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- EMDB-50119: CryoEM map of the F plasmid relaxosome with truncated TraI1-863 i... -

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Entry
Database: EMDB / ID: EMD-50119
TitleCryoEM map of the F plasmid relaxosome with truncated TraI1-863 in its TE mode. ss-27_+8ds+9_+143-R_deltaAH+CTD Locally-refined 3.42 A Map
Map dataF plasmid relaxosome with truncated relaxase TraI1-863: Local refinement map
Sample
  • Complex: Complex of the relaxosome containing oriT DNA, accessory proteins TraY and TraM, host protein IHF and truncated relaxase TraI1-863
    • Complex: Heteroduplex OriT DNA containing the nic site
      • DNA: T-strand DNA (96-MER)
      • DNA: R-strand DNA (85-MER)
    • Complex: IHF heterodimer
      • Protein or peptide: Integration host factor subunit alpha
      • Protein or peptide: Integration host factor subunit beta
    • Complex: Train of three TraY proteins
      • Protein or peptide: Relaxosome protein TraY
    • Complex: Relaxase/helicase protein TraI1-863 with active helicase and C-terminal domains deleted.
      • Protein or peptide: Multifunctional conjugation protein TraI
    • Complex: TraM tetramer
  • Ligand: MAGNESIUM ION
KeywordsRelaxosome / Bacterial Conjugation / DNA processing / Relaxase / DNA binding proteins / DNA BINDING PROTEIN
Function / homology
Function and homology information


IHF-DNA complex / DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / DNA-binding transcription activator activity / protein-DNA complex / structural constituent of chromatin / regulation of translation / chromosome / DNA helicase / DNA recombination ...IHF-DNA complex / DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / DNA-binding transcription activator activity / protein-DNA complex / structural constituent of chromatin / regulation of translation / chromosome / DNA helicase / DNA recombination / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / DNA replication / transcription cis-regulatory region binding / DNA-templated transcription / regulation of DNA-templated transcription / ATP hydrolysis activity / DNA binding / ATP binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Relaxosome protein TraY / TraY domain / DNA helicase, TraI type / Conjugative transfer relaxase protein TraI / TraI, 2B/2B-like domain / TraI, N-terminal subdomain / : / DNA helicase TraI, C-terminal / single-stranded DNA binding TraI N-terminal subdomain / DNA relaxase TraI 2B/2B-like domain ...Relaxosome protein TraY / TraY domain / DNA helicase, TraI type / Conjugative transfer relaxase protein TraI / TraI, 2B/2B-like domain / TraI, N-terminal subdomain / : / DNA helicase TraI, C-terminal / single-stranded DNA binding TraI N-terminal subdomain / DNA relaxase TraI 2B/2B-like domain / TraI helicase-associated ssDNA bd, N-terminal / Integration host factor, alpha subunit / Integration host factor, beta subunit / Conjugative relaxase, N-terminal / TrwC relaxase / TrwC relaxase / Histone-like DNA-binding protein, conserved site / Bacterial histone-like DNA-binding proteins signature. / Histone-like DNA-binding protein / Bacterial DNA-binding protein / bacterial (prokaryotic) histone like domain / Integration host factor (IHF)-like DNA-binding domain superfamily / AAA domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Relaxosome protein TraY / Integration host factor subunit alpha / Integration host factor subunit beta / Multifunctional conjugation protein TraI
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.42 Å
AuthorsWilliams SM / Waksman G
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Nat Commun / Year: 2025
Title: Cryo-EM Structure of the relaxosome, a complex essential for bacterial mating and the spread of antibiotic resistance genes.
Authors: Sunanda M Williams / Sandra Raffl / Sabine Kienesberger / Aravindan Ilangovan / Ellen L Zechner / Gabriel Waksman /
Abstract: Bacterial mating, or conjugation, was discovered nearly 80 years ago as a process transferring genes from one bacterial cell (the donor) to another (the recipient). It requires three key multiprotein ...Bacterial mating, or conjugation, was discovered nearly 80 years ago as a process transferring genes from one bacterial cell (the donor) to another (the recipient). It requires three key multiprotein complexes in the donor cell: a DNA-processing machinery called the relaxosome, a double-membrane spanning type 4 secretion system (T4SS), and an extracellular appendage termed pilus. While the near-atomic resolution structures of the T4SS and pilus are already known, that of the relaxosome has not been reported to date. Here, we describe the cryo-EM structure of the fully assembled relaxosome encoded by the paradigm F plasmid in two different states corresponding to distinct functional steps along the DNA processing reaction. By varying the structures of model DNAs we delineate conformational changes required to initiate conjugation. Mutational studies of the various protein-protein and protein-DNA interaction hubs suggest a complex sensitive to trigger signals, that could arise from cell-to-cell contacts with recipient cells.
History
DepositionApr 17, 2024-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50119.png

Downloads & links

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Map

FileDownload / File: emd_50119.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationF plasmid relaxosome with truncated relaxase TraI1-863: Local refinement map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 560 pix.
= 462. Å		0.83 Å/pix.
x 560 pix.
= 462. Å		0.83 Å/pix.
x 560 pix.
= 462. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-0.8200173 - 1.8061359
Average (Standard dev.)0.0008012993 (±0.022059534)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 462.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50119_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: DeepEMhancer Post-processed Map

Fileemd_50119_additional_1.map
AnnotationDeepEMhancer Post-processed Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: F plasmid relaxosome with truncated relaxase TraI1-863: Local...

Fileemd_50119_additional_2.map
AnnotationF plasmid relaxosome with truncated relaxase TraI1-863: Local refinement map unsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Local refinement map - Half-A

Fileemd_50119_half_map_1.map
AnnotationLocal refinement map - Half-A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Local refinement map - Half-B

Fileemd_50119_half_map_2.map
AnnotationLocal refinement map - Half-B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of the relaxosome containing oriT DNA, accessory proteins...

EntireName: Complex of the relaxosome containing oriT DNA, accessory proteins TraY and TraM, host protein IHF and truncated relaxase TraI1-863
Components
  • Complex: Complex of the relaxosome containing oriT DNA, accessory proteins TraY and TraM, host protein IHF and truncated relaxase TraI1-863
    • Complex: Heteroduplex OriT DNA containing the nic site
      • DNA: T-strand DNA (96-MER)
      • DNA: R-strand DNA (85-MER)
    • Complex: IHF heterodimer
      • Protein or peptide: Integration host factor subunit alpha
      • Protein or peptide: Integration host factor subunit beta
    • Complex: Train of three TraY proteins
      • Protein or peptide: Relaxosome protein TraY
    • Complex: Relaxase/helicase protein TraI1-863 with active helicase and C-terminal domains deleted.
      • Protein or peptide: Multifunctional conjugation protein TraI
    • Complex: TraM tetramer
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Complex of the relaxosome containing oriT DNA, accessory proteins...

SupramoleculeName: Complex of the relaxosome containing oriT DNA, accessory proteins TraY and TraM, host protein IHF and truncated relaxase TraI1-863
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6

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Supramolecule #2: Heteroduplex OriT DNA containing the nic site

SupramoleculeName: Heteroduplex OriT DNA containing the nic site / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Details: Prepared by annealing of chemically synthesised oligos
Source (natural)Organism: Escherichia coli K-12 (bacteria)

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Supramolecule #3: IHF heterodimer

SupramoleculeName: IHF heterodimer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Escherichia coli K-12 (bacteria)

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Supramolecule #4: Train of three TraY proteins

SupramoleculeName: Train of three TraY proteins / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Escherichia coli K-12 (bacteria)

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Supramolecule #5: Relaxase/helicase protein TraI1-863 with active helicase and C-te...

SupramoleculeName: Relaxase/helicase protein TraI1-863 with active helicase and C-terminal domains deleted.
type: complex / ID: 5 / Parent: 1 / Macromolecule list: #6
Source (natural)Organism: Escherichia coli K-12 (bacteria)

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Supramolecule #6: TraM tetramer

SupramoleculeName: TraM tetramer / type: complex / ID: 6 / Parent: 1
Details: Used for complex formation, but density was excluded from the local refinement. TraM is therefore not present in the model
Source (natural)Organism: Escherichia coli K-12 (bacteria)

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Macromolecule #1: T-strand DNA (96-MER)

MacromoleculeName: T-strand DNA (96-MER) / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 52.621707 KDa
SequenceString: (DC)(DC)(DT)(DA)(DC)(DA)(DA)(DA)(DA)(DC) (DG)(DG)(DT)(DG)(DT)(DC)(DG)(DG)(DC)(DG) (DC)(DG)(DT)(DT)(DG)(DT)(DT)(DG)(DT) (DA)(DG)(DC)(DC)(DG)(DC)(DG)(DC)(DC)(DG) (DA) (DC)(DA)(DC)(DC)(DG)(DC) ...String:
(DC)(DC)(DT)(DA)(DC)(DA)(DA)(DA)(DA)(DC) (DG)(DG)(DT)(DG)(DT)(DC)(DG)(DG)(DC)(DG) (DC)(DG)(DT)(DT)(DG)(DT)(DT)(DG)(DT) (DA)(DG)(DC)(DC)(DG)(DC)(DG)(DC)(DC)(DG) (DA) (DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT) (DT)(DT)(DT)(DT)(DA)(DA)(DA)(DT)(DA)(DT) (DC)(DA) (DT)(DA)(DA)(DA)(DG)(DA)(DG) (DA)(DG)(DT)(DA)(DA)(DG)(DA)(DG)(DA)(DA) (DA)(DC)(DT) (DA)(DA)(DT)(DT)(DT)(DT) (DT)(DC)(DA)(DT)(DA)(DA)(DC)(DA)(DC)(DT) (DC)(DT)(DA)(DT) (DT)(DT)(DA)(DT)(DA) (DA)(DA)(DG)(DA)(DA)(DA)(DA)(DA)(DT)(DC) (DA)(DG)(DC)(DA)(DA) (DA)(DA)(DA)(DC) (DT)(DT)(DG)(DT)(DT)(DT)(DT)(DT)(DG)(DC) (DG)(DT)(DG)(DG)(DG)(DG) (DT)(DG)(DT) (DG)(DG)(DT)(DG)(DC)(DT)(DT)(DT)(DT)(DG) (DG)(DT)(DG)(DG)(DT)(DG)(DA) (DG)(DA) (DA)(DC)(DC)(DA)(DC)(DC)(DA)(DA)

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Macromolecule #2: R-strand DNA (85-MER)

MacromoleculeName: R-strand DNA (85-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 41.662676 KDa
SequenceString: (DC)(DG)(DC)(DA)(DA)(DA)(DA)(DA)(DC)(DA) (DA)(DG)(DT)(DT)(DT)(DT)(DT)(DG)(DC)(DT) (DG)(DA)(DT)(DT)(DT)(DT)(DT)(DC)(DT) (DT)(DT)(DA)(DT)(DA)(DA)(DA)(DT)(DA)(DG) (DA) (DG)(DT)(DG)(DT)(DT)(DA) ...String:
(DC)(DG)(DC)(DA)(DA)(DA)(DA)(DA)(DC)(DA) (DA)(DG)(DT)(DT)(DT)(DT)(DT)(DG)(DC)(DT) (DG)(DA)(DT)(DT)(DT)(DT)(DT)(DC)(DT) (DT)(DT)(DA)(DT)(DA)(DA)(DA)(DT)(DA)(DG) (DA) (DG)(DT)(DG)(DT)(DT)(DA)(DT)(DG) (DA)(DA)(DA)(DA)(DA)(DT)(DT)(DA)(DG)(DT) (DT)(DT) (DC)(DT)(DC)(DT)(DT)(DA)(DC) (DT)(DC)(DT)(DC)(DT)(DT)(DT)(DA)(DT)(DG) (DA)(DT)(DA) (DT)(DT)(DT)(DA)(DA)(DA) (DA)(DA)(DA)(DG)(DC)(DG)(DG)(DT)(DG)(DT) (DC)(DG)(DG)(DC) (DG)(DC)(DG)(DG)(DC) (DT)(DA)(DC)(DA)(DA)(DC)(DA)(DA)(DC)(DG) (DC)(DG)(DC)(DC)(DG) (DA)(DC)(DA)(DC) (DC)(DG)(DT)(DT)(DT)(DT)(DG)(DT)(DA)(DG) (DG)

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Macromolecule #3: Integration host factor subunit alpha

MacromoleculeName: Integration host factor subunit alpha / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 11.373952 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MALTKAEMSE YLFDKLGLSK RDAKELVELF FEEIRRALEN GEQVKLSGFG NFDLRDKNQR PGRNPKTGED IPITARRVVT FRPGQKLKS RVENASPKDE

UniProtKB: Integration host factor subunit alpha

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Macromolecule #4: Integration host factor subunit beta

MacromoleculeName: Integration host factor subunit beta / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 10.671178 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MTKSELIERL ATQQSHIPAK TVEDAVKEML EHMASTLAQG ERIEIRGFGS FSLHYRAPRT GRNPKTGDKV ELEGKYVPHF KPGKELRDR ANIYG

UniProtKB: Integration host factor subunit beta

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Macromolecule #5: Relaxosome protein TraY

MacromoleculeName: Relaxosome protein TraY / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 15.210423 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MKRFGTRSAT GKMVKLKLPV DVESLLIEAS NRSGRSRSFE AVIRLKDHLH RYPKFNRAGN IYGKSLVKYL TMRLDDETNQ LLIAAKNRS GWCKTDEAAD RVIDHLIKFP DFYNSEIFRE ADKEEDITFN TL

UniProtKB: Relaxosome protein TraY

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Macromolecule #6: Multifunctional conjugation protein TraI

MacromoleculeName: Multifunctional conjugation protein TraI / type: protein_or_peptide / ID: 6
Details: TraI in its trans-esterase or relaxase conformation
Number of copies: 1 / Enantiomer: LEVO / EC number: DNA topoisomerase
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 95.347328 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MEFELGTMMS IAQVRSAGSA GNFYTDKDNY YVLGSMGERW AGRGAEQLGL QGSVDKDVFT RLLEGRLPDG ADLSRMQDGS NRHRPGYDL TFSAPKSVSM MAMLGGDKRL IDAHNQAVDF AVRQVEALAS TRVMTDGQSE TVLTGNLVMA LFNHDTSRDQ E PQLHTHAV ...String:
MEFELGTMMS IAQVRSAGSA GNFYTDKDNY YVLGSMGERW AGRGAEQLGL QGSVDKDVFT RLLEGRLPDG ADLSRMQDGS NRHRPGYDL TFSAPKSVSM MAMLGGDKRL IDAHNQAVDF AVRQVEALAS TRVMTDGQSE TVLTGNLVMA LFNHDTSRDQ E PQLHTHAV VANVTQHNGE WKTLSSDKVG KTGFIENVYA NQIAFGRLYR EKLKEQVEAL GYETEVVGKH GMWEMPGVPV EA FSGRSQT IREAVGEDAS LKSRDVAALD TRKSKQHVDP EIKMAEWMQT LKETGFDIRA YRDAADQRAD LRTLTPGPAS QDG PDVQQA VTQAIAGLSE RKVQFTYTDV LARTVGILPP ENGVIERARA GIDEAISREQ LIPLDREKGL FTSGIHVLDE LSVR ALSRD IMKQNRVTVH PEKSVPRTAG YSDAVSVLAQ DRPSLAIVSG QGGAAGQRER VAELVMMARE QGREVQIIAA DRRSQ MNMK QDERLSGELI TGRRQLLEGM AFTPGSTVIV DQGEKLSLKE TLTLLDGAAR HNVQVLITDS GQRTGTGSAL MAMKDA GVN TYRWQGGEQR PATIISEPDR NVRYARLAGD FAASVKAGEE SVAQVSGVRE QAILTQAIRS ELKTQGVLGL PEVTMTA LS PVWLDSRSRY LRDMYRPGMV MEQWNPETRS HDRYVIDRVT AQSHSLTLRD AQGETQVVRI SSLDSSWSLF RPEKMPVA D GERLRVTGKI PGLRVSGGDR LQVASVSEDA MTVVVPGRAE PATLPVSDSP FTALKLENGW VETPGHSVSD SATVFASVT QMAMDNATLN GLARSGRDVR LYSSLDETRT AEKLARHPSF TVVSEQIKTR AGETSLETAI SHQKSALHTP

UniProtKB: Multifunctional conjugation protein TraI

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Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5 / Details: 20 mM Hepes pH 7.5, 100 mM NaCl
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsThe complex after assembly and gel filtration was subjected to glutaraldehyde cross-linking

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 49.92 e/Å2
Details: Movies were collected in counting mode fractionated over 50 frames
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 8381227
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: CryoSPARC ab-initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 165577
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Details: CryoSPARC ab-initio
Final angle assignmentType: MAXIMUM LIKELIHOOD / Details: Local refinement
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-9f0z:
CryoEM structure of the F plasmid relaxosome with truncated TraI1-863 in its TE mode, derived from the ss-27_+8ds+9_+143-R_deltaAH+CTD Locally-refined 3.42 A Map

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