[English] 日本語
Yorodumi
- PDB-8y37: Cryo-EM structure of Staphylococcus aureus (15B196) 50S ribosome ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8y37
TitleCryo-EM structure of Staphylococcus aureus (15B196) 50S ribosome in complex with MCX-190.
Components
  • (Large ribosomal subunit protein ...) x 28
  • 23S ribosomal RNA
  • 5S ribosomal RNA
KeywordsRIBOSOME / antibiotic
Function / homology
Function and homology information


large ribosomal subunit / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome ...large ribosomal subunit / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / cytoplasm
Similarity search - Function
Ribosomal protein L31 type B / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L16 signature 1. ...Ribosomal protein L31 type B / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L16 signature 1. / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L32p, bacterial type / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / 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 L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 superfamily / Ribosomal protein L30, bacterial-type / : / Ribosomal protein L16 / L28p-like / 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 L32p / Ribosomal protein L24 / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L13, bacterial-type / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L5, conserved site / Ribosomal protein L5 signature. / Ribosomal protein L2 signature. / : / Ribosomal protein L2, conserved site / Ribosomal protein L15, conserved site / Ribosomal protein L15 signature. / Ribosomal protein L5, N-terminal / Ribosomal protein L5 / Ribosomal protein L5, C-terminal / ribosomal L5P family C-terminus / Ribosomal protein L5 / Ribosomal protein L5 domain superfamily / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L16p/L10e
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL2 ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL31B / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL33B / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein bL19
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.53 Å
AuthorsLi, Y. / Lu, G. / Li, J. / Pei, X. / Lin, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32130063 China
CitationJournal: Cell Discov / Year: 2024
Title: Synthetic macrolides overcoming MLSK-resistant pathogens.
Authors: Cong-Xuan Ma / Ye Li / Wen-Tian Liu / Yun Li / Fei Zhao / Xiao-Tian Lian / Jing Ding / Si-Meng Liu / Xie-Peng Liu / Bing-Zhi Fan / Li-Yong Liu / Feng Xue / Jian Li / Jue-Ru Zhang / Zhao Xue ...Authors: Cong-Xuan Ma / Ye Li / Wen-Tian Liu / Yun Li / Fei Zhao / Xiao-Tian Lian / Jing Ding / Si-Meng Liu / Xie-Peng Liu / Bing-Zhi Fan / Li-Yong Liu / Feng Xue / Jian Li / Jue-Ru Zhang / Zhao Xue / Xiao-Tong Pei / Jin-Zhong Lin / Jian-Hua Liang /
Abstract: Conventional macrolide-lincosamide-streptogramin B-ketolide (MLSK) antibiotics are unable to counter the growing challenge of antibiotic resistance that is conferred by the constitutive methylation ...Conventional macrolide-lincosamide-streptogramin B-ketolide (MLSK) antibiotics are unable to counter the growing challenge of antibiotic resistance that is conferred by the constitutive methylation of rRNA base A2058 or its G2058 mutation, while the presence of unmodified A2058 is crucial for high selectivity of traditional MLSK in targeting pathogens over human cells. The absence of effective modes of action reinforces the prevailing belief that constitutively antibiotic-resistant Staphylococcus aureus remains impervious to existing macrolides including telithromycin. Here, we report the design and synthesis of a novel series of macrolides, featuring the strategic fusion of ketolide and quinolone moieties. Our effort led to the discovery of two potent compounds, MCX-219 and MCX-190, demonstrating enhanced antibacterial efficacy against a broad spectrum of formidable pathogens, including A2058-methylated Staphylococcus aureus, Streptococcus pneumoniae, Streptococcus pyogenes, and notably, the clinical Mycoplasma pneumoniae isolates harboring A2058G mutations which are implicated in the recent pneumonia outbreak in China. Mechanistic studies reveal that the modified quinolone moiety of MCX-190 establishes a distinctive secondary binding site within the nascent peptide exit tunnel. Structure-activity relationship analysis underscores the importance of this secondary binding, maintained by a sandwich-like π-π stacking interaction and a water-magnesium bridge, for effective engagement with A2058-methylated ribosomes rather than topoisomerases targeted by quinolone antibiotics. Our findings not only highlight MCX-219 and MCX-190 as promising candidates for next-generation MLSK antibiotics to combat antibiotic resistance, but also pave the way for the future rational design of the class of MLSK antibiotics, offering a strategic framework to overcome the challenges posed by escalating antibiotic resistance.
History
DepositionJan 28, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: Large ribosomal subunit protein bL33B
2: Large ribosomal subunit protein bL34
3: Large ribosomal subunit protein bL35
4: Large ribosomal subunit protein bL36
A: 23S ribosomal RNA
B: 5S ribosomal RNA
C: Large ribosomal subunit protein uL2
D: Large ribosomal subunit protein uL3
E: Large ribosomal subunit protein uL4
F: Large ribosomal subunit protein uL5
G: Large ribosomal subunit protein uL6
H: Large ribosomal subunit protein uL13
I: Large ribosomal subunit protein uL14
J: Large ribosomal subunit protein uL15
K: Large ribosomal subunit protein uL16
L: Large ribosomal subunit protein bL17
M: Large ribosomal subunit protein uL18
N: Large ribosomal subunit protein bL19
O: Large ribosomal subunit protein bL20
P: Large ribosomal subunit protein bL21
Q: Large ribosomal subunit protein uL22
R: Large ribosomal subunit protein uL23
S: Large ribosomal subunit protein uL24
T: Large ribosomal subunit protein bL25
U: Large ribosomal subunit protein bL27
V: Large ribosomal subunit protein bL28
W: Large ribosomal subunit protein uL29
X: Large ribosomal subunit protein uL30
Y: Large ribosomal subunit protein bL31B
Z: Large ribosomal subunit protein bL32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,334,30843
Polymers1,333,04730
Non-polymers1,26113
Water1086
1


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

-
Components

+
Large ribosomal subunit protein ... , 28 types, 28 molecules 1234CDEFGHIJKLMNOPQRSTUVWXYZ

#1: Protein/peptide Large ribosomal subunit protein bL33B / 50S ribosomal protein L33 2


Mass: 5684.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: 15B196 / References: UniProt: P66232
#2: Protein/peptide Large ribosomal subunit protein bL34 / 50S ribosomal protein L34


Mass: 5252.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: 15B196 / References: UniProt: P66254
#3: Protein Large ribosomal subunit protein bL35 / 50S ribosomal protein L35


Mass: 7461.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: 15B196 / References: UniProt: P66277
#4: Protein/peptide Large ribosomal subunit protein bL36 / 50S ribosomal protein L36


Mass: 4318.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: 15B196 / References: UniProt: P66300
#7: Protein Large ribosomal subunit protein uL2 / 50S ribosomal protein L2


Mass: 29827.607 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Sequence reference for strain 15B196 is not available in UniProt at the time of biocuration. Current sequence references are from UniProt tax id 196620.
Source: (natural) Staphylococcus aureus (bacteria) / Strain: 15B196 / References: UniProt: P60433
#8: Protein Large ribosomal subunit protein uL3 / 50S ribosomal protein L3


Mass: 23199.545 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: 15B196 / References: UniProt: P60450
#9: Protein Large ribosomal subunit protein uL4 / 50S ribosomal protein L4


Mass: 22364.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: 15B196 / References: UniProt: P61060
#10: Protein Large ribosomal subunit protein uL5 / 50S ribosomal protein L5


Mass: 19731.893 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: 15B196 / References: UniProt: Q7A083
#11: Protein Large ribosomal subunit protein uL6 / 50S ribosomal protein L6


Mass: 19501.154 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: 15B196 / References: UniProt: Q7A084
#12: Protein Large ribosomal subunit protein uL13 / 50S ribosomal protein L13


Mass: 16359.427 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: 15B196 / References: UniProt: Q7A089
#13: Protein Large ribosomal subunit protein uL14 / 50S ribosomal protein L14


Mass: 13157.342 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: 15B196 / References: UniProt: Q7A081
#14: Protein Large ribosomal subunit protein uL15 / 50S ribosomal protein L15


Mass: 15628.890 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: 15B196 / References: UniProt: P0A0F7
#15: Protein Large ribosomal subunit protein uL16 / 50S ribosomal protein L16


Mass: 15599.435 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: 15B196 / References: UniProt: Q7A080
#16: Protein Large ribosomal subunit protein bL17 / 50S ribosomal protein L17


Mass: 13583.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: 15B196 / References: UniProt: Q7A087
#17: Protein Large ribosomal subunit protein uL18 / 50S ribosomal protein L18


Mass: 13124.093 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: 15B196 / References: UniProt: Q7A085
#18: Protein Large ribosomal subunit protein bL19 / 50S ribosomal protein L19


Mass: 13104.381 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: 15B196 / References: UniProt: Q8NX05
#19: Protein Large ribosomal subunit protein bL20 / 50S ribosomal protein L20


Mass: 13459.919 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: 15B196 / References: UniProt: P66109
#20: Protein Large ribosomal subunit protein bL21 / 50S ribosomal protein L21


Mass: 11354.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: 15B196 / References: UniProt: Q7A0Q2
#21: Protein Large ribosomal subunit protein uL22 / 50S ribosomal protein L22


Mass: 12857.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: 15B196 / References: UniProt: Q7A079
#22: Protein Large ribosomal subunit protein uL23 / 50S ribosomal protein L23


Mass: 10380.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: 15B196 / References: UniProt: Q7A078
#23: Protein Large ribosomal subunit protein uL24 / 50S ribosomal protein L24


Mass: 11316.205 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: 15B196 / References: UniProt: P60736
#24: Protein Large ribosomal subunit protein bL25 / 50S ribosomal protein L25 / General stress protein CTC


Mass: 10462.200 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: 15B196 / References: UniProt: Q7A1S4
#25: Protein Large ribosomal subunit protein bL27 / 50S ribosomal protein L27


Mass: 8911.099 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: 15B196 / References: UniProt: P66134
#26: Protein Large ribosomal subunit protein bL28 / 50S ribosomal protein L28


Mass: 6550.716 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: 15B196 / References: UniProt: P66154
#27: Protein Large ribosomal subunit protein uL29 / 50S ribosomal protein L29


Mass: 7845.942 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: 15B196 / References: UniProt: P66174
#28: Protein Large ribosomal subunit protein uL30 / 50S ribosomal protein L30


Mass: 6434.487 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: 15B196 / References: UniProt: P0A0G1
#29: Protein Large ribosomal subunit protein bL31B / 50S ribosomal protein L31 type B


Mass: 6909.694 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: 15B196 / References: UniProt: P66197
#30: Protein/peptide Large ribosomal subunit protein bL32 / 50S ribosomal protein L32


Mass: 5569.565 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: 15B196 / References: UniProt: P66211

-
RNA chain , 2 types, 2 molecules AB

#5: RNA chain 23S ribosomal RNA


Mass: 946121.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: 15B196 / References: GenBank: 1865318698
#6: RNA chain 5S ribosomal RNA


Mass: 36974.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: 15B196 / References: GenBank: 1760048038

-
Non-polymers , 3 types, 19 molecules

#31: Chemical ChemComp-A1D6G / 7-[4-[3-[[(1~{S},2~{R},5~{R},6~{S},7~{S},8~{R},9~{R},11~{R},13~{R},14~{R})-8-[(2~{S},3~{R},4~{S},6~{R})-4-(dimethylamino)-6-methyl-3-oxidanyl-oxan-2-yl]oxy-2-ethyl-9-methoxy-1,5,7,9,11,13-hexamethyl-4,12,16-tris(oxidanylidene)-3,17-dioxa-15-azabicyclo[12.3.0]heptadecan-6-yl]oxycarbonylamino]propoxy]but-1-ynyl]-1-methyl-4-oxidanylidene-quinoline-3-carboxylic acid / MCX-190


Mass: 969.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C50H72N4O15 / Feature type: SUBJECT OF INVESTIGATION
#32: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#33: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Staphylococcus aureus(15B196) 50S ribosome in complex with MCX-190.
Type: COMPLEX / Entity ID: #5-#30, #1-#4 / Source: NATURAL
Source (natural)Organism: Staphylococcus aureus (bacteria) / Strain: 15B196
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

CTF correctionType: NONE
3D reconstructionResolution: 2.53 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 68392 / Symmetry type: POINT

+
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://pdbjlvh1.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