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- PDB-6az1: Cryo-EM structure of the small subunit of Leishmania ribosome bou... -

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Basic information

Entry
Database: PDB / ID: 6az1
TitleCryo-EM structure of the small subunit of Leishmania ribosome bound to paromomycin
Components
  • (ribosomal protein ...) x 32
  • E-site tRNA
  • LACK1
  • P-site tRNA
  • mRNAMessenger RNA
  • ribosomal RNA 18S
  • tRNA-Phe
KeywordsRIBOSOME/ANTIBIOTIC / Leishmania donovani / ribosome / aminoglycoside / paromomycin / RIBOSOME-ANTIBIOTIC complex
Function / homology
Function and homology information


translation regulator activity / ribosomal small subunit assembly / cytosolic small ribosomal subunit / ribosome binding / small ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex ...translation regulator activity / ribosomal small subunit assembly / cytosolic small ribosomal subunit / ribosome binding / small ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / RNA binding / zinc ion binding / metal ion binding
Similarity search - Function
Ribosomal protein S17 / Ribosomal protein S26 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #1000 / Ribosomal protein S4, central domain / Ribosomal protein S21 / Alpha-Beta Plaits - #3370 / Hypothetical Cytosolic Protein; Chain: A; / Ribosomal protein S27 / first zn-finger domain of poly(adp-ribose) polymerase-1 / Diphtheria Toxin Repressor; domain 2 ...Ribosomal protein S17 / Ribosomal protein S26 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #1000 / Ribosomal protein S4, central domain / Ribosomal protein S21 / Alpha-Beta Plaits - #3370 / Hypothetical Cytosolic Protein; Chain: A; / Ribosomal protein S27 / first zn-finger domain of poly(adp-ribose) polymerase-1 / Diphtheria Toxin Repressor; domain 2 / Ribosomal protein S3, C-terminal domain / Ribosomal Protein S14/S29 / 30s Ribosomal Protein S14; Chain N / Ribosomal Protein S8; Chain: A, domain 1 - #30 / RNA-binding S4 domain / Ribosomal Protein S7 / Ribosomal protein S7/S5 / Ribosomal protein S3 C-terminal domain / Dna Ligase; domain 1 - #10 / Ribosomal protein S11/S14 / Ribosomal protein S10 / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / S15/NS1, RNA-binding / SH3 type barrels. - #30 / K homology (KH) domain / Ribosomal protein L30/S12 / Double Stranded RNA Binding Domain - #20 / Glucose-6-phosphate isomerase like protein; domain 1 / Ribosomal Protein S8; Chain: A, domain 1 / Ribosomal Protein S5; domain 2 - #10 / N-terminal domain of TfIIb / Ribosomal protein S12e / Small (40S) ribosomal subunit Asc1/RACK1 / GMP Synthetase; Chain A, domain 3 / S27a-like superfamily / Ribosomal Protein S5; domain 2 / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S25 / Ribosomal protein S2, eukaryotic / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S8e subdomain, eukaryotes / S25 ribosomal protein / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S19A/S15e / Ribosomal protein S30 / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S5, eukaryotic/archaeal / Double Stranded RNA Binding Domain / Ribosomal protein S8e, conserved site / 40S ribosomal protein S11, N-terminal / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S6, eukaryotic / Ribosomal protein S7e / 40S ribosomal protein S4, C-terminal domain / Ribosomal S17 / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S19e / Ribosomal protein S27, zinc-binding domain superfamily / 40S Ribosomal protein S10 / Ribosomal protein S27 / Ribosomal protein S28e conserved site / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S28e / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal_S17 N-terminal / Plectin/S10, N-terminal / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal protein S7e / YVTN repeat-like/Quinoprotein amine dehydrogenase / Plectin/S10 domain / Ribosomal protein S8e / Ribosomal protein S4, KOW domain / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S6e / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S6e / Ribosomal protein S4/S9, eukaryotic/archaeal / RS4NT (NUC023) domain / Ribosomal protein S27
Similarity search - Domain/homology
PAROMOMYCIN / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S5 / 40S ribosomal protein SA ...PAROMOMYCIN / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S5 / 40S ribosomal protein SA / 40S ribosomal protein S7 / 40S ribosomal protein S21, putative / 40S ribosomal protein S15A, putative / 40S ribosomal protein S12 / 40S ribosomal protein S4 / 40S ribosomal protein S23, putative / 40S ribosomal protein S15, putative / 40S ribosomal protein S8 / 40S ribosomal protein S25 / 40S ribosomal protein S16, putative / 40S ribosomal protein S33, putative / Ribosomal protein S10 / Ribosomal protein S29, putative / 40S ribosomal protein S17, putative / 40S ribosomal protein S26 / 40S ribosomal protein S30 / 40S ribosomal protein S14 / 40S ribosomal protein S2 / 40S ribosomal protein S13, putative / 40S ribosomal protein S3, putative / 40S ribosomal protein S19 protein, putative / 40S ribosomal protein S3a / 60S ribosomal protein L40 / 40S ribosomal protein S18, putative / 40S ribosomal protein S10, putative / 40S ribosomal protein S9, putative / 40S ribosomal protein S24 / 40S ribosomal protein S27-1, putative / 40S ribosomal protein S6 / Guanine nucleotide-binding protein subunit beta-like protein / 40S ribosomal protein S11, putative
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsShalev-Benami, M. / Zhang, Y. / Rozenberg, H. / Matzov, D. / Zimmerman, E. / Bashan, A. / Jaffe, C.L. / Yonath, A. / Skiniotis, G.
CitationJournal: Nat Commun / Year: 2017
Title: Atomic resolution snapshot of Leishmania ribosome inhibition by the aminoglycoside paromomycin.
Authors: Moran Shalev-Benami / Yan Zhang / Haim Rozenberg / Yuko Nobe / Masato Taoka / Donna Matzov / Ella Zimmerman / Anat Bashan / Toshiaki Isobe / Charles L Jaffe / Ada Yonath / Georgios Skiniotis /
Abstract: Leishmania is a single-celled eukaryotic parasite afflicting millions of humans worldwide, with current therapies limited to a poor selection of drugs that mostly target elements in the parasite's ...Leishmania is a single-celled eukaryotic parasite afflicting millions of humans worldwide, with current therapies limited to a poor selection of drugs that mostly target elements in the parasite's cell envelope. Here we determined the atomic resolution electron cryo-microscopy (cryo-EM) structure of the Leishmania ribosome in complex with paromomycin (PAR), a highly potent compound recently approved for treatment of the fatal visceral leishmaniasis (VL). The structure reveals the mechanism by which the drug induces its deleterious effects on the parasite. We further show that PAR interferes with several aspects of cytosolic translation, thus highlighting the cytosolic rather than the mitochondrial ribosome as the primary drug target. The results also highlight unique as well as conserved elements in the PAR-binding pocket that can serve as hotspots for the development of novel therapeutics.
History
DepositionSep 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation
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
Revision 2.0Jul 3, 2019Group: Data collection / Non-polymer description / Structure summary
Category: chem_comp / entity
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight

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Assembly

Deposited unit
A: Ribosomal protein s1e
B: ribosomal protein S2
C: ribosomal protein S3
D: ribosomal protein S4
E: ribosomal protein S4e
F: ribosomal protein S5
G: ribosomal protein S6e
H: ribosomal protein S7
I: ribosomal protein S7e
J: ribosomal protein S8
K: ribosomal protein S8e
L: ribosomal protein S9
M: ribosomal protein S10
N: ribosomal protein S10e
O: ribosomal protein S11
P: ribosomal protein S12
Q: ribosomal protein S12e
R: ribosomal protein S13
S: ribosomal protein S14
T: ribosomal protein S15
U: ribosomal protein S17
V: ribosomal protein S17e
W: ribosomal protein S19
X: ribosomal protein S19e
Y: ribosomal protein S21e
Z: ribosomal protein S24e
a: ribosomal protein S25e
b: ribosomal protein S26e
c: ribosomal protein S27e
d: ribosomal protein S28e
e: ribosomal protein S30e
f: ribosomal protein S31e
g: LACK1
1: ribosomal RNA 18S
2: tRNA-Phe
3: P-site tRNA
4: E-site tRNA
5: mRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,416,65868
Polymers1,412,38138
Non-polymers4,27730
Water4,720262
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area233520 Å2
ΔGint-1705 kcal/mol
Surface area417100 Å2

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Components

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Ribosomal protein ... , 32 types, 32 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZabcdef

#1: Protein Ribosomal protein s1e / Ribosome


Mass: 30092.064 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BRS2
#2: Protein ribosomal protein S2 /


Mass: 27564.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: A4IDS4*PLUS
#3: Protein ribosomal protein S3 /


Mass: 24511.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BQ25
#4: Protein ribosomal protein S4 /


Mass: 22184.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BTJ0
#5: Protein ribosomal protein S4e / Ribosome


Mass: 30711.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BBI6
#6: Protein ribosomal protein S5 /


Mass: 28803.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BNF0
#7: Protein ribosomal protein S6e / Ribosome


Mass: 28341.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: O44012*PLUS
#8: Protein ribosomal protein S7 /


Mass: 21311.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: A0A381MCG8*PLUS
#9: Protein ribosomal protein S7e / Ribosome


Mass: 23867.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9B7A8
#10: Protein ribosomal protein S8 /


Mass: 14719.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BAV6
#11: Protein ribosomal protein S8e / Ribosome


Mass: 25038.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BH78
#12: Protein ribosomal protein S9 /


Mass: 16718.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BI96
#13: Protein ribosomal protein S10 /


Mass: 13049.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BJI2*PLUS
#14: Protein ribosomal protein S10e / Ribosome


Mass: 17432.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BTG4
#15: Protein ribosomal protein S11 /


Mass: 15609.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BMA8
#16: Protein ribosomal protein S12 /


Mass: 15952.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BFB6
#17: Protein ribosomal protein S12e / Ribosome


Mass: 15611.837 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BBC0
#18: Protein ribosomal protein S13 /


Mass: 17443.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BTF9
#19: Protein ribosomal protein S14 /


Mass: 6696.929 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BJV7
#20: Protein ribosomal protein S15 /


Mass: 17455.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BPR7
#21: Protein ribosomal protein S17 /


Mass: 19985.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: Q9TXA6*PLUS
#22: Protein ribosomal protein S17e / Ribosome


Mass: 16521.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BJZ5
#23: Protein ribosomal protein S19 / 40S ribosomal protein S19


Mass: 17528.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BFQ0*PLUS
#24: Protein ribosomal protein S19e / Ribosome


Mass: 20188.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BR60
#25: Protein ribosomal protein S21e / Ribosome


Mass: 16669.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BAR6*PLUS
#26: Protein ribosomal protein S24e / Ribosome


Mass: 15808.882 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BU11
#27: Protein ribosomal protein S25e / Ribosome


Mass: 13071.399 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BHM6
#28: Protein ribosomal protein S26e / Ribosome


Mass: 12794.251 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BK95
#29: Protein ribosomal protein S27e / Ribosome


Mass: 9819.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BUA2
#30: Protein ribosomal protein S28e / Ribosome


Mass: 9763.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BIH3
#31: Protein ribosomal protein S30e / Ribosome


Mass: 7394.894 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BLG3
#32: Protein ribosomal protein S31e / Ribosome


Mass: 17015.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BTC5

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Protein , 1 types, 1 molecules g

#33: Protein LACK1


Mass: 34459.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: Q9BIJ5

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RNA chain , 5 types, 5 molecules 12345

#34: RNA chain ribosomal RNA 18S


Mass: 710287.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: GenBank: 322500086
#35: RNA chain tRNA-Phe


Mass: 24599.748 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) / References: GenBank: 1229082179
#36: RNA chain P-site tRNA


Mass: 24786.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 817573384
#37: RNA chain E-site tRNA


Mass: 24485.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1229082179
#38: RNA chain mRNA / Messenger RNA


Mass: 4085.501 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Leishmania donovani (eukaryote)

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Non-polymers , 3 types, 292 molecules

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


Mass: 24.305 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Mg
#40: Chemical
ChemComp-PAR / PAROMOMYCIN / PAROMOMYCIN I, AMMINOSIDIN, CATENULIN, CRESTOMYCIN, MONOMYCIN A, NEOMYCIN E / Paromomycin


Mass: 615.628 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C23H45N5O14 / Comment: Antimicrobial, medication*YM
#41: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O

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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 donovani 91S ribosome SSU / Type: RIBOSOME / Entity ID: #1-#38 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Leishmania donovani (eukaryote)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 FIELDBright-field microscopy
Image recordingElectron dose: 1 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: dev-2686_1692: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 141028 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0186381
ELECTRON MICROSCOPYf_angle_d1.166126481
ELECTRON MICROSCOPYf_dihedral_angle_d18.20947125
ELECTRON MICROSCOPYf_chiral_restr0.06115904
ELECTRON MICROSCOPYf_plane_restr0.0088580

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