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- EMDB-21617: Structure of a substrate-bound DQC ubiquitin ligase -

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Basic information

Entry
Database: EMDB / ID: EMD-21617
TitleStructure of a substrate-bound DQC ubiquitin ligase
Map dataUnfiltered half-map from RELION auto-refinement
Sample
  • Complex: CUL1-SKP1-FBXL17-KEAP1 complex
    • Protein or peptide: S-phase kinase-associated protein 1
    • Protein or peptide: F-box/LRR-repeat protein 17
    • Protein or peptide: Kelch-like ECH-associated protein 1
    • Protein or peptide: Cullin-1
Keywordsubiquitin / E3-ligase / multiprotein complex / substrate recognition / LIGASE
Function / homology
Function and homology information


Parkin-FBXW7-Cul1 ubiquitin ligase complex / F-box domain binding / PcG protein complex / regulation of epidermal cell differentiation / cullin-RING ubiquitin ligase complex / positive regulation of ubiquitin protein ligase activity / Cul7-RING ubiquitin ligase complex / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / maintenance of protein location in nucleus / regulation of smoothened signaling pathway ...Parkin-FBXW7-Cul1 ubiquitin ligase complex / F-box domain binding / PcG protein complex / regulation of epidermal cell differentiation / cullin-RING ubiquitin ligase complex / positive regulation of ubiquitin protein ligase activity / Cul7-RING ubiquitin ligase complex / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / maintenance of protein location in nucleus / regulation of smoothened signaling pathway / Nuclear events mediated by NFE2L2 / neural crest cell differentiation / negative regulation of response to oxidative stress / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul3-RING ubiquitin ligase complex / Prolactin receptor signaling / ubiquitin ligase complex scaffold activity / protein quality control for misfolded or incompletely synthesized proteins / cullin family protein binding / protein monoubiquitination / ubiquitin-like ligase-substrate adaptor activity / protein K48-linked ubiquitination / transcription regulator inhibitor activity / Nuclear events stimulated by ALK signaling in cancer / inclusion body / cellular response to interleukin-4 / intrinsic apoptotic signaling pathway / Regulation of BACH1 activity / molecular function activator activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / animal organ morphogenesis / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / actin filament / Vpu mediated degradation of CD4 / Dectin-1 mediated noncanonical NF-kB signaling / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / Iron uptake and transport / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Negative regulation of NOTCH4 signaling / G1/S transition of mitotic cell cycle / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Degradation of beta-catenin by the destruction complex / beta-catenin binding / NOTCH1 Intracellular Domain Regulates Transcription / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / FCERI mediated NF-kB activation / centriolar satellite / Interleukin-1 signaling / Orc1 removal from chromatin / protein polyubiquitination / Regulation of RUNX2 expression and activity / disordered domain specific binding / Cyclin D associated events in G1 / KEAP1-NFE2L2 pathway / : / Regulation of PLK1 Activity at G2/M Transition / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / nervous system development / Neddylation / cellular response to oxidative stress / midbody / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / in utero embryonic development / Potential therapeutics for SARS / proteasome-mediated ubiquitin-dependent protein catabolic process / RNA polymerase II-specific DNA-binding transcription factor binding / cell population proliferation / positive regulation of canonical NF-kappaB signal transduction / Ub-specific processing proteases / regulation of autophagy / protein ubiquitination / chromatin remodeling / protein domain specific binding / ubiquitin protein ligase binding / centrosome / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / A Receptor for Ubiquitination Targets / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / F-box domain profile. / F-box-like / F-box-like domain superfamily / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily ...: / A Receptor for Ubiquitination Targets / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / F-box domain profile. / F-box-like / F-box-like domain superfamily / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / Kelch-like ECH-associated protein 1 / : / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / F-box domain / Cullin protein neddylation domain / BTB-kelch protein / BTB/Kelch-associated / Cullin, conserved site / BTB And C-terminal Kelch / Cullin family signature. / BTB And C-terminal Kelch / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Kelch motif / Kelch / Kelch repeat type 1 / Leucine Rich repeat / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin alpha solenoid domain / Cullin family profile. / Kelch-type beta propeller / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
S-phase kinase-associated protein 1 / Cullin-1 / Kelch-like ECH-associated protein 1 / F-box/LRR-repeat protein 17
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.5 Å
AuthorsMena EL / Jevtic P
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2020
Title: Structural basis for dimerization quality control.
Authors: Elijah L Mena / Predrag Jevtić / Basil J Greber / Christine L Gee / Brandon G Lew / David Akopian / Eva Nogales / John Kuriyan / Michael Rape /
Abstract: Most quality control pathways target misfolded proteins to prevent toxic aggregation and neurodegeneration. Dimerization quality control further improves proteostasis by eliminating complexes of ...Most quality control pathways target misfolded proteins to prevent toxic aggregation and neurodegeneration. Dimerization quality control further improves proteostasis by eliminating complexes of aberrant composition, but how it detects incorrect subunits remains unknown. Here we provide structural insight into target selection by SCF-FBXL17, a dimerization-quality-control E3 ligase that ubiquitylates and helps to degrade inactive heterodimers of BTB proteins while sparing functional homodimers. We find that SCF-FBXL17 disrupts aberrant BTB dimers that fail to stabilize an intermolecular β-sheet around a highly divergent β-strand of the BTB domain. Complex dissociation allows SCF-FBXL17 to wrap around a single BTB domain, resulting in robust ubiquitylation. SCF-FBXL17 therefore probes both shape and complementarity of BTB domains, a mechanism that is well suited to establish quality control of complex composition for recurrent interaction modules.
History
DepositionMar 31, 2020-
Header (metadata) releaseAug 19, 2020-
Map releaseAug 19, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6wcq
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6wcq
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21617.png

Downloads & links

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Map

FileDownload / File: emd_21617.map.gz / Format: CCP4 / Size: 5.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnfiltered half-map from RELION auto-refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.28 Å/pix.
x 112 pix.
= 255.36 Å		2.28 Å/pix.
x 112 pix.
= 255.36 Å		2.28 Å/pix.
x 112 pix.
= 255.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.28 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.045 / Movie #1: 0.045
Minimum - Maximum-0.086691014 - 0.19979686
Average (Standard dev.)0.0004120202 (±0.008419467)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions112112112
Spacing112112112
CellA=B=C: 255.36 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.282.282.28
M x/y/z112112112
origin x/y/z0.0000.0000.000
length x/y/z255.360255.360255.360
α/β/γ90.00090.00090.000
start NX/NY/NZ-205-205-205
NX/NY/NZ411411411
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS112112112
D min/max/mean-0.0870.2000.000

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Supplemental data

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Half map: Unfiltered half-map from RELION auto-refinement

Fileemd_21617_half_map_1.map
AnnotationUnfiltered half-map from RELION auto-refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half-map from RELION auto-refinement

Fileemd_21617_half_map_2.map
AnnotationUnfiltered half-map from RELION auto-refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CUL1-SKP1-FBXL17-KEAP1 complex

EntireName: CUL1-SKP1-FBXL17-KEAP1 complex
Components
  • Complex: CUL1-SKP1-FBXL17-KEAP1 complex
    • Protein or peptide: S-phase kinase-associated protein 1
    • Protein or peptide: F-box/LRR-repeat protein 17
    • Protein or peptide: Kelch-like ECH-associated protein 1
    • Protein or peptide: Cullin-1

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Supramolecule #1: CUL1-SKP1-FBXL17-KEAP1 complex

SupramoleculeName: CUL1-SKP1-FBXL17-KEAP1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: S-phase kinase-associated protein 1

MacromoleculeName: S-phase kinase-associated protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.679965 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MPSIKLQSSD GEIFEVDVEI AKQSVTIKTM LEDLGMDDEG DDDPVPLPNV NAAILKKVIQ WCTHHKDDPP PPEDDENKEK RTDDIPVWD QEFLKVDQGT LFELILAANY LDIKGLLDVT CKTVANMIKG KTPEEIRKTF NIKNDFTEEE EAQVRKENQW C EEK

UniProtKB: S-phase kinase-associated protein 1

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Macromolecule #2: F-box/LRR-repeat protein 17

MacromoleculeName: F-box/LRR-repeat protein 17 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.970043 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GEFMCHREPP PETPDINQLP PSILLKIFSN LSLDERCLSA SLVCKYWRDL CLDFQFWKQL DLSSRQQVTD ELLEKIASRS QNIIEINIS DCRSMSDNGV CVLAFKCPGL LRYTAYRCKQ LSDTSIIAVA SHCPLLQKVH VGNQDKLTDE GLKQLGSKCR E LKDIHFGQ ...String:
GEFMCHREPP PETPDINQLP PSILLKIFSN LSLDERCLSA SLVCKYWRDL CLDFQFWKQL DLSSRQQVTD ELLEKIASRS QNIIEINIS DCRSMSDNGV CVLAFKCPGL LRYTAYRCKQ LSDTSIIAVA SHCPLLQKVH VGNQDKLTDE GLKQLGSKCR E LKDIHFGQ CYKISDEGMI VIAKGCLKLQ RIYMQENKLV TDQSVKAFAE HCPELQYVGF MGCSVTSKGV IHLTKLRNLS SL DLRHITE LDNETVMEIV KRCKNLSSLN LCLNWIINDR CVEVIAKEGQ NLKELYLVSC KITDYALIAI GRYSMTIETV DVG WCKEIT DQGATLIAQS SKSLRYLGLM RCDKVNEVTV EQLVQQYPHI TFSTVLQDCK RTLERAYQMG WTPNMSAASS

UniProtKB: F-box/LRR-repeat protein 17

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Macromolecule #3: Kelch-like ECH-associated protein 1

MacromoleculeName: Kelch-like ECH-associated protein 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 70.173484 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GGGSGGSMQP DPRPSGAGAC CRFLPLQSQC PEGAGDAVMY ASTECKAEVT PSQHGNRTFS YTLEDHTKQA FGIMNELRLS QQLCDVTLQ VKYQDAPAAQ FMAHKVALAS SSPVFKAMFT NGLREQGMEV VSIEGIHPKV MERLIEFAYT ASISMGEKCV L HVMNGAVM ...String:
GGGSGGSMQP DPRPSGAGAC CRFLPLQSQC PEGAGDAVMY ASTECKAEVT PSQHGNRTFS YTLEDHTKQA FGIMNELRLS QQLCDVTLQ VKYQDAPAAQ FMAHKVALAS SSPVFKAMFT NGLREQGMEV VSIEGIHPKV MERLIEFAYT ASISMGEKCV L HVMNGAVM YQIDSVVRAC SDFLVQQLDP SNAIGIANFA EQIGCVELHQ RAREYIYMHF GEVAKQEEFF NLSHCQLVTL IS RDDLNVR CESEVFHACI NWVKYDCEQR RFYVQALLRA VRCHSLTPNF LQMQLQKCEI LQSDSRCKDY LVKIFEELTL HKP TQVMPC RAPKVGRLIY TAGGYFRQSL SYLEAYNPSD GTWLRLADLQ VPRSGLAGCV VGGLLYAVGG RNNSPDGNTD SSAL DCYNP MTNQWSPCAP MSVPRNRIGV GVIDGHIYAV GGSHGCIHHN SVERYEPERD EWHLVAPMLT RRIGVGVAVL NRLLY AVGG FDGTNRLNSA ECYYPERNEW RMITAMNTIR SGAGVCVLHN CIYAAGGYDG QDQLNSVERY DVETETWTFV APMKHR RSA LGITVHQGRI YVLGGYDGHT FLDSVECYDP DTDTWSEVTR MTSGRSGVGV AVTMEPCRKQ IDQQNCTC

UniProtKB: Kelch-like ECH-associated protein 1

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Macromolecule #4: Cullin-1

MacromoleculeName: Cullin-1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.92652 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSSTRSQNPH GLKQIGLDQI WDDLRAGIQQ VYTRQSMAKS RYMELYTHVY NYCTSVHQSN QARGAGVPPS KSKKGQTPGG AQFVGLELY KRLKEFLKNY LTNLLKDGED LMDESVLKFY TQQWEDYRFS SKVLNGICAY LNRHWVRREC DEGRKGIYEI Y SLALVTWR ...String:
MSSTRSQNPH GLKQIGLDQI WDDLRAGIQQ VYTRQSMAKS RYMELYTHVY NYCTSVHQSN QARGAGVPPS KSKKGQTPGG AQFVGLELY KRLKEFLKNY LTNLLKDGED LMDESVLKFY TQQWEDYRFS SKVLNGICAY LNRHWVRREC DEGRKGIYEI Y SLALVTWR DCLFRPLNKQ VTNAVLKLIE KERNGETINT RLISGVVQSY VELGLNEDDA FAKGPTLTVY KESFESQFLA DT ERFYTRE STEFLQQNPV TEYMKKAEAR LLEEQRRVQV YLHESTQDEL ARKCEQVLIE KHLEIFHTEF QNLLDADKNE DLG RMYNLV SRIQDGLGEL KKLLETHIHN QGLAAIEKCG EAALNDPKMY VQTVLDVHKK YNALVMSAFN NDAGFVAALD KACG RFINN NAVTKMAQSS SKSPELLARY CDSLLKKSS

UniProtKB: Cullin-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 #1

Preparation ID1
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
20.0 mMHEPES-NaOH
1.0 mMDTT
GridModel: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Film type ID: 1 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
Details: Glow discharge before deposition of graphene oxide.
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsCrosslinked with BS3

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Sample preparation #2

Preparation ID2
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
20.0 mMHEPES-NaOH
1.0 mMDTT
GridModel: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Film type ID: 1 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
Details: Glow discharge before deposition of graphene oxide.
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsCrosslinked with BS3

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Electron microscopy #1

Microscopy ID1
MicroscopeFEI TALOS ARCTICA
Image recordingImage recording ID: 1 / Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 2.0 µm
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Electron microscopy #1~

Microscopy ID1
MicroscopeFEI TALOS ARCTICA
Image recordingImage recording ID: 2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Image recording ID1
DetailsDatasets from K3 and K2 were joined for the final reconstruction.
Particle selectionNumber selected: 824561
Details: Total number of particles for both datasets. Selected using RELION auto-picking (Laplacian-of-Gaussian).
Startup modelType of model: INSILICO MODEL
Details: Initial models were generated from molecular structures and by ab-initio model generation in cryoSPARC (with consistent results).
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 8.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 160256
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software: (Name: RELION (ver. 3), cryoSPARC)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)

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Atomic model buiding 1

Initial model
PDB IDChain

1ldk

source_name: PDB, initial_model_type: experimental model

1x1x

source_name: PDB, initial_model_type: experimental model
DetailsCoordinates were fitted as rigid bodies or fragments in Chimera and subsequently geometry-optimized using PHENIX real space refinement.
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-6wcq:
Structure of a substrate-bound DQC ubiquitin ligase

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