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- PDB-8s1u: YlmH bound to stalled 50S subunits with RqcH and PtRNA -

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Basic information

Entry
Database: PDB / ID: 8s1u
TitleYlmH bound to stalled 50S subunits with RqcH and PtRNA
Components
  • (50S ribosomal protein ...) x 22
  • (Large ribosomal subunit protein ...) x 5
  • 23S rRNA
  • 5S rRNA
  • P-tRNA
  • Putative RNA-binding protein YlmH
  • Rqc2 homolog RqcH
KeywordsRIBOSOME / LSU / 50S / RQC / YlmH / RqcH
Function / homology
Function and homology information


regulation of mitochondrial transcription / RQC complex / positive regulation of rRNA processing / nucleoid / ribosome-associated ubiquitin-dependent protein catabolic process / ribosomal large subunit binding / rescue of stalled ribosome / rRNA processing / large ribosomal subunit / ribosomal small subunit biogenesis ...regulation of mitochondrial transcription / RQC complex / positive regulation of rRNA processing / nucleoid / ribosome-associated ubiquitin-dependent protein catabolic process / ribosomal large subunit binding / rescue of stalled ribosome / rRNA processing / large ribosomal subunit / ribosomal small subunit biogenesis / small 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 / DNA binding / RNA binding / metal ion binding / cytoplasm
Similarity search - Function
: / YlmH, N-terminal / YlmH, putative RNA-binding domain / Putative RNA-binding domain in YlmH / NFACT protein RNA binding domain / Rqc2 homolog RqcH, bacterial / NFACT, RNA-binding domain / NFACT protein RNA binding domain / NFACT N-terminal and middle domains / Ribosomal protein L31 type A ...: / YlmH, N-terminal / YlmH, putative RNA-binding domain / Putative RNA-binding domain in YlmH / NFACT protein RNA binding domain / Rqc2 homolog RqcH, bacterial / NFACT, RNA-binding domain / NFACT protein RNA binding domain / NFACT N-terminal and middle domains / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / 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 protein L36 signature. / Ribosomal protein L28/L24 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 L6, bacterial-type / Ribosomal protein L18, 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 L33 superfamily / Ribosomal protein L30, bacterial-type / : / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / 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 L24 / Ribosomal protein L32p / 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 L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal protein L30, conserved site / Ribosomal protein L30 signature. / Ribosomal protein L5, conserved site / Ribosomal protein L5 signature. / Ribosomal protein L2 signature. / Ribosomal protein L29, conserved site / Ribosomal protein L29 signature. / : / Ribosomal protein L2, conserved site / Ribosomal protein L15, conserved site / Ribosomal protein L15 signature.
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL32 / Rqc2 homolog RqcH ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL32 / Rqc2 homolog RqcH / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL33A / Large ribosomal subunit protein uL13 / Putative RNA-binding protein YlmH / Large ribosomal subunit protein bL31
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsPaternoga, H. / Wilson, D.N.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)WI3285/11-1 Germany
CitationJournal: Nucleic Acids Res / Year: 2024
Title: A role for the S4-domain containing protein YlmH in ribosome-associated quality control in Bacillus subtilis.
Authors: Hiraku Takada / Helge Paternoga / Keigo Fujiwara / Jose A Nakamoto / Esther N Park / Lyudmila Dimitrova-Paternoga / Bertrand Beckert / Merilin Saarma / Tanel Tenson / Allen R Buskirk / Gemma ...Authors: Hiraku Takada / Helge Paternoga / Keigo Fujiwara / Jose A Nakamoto / Esther N Park / Lyudmila Dimitrova-Paternoga / Bertrand Beckert / Merilin Saarma / Tanel Tenson / Allen R Buskirk / Gemma C Atkinson / Shinobu Chiba / Daniel N Wilson / Vasili Hauryliuk /
Abstract: Ribosomes trapped on mRNAs during protein synthesis need to be rescued for the cell to survive. The most ubiquitous bacterial ribosome rescue pathway is trans-translation mediated by tmRNA and SmpB. ...Ribosomes trapped on mRNAs during protein synthesis need to be rescued for the cell to survive. The most ubiquitous bacterial ribosome rescue pathway is trans-translation mediated by tmRNA and SmpB. Genetic inactivation of trans-translation can be lethal, unless ribosomes are rescued by ArfA or ArfB alternative rescue factors or the ribosome-associated quality control (RQC) system, which in Bacillus subtilis involves MutS2, RqcH, RqcP and Pth. Using transposon sequencing in a trans-translation-incompetent B. subtilis strain we identify a poorly characterized S4-domain-containing protein YlmH as a novel potential RQC factor. Cryo-EM structures reveal that YlmH binds peptidyl-tRNA-50S complexes in a position analogous to that of S4-domain-containing protein RqcP, and that, similarly to RqcP, YlmH can co-habit with RqcH. Consistently, we show that YlmH can assume the role of RqcP in RQC by facilitating the addition of poly-alanine tails to truncated nascent polypeptides. While in B. subtilis the function of YlmH is redundant with RqcP, our taxonomic analysis reveals that in multiple bacterial phyla RqcP is absent, while YlmH and RqcH are present, suggesting that in these species YlmH plays a central role in the RQC.
History
DepositionFeb 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
c: P-tRNA
0: 50S ribosomal protein L32
1: 50S ribosomal protein L33 1
2: 50S ribosomal protein L34
3: 50S ribosomal protein L35
4: 50S ribosomal protein L36
6: 50S ribosomal protein L31
B: 5S rRNA
C: 50S ribosomal protein L2
D: 50S ribosomal protein L3
E: 50S ribosomal protein L4
F: 50S ribosomal protein L5
G: Large ribosomal subunit protein uL6
J: 50S ribosomal protein L13
K: 50S ribosomal protein L14
L: 50S ribosomal protein L15
M: 50S ribosomal protein L16
N: 50S ribosomal protein L17
O: 50S ribosomal protein L18
P: 50S ribosomal protein L19
Q: Large ribosomal subunit protein bL20
R: 50S ribosomal protein L21
S: 50S ribosomal protein L22
T: Large ribosomal subunit protein uL23
U: 50S ribosomal protein L24
V: Putative RNA-binding protein YlmH
W: Large ribosomal subunit protein bL27
X: 50S ribosomal protein L28
Y: 50S ribosomal protein L29
Z: Large ribosomal subunit protein uL30
a: P-tRNA
H: Rqc2 homolog RqcH
A: 23S rRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,476,70548
Polymers1,476,11833
Non-polymers58615
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11c
21c

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: G / Beg label comp-ID: G / End auth comp-ID: C / End label comp-ID: C / Auth asym-ID: c / Label asym-ID: A / Auth seq-ID: 1 - 71 / Label seq-ID: 1 - 71

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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RNA chain , 3 types, 4 molecules caBA

#1: RNA chain P-tRNA


Mass: 24491.547 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: GenBank: 1837880844
#8: RNA chain 5S rRNA


Mass: 36157.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: GenBank: 1150402534
#32: RNA chain 23S rRNA


Mass: 949761.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)

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50S ribosomal protein ... , 22 types, 22 molecules 012346CDEFJKLMNOPRSUXY

#2: Protein 50S ribosomal protein L32


Mass: 6745.073 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: O34687
#3: Protein/peptide 50S ribosomal protein L33 1


Mass: 5915.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P56849
#4: Protein/peptide 50S ribosomal protein L34


Mass: 5271.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P05647
#5: Protein 50S ribosomal protein L35


Mass: 7581.128 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P55874
#6: Protein/peptide 50S ribosomal protein L36 / BL38 / Ribosomal protein B / Ribosomal protein II


Mass: 4318.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P20278
#7: Protein 50S ribosomal protein L31


Mass: 7458.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: Q03223
#9: Protein 50S ribosomal protein L2 / BL2


Mass: 30335.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42919
#10: Protein 50S ribosomal protein L3 / BL3


Mass: 22723.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42920
#11: Protein 50S ribosomal protein L4


Mass: 22424.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42921
#12: Protein 50S ribosomal protein L5 / BL6


Mass: 20177.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12877
#14: Protein 50S ribosomal protein L13


Mass: 16407.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P70974
#15: Protein 50S ribosomal protein L14


Mass: 13175.288 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12875
#16: Protein 50S ribosomal protein L15


Mass: 15410.694 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P19946
#17: Protein 50S ribosomal protein L16


Mass: 16223.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P14577
#18: Protein 50S ribosomal protein L17 / BL15 / BL21


Mass: 13774.806 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P20277
#19: Protein 50S ribosomal protein L18 / BL16


Mass: 12993.829 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P46899
#20: Protein 50S ribosomal protein L19


Mass: 13416.853 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: O31742
#22: Protein 50S ribosomal protein L21 / BL20


Mass: 11296.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P26908
#23: Protein 50S ribosomal protein L22


Mass: 12481.608 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42060
#25: Protein 50S ribosomal protein L24 / 12 kDa DNA-binding protein / BL23 / HPB12


Mass: 11166.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P0CI78
#28: Protein 50S ribosomal protein L28


Mass: 6826.144 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P37807
#29: Protein 50S ribosomal protein L29


Mass: 7728.029 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12873

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Large ribosomal subunit protein ... , 5 types, 5 molecules GQTWZ

#13: Protein Large ribosomal subunit protein uL6


Mass: 19543.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P46898
#21: Protein Large ribosomal subunit protein bL20


Mass: 13669.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P55873
#24: Protein Large ribosomal subunit protein uL23


Mass: 10978.813 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42924
#27: Protein Large ribosomal subunit protein bL27


Mass: 10391.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P05657
#30: Protein Large ribosomal subunit protein uL30


Mass: 6650.795 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P19947

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Protein , 2 types, 2 molecules VH

#26: Protein Putative RNA-binding protein YlmH


Mass: 30823.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: ylmH, BSU15410 / Production host: Bacillus subtilis (bacteria) / References: UniProt: P71020
#31: Protein Rqc2 homolog RqcH / RqcH


Mass: 65307.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: O34693

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Non-polymers , 1 types, 15 molecules

#33: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: K

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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

ComponentName: 50S ribosomal subunit with stalled P-tRNA-nascent chain, bound by YlmH
Type: RIBOSOME / Entity ID: #1-#32 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R3/3
VitrificationCryogen name: ETHANE-PROPANE / Humidity: 100 %

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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 FIELD / Nominal defocus max: 900 nm / Nominal defocus min: 400 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
1crYOLO1.8.3particle selectiongeneral model used: gmodel_phosnet_202005_N63_c17.h5
4RELION4.0.1CTF correction
10RELION4.0.1initial Euler assignment
11RELION4.0.1final Euler assignment
13RELION4.0.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2550984
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3770 / Symmetry type: POINT
RefinementResolution: 3.4→3.4 Å / Cor.coef. Fo:Fc: 0.827 / WRfactor Rwork: 0.339 / SU B: 31.516 / SU ML: 0.475 / Average fsc free: 0 / Average fsc overall: 0.8044 / Average fsc work: 0.8044 / ESU R: 0.583
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rwork0.3394 717030 -
all0.339 --
Rfree--0 %
obs--100 %
Solvent computationSolvent model: NONE
Displacement parametersBiso mean: 93.78 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0060.011101392
ELECTRON MICROSCOPYr_bond_other_d0.0010.01757253
ELECTRON MICROSCOPYr_ext_dist_refined_b00.1158377
ELECTRON MICROSCOPYr_angle_refined_deg1.0891.844152002
ELECTRON MICROSCOPYr_angle_other_deg0.4221.726135620
ELECTRON MICROSCOPYr_dihedral_angle_1_deg8.35153751
ELECTRON MICROSCOPYr_dihedral_angle_2_deg2.9752.093289
ELECTRON MICROSCOPYr_dihedral_angle_other_2_deg1.37552451
ELECTRON MICROSCOPYr_dihedral_angle_3_deg13.125105116
ELECTRON MICROSCOPYr_dihedral_angle_6_deg13.23101087
ELECTRON MICROSCOPYr_chiral_restr0.0440.219524
ELECTRON MICROSCOPYr_chiral_restr_other0.0850.23
ELECTRON MICROSCOPYr_gen_planes_refined0.0090.0270695
ELECTRON MICROSCOPYr_gen_planes_other0.0030.0217959
ELECTRON MICROSCOPYr_nbd_refined0.1470.217720
ELECTRON MICROSCOPYr_symmetry_nbd_other0.1660.259850
ELECTRON MICROSCOPYr_nbtor_refined0.2170.239231
ELECTRON MICROSCOPYr_symmetry_nbtor_other0.0760.236024
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.1220.22985
ELECTRON MICROSCOPYr_symmetry_xyhbond_nbd_other0.0740.210
ELECTRON MICROSCOPYr_metal_ion_refined0.1980.216
ELECTRON MICROSCOPYr_mcbond_it9.99713.75115103
ELECTRON MICROSCOPYr_mcbond_other9.99613.75115103
ELECTRON MICROSCOPYr_mcangle_it17.94824.76518821
ELECTRON MICROSCOPYr_mcangle_other17.94824.76918822
ELECTRON MICROSCOPYr_scbond_it7.8788.69986289
ELECTRON MICROSCOPYr_scbond_other7.8788.69986290
ELECTRON MICROSCOPYr_scangle_it13.61515.869133181
ELECTRON MICROSCOPYr_scangle_other13.61515.869133182
ELECTRON MICROSCOPYr_lrange_it42.999291.118278264
ELECTRON MICROSCOPYr_lrange_other42.999291.118278265
ELECTRON MICROSCOPYr_ncsr_local_group_10.1950.056403
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11cELECTRON MICROSCOPYLocal ncs0.195060.05007
12cELECTRON MICROSCOPYLocal ncs0.195060.05007
LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: _ / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc workWRfactor Rwork
3.3-3.3860.595532260.595532260.5850.595
3.386-3.4780.461515940.461515940.6580.461
3.478-3.5790.429504030.429504030.6950.429
3.579-3.6890.396487620.396487620.7360.396
3.689-3.810.374472360.374472360.770.374
3.81-3.9440.358457840.358457840.7960.358
3.944-4.0930.347442590.347442590.8130.347
4.093-4.260.332425010.332425010.8370.332
4.26-4.4490.321407570.321407570.8540.321
4.449-4.6660.31389670.31389670.8740.31
4.666-4.9190.3369670.3369670.8850.3
4.919-5.2170.293350990.293350990.8930.293
5.217-5.5770.285329310.285329310.8980.285
5.577-6.0240.282306350.282306350.8990.282
6.024-6.5980.286281960.286281960.8890.286
6.598-7.3760.274255340.274255340.8970.274
7.376-8.5160.27224730.27224730.8960.27
8.516-10.4260.258189770.258189770.9090.258
10.426-14.7310.267146690.267146690.9250.267
14.731-236.80.34780600.34780600.9110.347

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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

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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

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