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- EMDB-8624: Cryo EM structure of anti-CRISPRs, AcrF1 and AcrF2, bound to type... -

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Basic information

Entry
Database: EMDB / ID: EMD-8624
TitleCryo EM structure of anti-CRISPRs, AcrF1 and AcrF2, bound to type I-F crRNA-guided CRISPR surveillance complex
Map dataCryo EM map of the Csy-Acr complex.
Sample
  • Complex: Anti-CRISPRs AcrF1 and AcrF2 bound P. aeruginosa crRNA-guided CRISPR surveillance(Csy)complex.
    • Protein or peptide: CRISPR-associated protein Csy1
    • Protein or peptide: CRISPR-associated protein Csy2
    • Protein or peptide: CRISPR-associated protein Csy3
    • Protein or peptide: Anti-CRISPR protein Acr30-35
    • Protein or peptide: Anti-CRISPR protein 30
    • Protein or peptide: CRISPR-associated endonuclease Cas6/Csy4
    • RNA: CRISPR RNA (60-MER)
KeywordsCRISPR RNA-recognition-motif (RRM) / pseudo-helical / Type 1-F CRISPR / IMMUNE SYSTEM-RNA complex
Function / homology
Function and homology information


symbiont-mediated suppression of host adaptive immune response / symbiont-mediated suppression of host CRISPR-cas system / maintenance of CRISPR repeat elements / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / : / RNA binding
Similarity search - Function
: / Anti-CRISPR protein Acr30-35/AcrF1 / CRISPR-associated protein Csy1 / CRISPR-associated protein (Cas_Csy1) / CRISPR-associated endoribonuclease Cas6/Csy4, subtype I-F/YPEST / CRISPR-associated endoribonuclease Cas6/Csy4, subtype I-F/YPEST superfamily / CRISPR-associated protein (Cas_Csy4) / CRISPR-associated protein Csy2 / CRISPR-associated protein (Cas_Csy2) / CRISPR-associated protein Csy3 / CRISPR-associated protein (Cas_Csy3)
Similarity search - Domain/homology
Uncharacterized protein / CRISPR-associated protein Csy1 / CRISPR-associated protein Csy2 / CRISPR-associated protein Csy3 / CRISPR-associated endonuclease Cas6/Csy4 / Anti-CRISPR protein 30
Similarity search - Component
Biological speciesPseudomonas aeruginosa UCBPP-PA14 (bacteria) / Pseudomonas aeruginosa (strain UCBPP-PA14) (bacteria) / Pseudomonas phage JBD30 (virus) / Pseudomonas phage D3112 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsChowdhury S / Carter J
Funding support United States, Canada, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103500, P30GM110732-03, R01GM110270, R01GM108888, P20GM103474, F32GM108436, DP2EB020402, DP5OD021344 United States
National Science Foundation (NSF, United States)EPS-110134 United States
Canadian Institutes of Health Research (CIHR)MOP-130482, MOP-136845 Canada
CitationJournal: Cell / Year: 2017
Title: Structure Reveals Mechanisms of Viral Suppressors that Intercept a CRISPR RNA-Guided Surveillance Complex.
Authors: Saikat Chowdhury / Joshua Carter / MaryClare F Rollins / Sarah M Golden / Ryan N Jackson / Connor Hoffmann / Lyn'Al Nosaka / Joseph Bondy-Denomy / Karen L Maxwell / Alan R Davidson / ...Authors: Saikat Chowdhury / Joshua Carter / MaryClare F Rollins / Sarah M Golden / Ryan N Jackson / Connor Hoffmann / Lyn'Al Nosaka / Joseph Bondy-Denomy / Karen L Maxwell / Alan R Davidson / Elizabeth R Fischer / Gabriel C Lander / Blake Wiedenheft /
Abstract: Genetic conflict between viruses and their hosts drives evolution and genetic innovation. Prokaryotes evolved CRISPR-mediated adaptive immune systems for protection from viral infection, and viruses ...Genetic conflict between viruses and their hosts drives evolution and genetic innovation. Prokaryotes evolved CRISPR-mediated adaptive immune systems for protection from viral infection, and viruses have evolved diverse anti-CRISPR (Acr) proteins that subvert these immune systems. The adaptive immune system in Pseudomonas aeruginosa (type I-F) relies on a 350 kDa CRISPR RNA (crRNA)-guided surveillance complex (Csy complex) to bind foreign DNA and recruit a trans-acting nuclease for target degradation. Here, we report the cryo-electron microscopy (cryo-EM) structure of the Csy complex bound to two different Acr proteins, AcrF1 and AcrF2, at an average resolution of 3.4 Å. The structure explains the molecular mechanism for immune system suppression, and structure-guided mutations show that the Acr proteins bind to residues essential for crRNA-mediated detection of DNA. Collectively, these data provide a snapshot of an ongoing molecular arms race between viral suppressors and the immune system they target.
History
DepositionFeb 25, 2017-
Header (metadata) releaseApr 26, 2017-
Map releaseApr 26, 2017-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0274
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0274
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5uz9
  • Surface level: 0.0274
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8624.png

Downloads & links

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Map

FileDownload / File: emd_8624.map.gz / Format: CCP4 / Size: 35.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo EM map of the Csy-Acr complex.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 210 pix.
= 216.3 Å		1.03 Å/pix.
x 210 pix.
= 216.3 Å		1.03 Å/pix.
x 210 pix.
= 216.3 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0274 / Movie #1: 0.0274
Minimum - Maximum-0.10289869 - 0.17144284
Average (Standard dev.)0.0007336988 (±0.006945551)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions210210210
Spacing210210210
CellA=B=C: 216.29999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z210210210
origin x/y/z0.0000.0000.000
length x/y/z216.300216.300216.300
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-36
NX/NY/NZ528549
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS210210210
D min/max/mean-0.1030.1710.001

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Supplemental data

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Additional map: Focused map of the "tail" region of Csy-Acr...

Fileemd_8624_additional_1.map
AnnotationFocused map of the "tail" region of Csy-Acr complex, comprising of Cas5, Cas8 and Acr2 subunits.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened Cryo EM map of the Csy-Acr complex.

Fileemd_8624_additional_2.map
AnnotationUnsharpened Cryo EM map of the Csy-Acr complex.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 2 of the Csy-Acr complex.

Fileemd_8624_half_map_1.map
AnnotationHalf-map 2 of the Csy-Acr complex.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 1 of the Csy-Acr complex.

Fileemd_8624_half_map_2.map
AnnotationHalf-map 1 of the Csy-Acr complex.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Anti-CRISPRs AcrF1 and AcrF2 bound P. aeruginosa crRNA-guided CRI...

EntireName: Anti-CRISPRs AcrF1 and AcrF2 bound P. aeruginosa crRNA-guided CRISPR surveillance(Csy)complex.
Components
  • Complex: Anti-CRISPRs AcrF1 and AcrF2 bound P. aeruginosa crRNA-guided CRISPR surveillance(Csy)complex.
    • Protein or peptide: CRISPR-associated protein Csy1
    • Protein or peptide: CRISPR-associated protein Csy2
    • Protein or peptide: CRISPR-associated protein Csy3
    • Protein or peptide: Anti-CRISPR protein Acr30-35
    • Protein or peptide: Anti-CRISPR protein 30
    • Protein or peptide: CRISPR-associated endonuclease Cas6/Csy4
    • RNA: CRISPR RNA (60-MER)

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Supramolecule #1: Anti-CRISPRs AcrF1 and AcrF2 bound P. aeruginosa crRNA-guided CRI...

SupramoleculeName: Anti-CRISPRs AcrF1 and AcrF2 bound P. aeruginosa crRNA-guided CRISPR surveillance(Csy)complex.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Cas5F, Cas6F, Cas7F, Cas8F and CRISPR RNA (crRNA) forms the Csy surveillance complex. Cas5F, Cas8F and 5'crRNA handle forms the "tail" of the complex, and 3' crRNA stem-loop along with Cas6F ...Details: Cas5F, Cas6F, Cas7F, Cas8F and CRISPR RNA (crRNA) forms the Csy surveillance complex. Cas5F, Cas8F and 5'crRNA handle forms the "tail" of the complex, and 3' crRNA stem-loop along with Cas6F forms the "head". Six copies Cas7F along with crRNA spacer forms the "core" of the complex.
Source (natural)Organism: Pseudomonas aeruginosa UCBPP-PA14 (bacteria)
Molecular weightTheoretical: 450 KDa

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Macromolecule #1: CRISPR-associated protein Csy1

MacromoleculeName: CRISPR-associated protein Csy1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (strain UCBPP-PA14) (bacteria)
Strain: UCBPP-PA14
Molecular weightTheoretical: 49.194168 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MTSPLPTPTW QELRQFIESF IQERLQGKLD KLQPDEDDKR QTLLATHRRE AWLADAARRV GQLQLVTHTL KPIHPDARGS NLHSLPQAP GQPGLAGSHE LGDRLVSDVV GNAAALDVFK FLSLQYQGKN LLNWLTEDSA EALQALSDNA EQAREWRQAF I GITTVKGA ...String:
MTSPLPTPTW QELRQFIESF IQERLQGKLD KLQPDEDDKR QTLLATHRRE AWLADAARRV GQLQLVTHTL KPIHPDARGS NLHSLPQAP GQPGLAGSHE LGDRLVSDVV GNAAALDVFK FLSLQYQGKN LLNWLTEDSA EALQALSDNA EQAREWRQAF I GITTVKGA PASHSLAKQL YFPLPGSGYH LLAPLFPTSL VHHVHALLRE ARFGDAAKAA REARSRQESW PHGFSEYPNL AI QKFGGTK PQNISQLNNE RRGENWLLPS LPPNWQRQNV NAPMRHSSVF EHDFGRTPEV SRLTRTLQRF LAKTVHNNLA IRQ RRAQLV AQICDEALQY AARLRELEPG WSATPGCQLH DAEQLWLDPL RAQTDETFLQ RRLRGDWPAE VGNRFANWLN RAVS SDSQI LGSPEAAQWS QELSKELTMF KEILEDERD

UniProtKB: CRISPR-associated protein Csy1

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Macromolecule #2: CRISPR-associated protein Csy2

MacromoleculeName: CRISPR-associated protein Csy2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (strain UCBPP-PA14) (bacteria)
Strain: UCBPP-PA14
Molecular weightTheoretical: 36.244074 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSVTDPEALL LLPRLSIQNA NAISSPLTWG FPSPGAFTGF VHALQRRVGI SLDIELDGVG IVCHRFEAQI SQPAGKRTKV FNLTRNPLN RDGSTAAIVE EGRAHLEVSL LLGVHGDGLD DHPAQEIARQ VQEQAGAMRL AGGSILPWCN ERFPAPNAEL L MLGGSDEQ ...String:
MSVTDPEALL LLPRLSIQNA NAISSPLTWG FPSPGAFTGF VHALQRRVGI SLDIELDGVG IVCHRFEAQI SQPAGKRTKV FNLTRNPLN RDGSTAAIVE EGRAHLEVSL LLGVHGDGLD DHPAQEIARQ VQEQAGAMRL AGGSILPWCN ERFPAPNAEL L MLGGSDEQ RRKNQRRLTR RLLPGFALVS REALLQQHLE TLRTTLPEAT TLDALLDLCR INFEPPATSS EEEASPPDAA WQ VRDKPGW LVPIPAGYNA LSPLYLPGEV RNARDRETPL RFVENLFGLG EWLSPHRVAA LSDLLWYHHA EPDKGLYRWS TPR FVEHAI A

UniProtKB: CRISPR-associated protein Csy2

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Macromolecule #3: CRISPR-associated protein Csy3

MacromoleculeName: CRISPR-associated protein Csy3 / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (strain UCBPP-PA14) (bacteria)
Strain: UCBPP-PA14
Molecular weightTheoretical: 37.448078 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: SKPILSTASV LAFERKLDPS DALMSAGAWA QRDASQEWPA VTVREKSVRG TISNRLKTKD RDPAKLDASI QSPNLQTVDV ANLPSDADT LKVRFTLRVL GGAGTPSACN DAAYRDKLLQ TVATYVNDQG FAELARRYAH NLANARFLWR NRVGAEAVEV R INHIRQGE ...String:
SKPILSTASV LAFERKLDPS DALMSAGAWA QRDASQEWPA VTVREKSVRG TISNRLKTKD RDPAKLDASI QSPNLQTVDV ANLPSDADT LKVRFTLRVL GGAGTPSACN DAAYRDKLLQ TVATYVNDQG FAELARRYAH NLANARFLWR NRVGAEAVEV R INHIRQGE VARAWRFDAL AIGLRDFKAD AELDALAELI ASGLSGSGHV LLEVVAFARI GDGQEVFPSQ ELILDKGDKK GQ KSKTLYS VRDAAAIHSQ KIGNALRTID TWYPDEDGLG PIAVEPYGSV TSQGKAYRQP KQKLDFYTLL DNWVLRDEAP AVE QQHYVI ANLIRGGVFG EAEEK

UniProtKB: CRISPR-associated protein Csy3

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Macromolecule #4: Anti-CRISPR protein Acr30-35

MacromoleculeName: Anti-CRISPR protein Acr30-35 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage JBD30 (virus)
Molecular weightTheoretical: 8.693734 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
KFIKYLSTAH LNYMNIAVYE NGSKIKARVE NVVNGKSVGA RDFDSTEQLE SWFYGLPGSG LGRIENAMNE ISRRENP

UniProtKB: Uncharacterized protein

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Macromolecule #5: Anti-CRISPR protein 30

MacromoleculeName: Anti-CRISPR protein 30 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage D3112 (virus)
Molecular weightTheoretical: 10.760481 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MHHHHHHIAQ QHKDTVAACE AAEAIAIAKD QVWDGEGYTK YTFDDNSVLI QSGTTQYAMD ADDADSIKGY ADWLDDEARS AEASEIERL LESVEEE

UniProtKB: Anti-CRISPR protein 30

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Macromolecule #6: CRISPR-associated endonuclease Cas6/Csy4

MacromoleculeName: CRISPR-associated endonuclease Cas6/Csy4 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds
Source (natural)Organism: Pseudomonas aeruginosa (strain UCBPP-PA14) (bacteria)
Strain: UCBPP-PA14
Molecular weightTheoretical: 21.691848 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
FTMDHYLDIR LRPDPEFPPA QLMCVLFGKL HQALVAQGGD RIGVSFPDLD ESRSRLGERL RIHASADDLR ALLARPWLEG LRDHLQFGE PAVVPHPTPY RQVSRVQAKS NPERLRRRLM RRHDLSEEEA RKRIPDTVAR ALDLPFVTLR SQSTGQHFRL F IRHGPLQV TAEEGGFTCY GLSKGGFVPW F

UniProtKB: CRISPR-associated endonuclease Cas6/Csy4

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Macromolecule #7: CRISPR RNA (60-MER)

MacromoleculeName: CRISPR RNA (60-MER) / type: rna / ID: 7 / Number of copies: 1
Source (natural)Organism: Pseudomonas aeruginosa UCBPP-PA14 (bacteria)
Molecular weightTheoretical: 19.249404 KDa
SequenceString:
CUAAGAAAUU CACGGCGGGC UUGAUGUCCG CGUCUACCUG GUUCACUGCC GUAUAGGCAG

GENBANK: GENBANK: CP000438.1

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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

Concentration0.1 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3Tris
100.0 mMKClPotassium Chloride
1.0 mMC9H15O6PTCEP

Details: Buffer was filtered before use.
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 5 sec. / Pretreatment - Atmosphere: OTHER
Details: Holey grid was coated with an amorphous carbon film.
VitrificationCryogen name: ETHANE / Chamber humidity: 98 % / Chamber temperature: 277 K / Instrument: HOMEMADE PLUNGER
Details: Sample was applied to poly-L-lysine hydrobromide pre-treated amorphous carbon film coated over a holey grid. Excess sample was blotted with Whatman-1 filter paper and plunge frozen. Manual ...Details: Sample was applied to poly-L-lysine hydrobromide pre-treated amorphous carbon film coated over a holey grid. Excess sample was blotted with Whatman-1 filter paper and plunge frozen. Manual plunge freezing was performed in a cold room..
DetailsSample was free from any aggregation and monodisperse.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 77.0 K / Max: 79.0 K
DetailsObjective astigmatism was corrected at nominal magnification of 29000X, using Thon rings visualized with a K2 camera.
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-30 / Number grids imaged: 2 / Number real images: 2261 / Average exposure time: 6.0 sec. / Average electron dose: 46.0 e/Å2
Details: Images were collected in movie mode using Leginon automated data acquisition software. Movie frames were aligned using MotionCorr program.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 29000
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

DetailsRaw movie frames were aligned using MotionCorr.
Particle selectionNumber selected: 199348
Details: Template based particle picking was done using FindEM program implemented in Appion processing package.
Startup modelType of model: OTHER
Details: A negative stain reconstruction was used as initial model.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4)
Details: Per-frame dose weighting was performed using the RELION particle polishing method. A B-factor of -71 square angstrom was applied to sharpen the final map. Signal subtracted focused ...Details: Per-frame dose weighting was performed using the RELION particle polishing method. A B-factor of -71 square angstrom was applied to sharpen the final map. Signal subtracted focused classification and refinement was performed for the "tail" region of the complex. This lead to a 4 angstrom (Gold standard FSC 0.143) map.
Number images used: 51212
Initial angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final 3D classificationSoftware - Name: RELION (ver. 1.4)
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsTop scoring five models out of two hundred models generated using Rosetta were refined using Phenix and deposited as an ensemble atomic model for the final EM map.
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-5uz9:
Cryo EM structure of anti-CRISPRs, AcrF1 and AcrF2, bound to type I-F crRNA-guided CRISPR surveillance complex

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Atomic model buiding 2

DetailsThe docked Cas6F structure in the "head" region of the complex was reduced to C-alpha backbone.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-5uz9:
Cryo EM structure of anti-CRISPRs, AcrF1 and AcrF2, bound to type I-F crRNA-guided CRISPR surveillance complex

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Atomic model buiding 3

DetailsInitially two copies were fitted using Chimera and then backbones and side chains were fixed using Coot, followed by real space refinement in Phenix.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-5uz9:
Cryo EM structure of anti-CRISPRs, AcrF1 and AcrF2, bound to type I-F crRNA-guided CRISPR surveillance complex

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