOSOMAL PROTEIN S4 /


Mass: 23383.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: KASUGAMYCIN RESISTANT / Strain: MRE600 / References: UniProt: P0A7V8
#5: Protein 30S RIBOSOMAL PROTEIN S5 /


Mass: 17498.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: KASUGAMYCIN RESISTANT / Strain: MRE600 / References: UniProt: P0A7W1
#6: Protein 30S RIBOSOMAL PROTEIN S6 /


Mass: 15727.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: KASUGAMYCIN RESISTANT / Strain: MRE600 / References: UniProt: P02358
#7: Protein 30S RIBOSOMAL PROTEIN S7 /


Mass: 19923.959 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: KASUGAMYCIN RESISTANT / Strain: MRE600 / References: UniProt: P02359
#8: Protein 30S RIBOSOMAL PROTEIN S8 /


Mass: 14015.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: KASUGAMYCIN RESISTANT / Strain: MRE600 / References: UniProt: P0A7W7
#9: Protein 30S RIBOSOMAL PROTEIN S9 /


Mass: 14755.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: KASUGAMYCIN RESISTANT / Strain: MRE600 / References: UniProt: P0A7X3
#10: Protein 30S RIBOSOMAL PROTEIN S10 /


Mass: 11755.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: KASUGAMYCIN RESISTANT / Strain: MRE600 / References: UniProt: P0A7R5
#11: Protein 30S RIBOSOMAL PROTEIN S11 /


Mass: 13739.778 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: KASUGAMYCIN RESISTANT / Strain: MRE600 / References: UniProt: P0A7R9
#12: Protein 30S RIBOSOMAL PROTEIN S12 /


Mass: 13636.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: KASUGAMYCIN RESISTANT / Strain: MRE600 / References: UniProt: P0A7S3
#13: Protein 30S RIBOSOMAL PROTEIN S13 /


Mass: 12997.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: KASUGAMYCIN RESISTANT / Strain: MRE600 / References: UniProt: P0A7S9
#14: Protein 30S RIBOSOMAL PROTEIN S14 /


Mass: 11475.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: KASUGAMYCIN RESISTANT / Strain: MRE600 / References: UniProt: P02370, UniProt: P0AG59*PLUS
#15: Protein 30S RIBOSOMAL PROTEIN S15 /


Mass: 10319.882 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: KASUGAMYCIN RESISTANT / Strain: MRE600 / References: UniProt: P02371, UniProt: P0ADZ4*PLUS
#16: Protein 30S RIBOSOMAL PROTEIN S16 /


Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: KASUGAMYCIN RESISTANT / Strain: MRE600 / References: UniProt: P0A7T3
#17: Protein 30S RIBOSOMAL PROTEIN S17 /


Mass: 9593.296 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: KASUGAMYCIN RESISTANT / Strain: MRE600 / References: UniProt: P02373, UniProt: P0AG63*PLUS
#18: Protein 30S RIBOSOMAL PROTEIN S18 /


Mass: 8874.276 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: KASUGAMYCIN RESISTANT / Strain: MRE600 / References: UniProt: P0A7T7
#19: Protein 30S RIBOSOMAL PROTEIN S19 /


Mass: 10324.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: KASUGAMYCIN RESISTANT / Strain: MRE600 / References: UniProt: P0A7U3
#20: Protein 30S RIBOSOMAL PROTEIN S20 /


Mass: 9577.268 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: KASUGAMYCIN RESISTANT / Strain: MRE600 / References: UniProt: P0A7U7
#21: Protein 30S RIBOSOMAL PROTEIN S21 /


Mass: 8524.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: KASUGAMYCIN RESISTANT / Strain: MRE600 / References: UniProt: P68679

-
RNA chain / Protein / Non-polymers , 3 types, 141 molecules AV

#1: RNA chain 16S RIBOSOMAL RNA /


Mass: 499690.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: KASUGAMYCIN RESISTANT / Strain: MRE600 / References: GenBank: 33357879
#22: Protein RIBOSOMAL RNA SMALL SUBUNIT METHYLTRANSFERASE A / / 16S RRNA (ADENINE(1518)-N(6)/ADENINE(1519)-N(6))-DIMETHYLTRANSFERASE / 16S RRNA DIMETHYLADENOSINE ...16S RRNA (ADENINE(1518)-N(6)/ADENINE(1519)-N(6))-DIMETHYLTRANSFERASE / 16S RRNA DIMETHYLADENOSINE TRANSFERASE / 16S RRNA DIMETHYLASE / HIGH LEVEL KASUGAMYCIN RESISTANCE PROTEIN KSGA / KASUGAMYCIN DIMETHYLTRANSFERASE / S-ADENOSYLMETHIONINE-6-N\ / N'-ADENOSYL(RRNA) DIMETHYLTRANSFERASE / METHYLTRANSFERASE KSGA


Mass: 27988.273 Da / Num. of mol.: 1 / Fragment: RESIDUES 17-268
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): HMS174
References: UniProt: P06992, 16S rRNA (adenine1518-N6/adenine1519-N6)-dimethyltransferase
#23: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: E. COLI METHYLTRANSFERASE KSGA BOUND TO THE E. COLI 30S RIBOSOMAL SUBUNIT
Type: COMPLEX
Buffer solutionName: 40 MM KCL, 4MM MGCL2, 20 MM HEPES/KOH PH 7. 6, 6 MM 2- MERCAPTOETHANOL
pH: 7.6
Details: 40 MM KCL, 4MM MGCL2, 20 MM HEPES/KOH PH 7. 6, 6 MM 2- MERCAPTOETHANOL
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- PLUNGER,

-
Electron microscopy imaging

MicroscopyModel: FEI TECNAI 20
Details: SEMI-AUTOMATIC DATA ACQUISITION WITH SERIAL EM SCRIPT
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 62000 X / Calibrated magnification: 82000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm
Image recordingElectron dose: 20 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Radiation wavelengthRelative weight: 1

-
Processing

EM software
IDNameVersionCategory
1UCSF Chimeramodel fitting
2IMAGIC53D reconstruction
3SPIDER3D reconstruction
CTF correctionDetails: PER IMAGE, CTFFIND3
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: ANGULAR RECONSTITUTION, PROJECTION MATCHING / Resolution: 13.5 Å / Num. of particles: 23343 / Actual pixel size: 3.07 Å
Details: 30S RIBOSOMAL SUBUNIT HEAD AND BODY WERE FITTED SEPARATELY AS RIGID BODIES. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2017. (DEPOSITION ID: 10519).
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient / Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--XRAY
Atomic model building
IDPDB-ID 3D fitting-ID
12AVY

2avy
PDB Unreleased entry

1
21QYR

1qyr

1
RefinementHighest resolution: 13.5 Å
Refinement stepCycle: LAST / Highest resolution: 13.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20487 30262 0 139 50888

+
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