[English] 日本語
Yorodumi
- EMDB-26855: Arabidopsis DDM1 bound to nucleosome (H2A.W, H2B, H3.3, H4, with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-26855
TitleArabidopsis DDM1 bound to nucleosome (H2A.W, H2B, H3.3, H4, with 147 bp DNA)
Map dataArabidopsis DDM1 bound to nucleosome (H2AW, H2B, H3.3, H4, with 147 bp DNA), final density-modified map, corresponds to molecular model
Sample
  • Complex: Arabidopsis DDM1 bound to nucleosome (H2A.W, H2B, H3.3, H4, with 147 bp DNA)
    • Complex: DDM1
      • Protein or peptide: ATP-dependent DNA helicase DDM1
    • Complex: Nucleosome core particleNucleosome
      • Complex: Histone octamer
        • Protein or peptide: Probable histone H2A.7
        • Protein or peptide: Histone H2B
        • Protein or peptide: Histone H3.3H3F3A
        • Protein or peptide: Histone H4
      • Complex: DNA double helixNucleic acid double helix
        • DNA: DNA (sense strand)
        • DNA: DNA (antisense strand)
KeywordsChromatin remodeler / Helicase / ATPase / Complex / Gene regulation
Function / homology
Function and homology information


rDNA protrusion / DNA-mediated transformation / retrotransposition / heterochromatin organization / plasmodesma / DNA methylation-dependent heterochromatin formation / ATP-dependent chromatin remodeler activity / plastid / heterochromatin / pericentric heterochromatin ...rDNA protrusion / DNA-mediated transformation / retrotransposition / heterochromatin organization / plasmodesma / DNA methylation-dependent heterochromatin formation / ATP-dependent chromatin remodeler activity / plastid / heterochromatin / pericentric heterochromatin / heterochromatin formation / epigenetic regulation of gene expression / DNA helicase activity / structural constituent of chromatin / nucleosome / DNA helicase / chromatin remodeling / protein heterodimerization activity / chromatin binding / nucleolus / ATP hydrolysis activity / DNA binding / ATP binding / nucleus / plasma membrane
Similarity search - Function
HELLS, N-terminal / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. ...HELLS, N-terminal / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Helicase conserved C-terminal domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Histone H3.3 / Histone H4 / Histone H2B / Probable histone H2A.7 / ATP-dependent DNA helicase DDM1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress) / Xenopus laevis (African clawed frog) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsIpsaro JJ / Adams DW / Joshua-Tor L
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Cell / Year: 2023
Title: Chromatin remodeling of histone H3 variants by DDM1 underlies epigenetic inheritance of DNA methylation.
Authors: Seung Cho Lee / Dexter W Adams / Jonathan J Ipsaro / Jonathan Cahn / Jason Lynn / Hyun-Soo Kim / Benjamin Berube / Viktoria Major / Joseph P Calarco / Chantal LeBlanc / Sonali Bhattacharjee ...Authors: Seung Cho Lee / Dexter W Adams / Jonathan J Ipsaro / Jonathan Cahn / Jason Lynn / Hyun-Soo Kim / Benjamin Berube / Viktoria Major / Joseph P Calarco / Chantal LeBlanc / Sonali Bhattacharjee / Umamaheswari Ramu / Daniel Grimanelli / Yannick Jacob / Philipp Voigt / Leemor Joshua-Tor / Robert A Martienssen /
Abstract: Nucleosomes block access to DNA methyltransferase, unless they are remodeled by DECREASE in DNA METHYLATION 1 (DDM1), a Snf2-like master regulator of epigenetic inheritance. We show that DDM1 ...Nucleosomes block access to DNA methyltransferase, unless they are remodeled by DECREASE in DNA METHYLATION 1 (DDM1), a Snf2-like master regulator of epigenetic inheritance. We show that DDM1 promotes replacement of histone variant H3.3 by H3.1. In ddm1 mutants, DNA methylation is partly restored by loss of the H3.3 chaperone HIRA, while the H3.1 chaperone CAF-1 becomes essential. The single-particle cryo-EM structure at 3.2 Å of DDM1 with a variant nucleosome reveals engagement with histone H3.3 near residues required for assembly and with the unmodified H4 tail. An N-terminal autoinhibitory domain inhibits activity, while a disulfide bond in the helicase domain supports activity. DDM1 co-localizes with H3.1 and H3.3 during the cell cycle, and with the DNA methyltransferase MET1, but is blocked by H4K16 acetylation. The male germline H3.3 variant MGH3/HTR10 is resistant to remodeling by DDM1 and acts as a placeholder nucleosome in sperm cells for epigenetic inheritance.
History
DepositionMay 5, 2022-
Header (metadata) releaseAug 9, 2023-
Map releaseAug 9, 2023-
UpdateSep 27, 2023-
Current statusSep 27, 2023Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_26855.png

Downloads & links

-
Map

FileDownload / File: emd_26855.map.gz / Format: CCP4 / Size: 4.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationArabidopsis DDM1 bound to nucleosome (H2AW, H2B, H3.3, H4, with 147 bp DNA), final density-modified map, corresponds to molecular model
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-10.712865000000001 - 18.843906
Average (Standard dev.)-0.000000000012646 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin11390123
Dimensions10013781
Spacing81100137
CellA: 89.1 Å / B: 110.0 Å / C: 150.7 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Arabidopsis DDM1 bound to nucleosome (H2AW, H2B, H3.3,...

Fileemd_26855_additional_1.map
AnnotationArabidopsis DDM1 bound to nucleosome (H2AW, H2B, H3.3, H4, with 147 bp DNA), non-uniform refined map, prior to density modification
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Arabidopsis DDM1 bound to nucleosome (H2AW, H2B, H3.3,...

Fileemd_26855_half_map_1.map
AnnotationArabidopsis DDM1 bound to nucleosome (H2AW, H2B, H3.3, H4, with 147 bp DNA), half map A, used for FSC calculation
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Arabidopsis DDM1 bound to nucleosome (H2AW, H2B, H3.3,...

Fileemd_26855_half_map_2.map
AnnotationArabidopsis DDM1 bound to nucleosome (H2AW, H2B, H3.3, H4, with 147 bp DNA), half map A, used for FSC calculation
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Arabidopsis DDM1 bound to nucleosome (H2A.W, H2B, H3.3, H4, with ...

EntireName: Arabidopsis DDM1 bound to nucleosome (H2A.W, H2B, H3.3, H4, with 147 bp DNA)
Components
  • Complex: Arabidopsis DDM1 bound to nucleosome (H2A.W, H2B, H3.3, H4, with 147 bp DNA)
    • Complex: DDM1
      • Protein or peptide: ATP-dependent DNA helicase DDM1
    • Complex: Nucleosome core particleNucleosome
      • Complex: Histone octamer
        • Protein or peptide: Probable histone H2A.7
        • Protein or peptide: Histone H2B
        • Protein or peptide: Histone H3.3H3F3A
        • Protein or peptide: Histone H4
      • Complex: DNA double helixNucleic acid double helix
        • DNA: DNA (sense strand)
        • DNA: DNA (antisense strand)

+
Supramolecule #1: Arabidopsis DDM1 bound to nucleosome (H2A.W, H2B, H3.3, H4, with ...

SupramoleculeName: Arabidopsis DDM1 bound to nucleosome (H2A.W, H2B, H3.3, H4, with 147 bp DNA)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Complex contains two copies of each histone (H2A.W, H2B, H3.3, and H4), 147 base pairs of DNA, and 1 copy of Arabidopsis DDM1
Molecular weightTheoretical: 91 KDa

+
Supramolecule #2: DDM1

SupramoleculeName: DDM1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Arabidopsis thaliana (thale cress) / Location in cell: nucleus

+
Supramolecule #3: Nucleosome core particle

SupramoleculeName: Nucleosome core particle / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#4, #6-#7
Details: Complex contains two copies of each histone (H2A.W, H2B, H3.3, and H4) and 147 base pairs of DNA

+
Supramolecule #4: Histone octamer

SupramoleculeName: Histone octamer / type: complex / ID: 4 / Parent: 3 / Macromolecule list: #1-#4
Details: Contains two copies each of H2A.W, H2B, H3.3, and H4
Source (natural)Organism: Arabidopsis thaliana (thale cress) / Location in cell: nucleus

+
Supramolecule #5: DNA double helix

SupramoleculeName: DNA double helix / type: complex / ID: 5 / Parent: 3 / Macromolecule list: #6-#7 / Details: Generated by PCR amplification

+
Macromolecule #1: Probable histone H2A.7

MacromoleculeName: Probable histone H2A.7 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 15.997942 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MESTGKVKKA FGGRKPPGAP KTKSVSKSMK AGLQFPVGRI TRFLKKGRYA QRLGGGAPVY MAAVLEYLAA EVLELAGNAA RDNKKSRII PRHLLLAIRN DEELGKLLSG VTIAHGGVLP NINSVLLPKK SATKPAEEKA TKSPVKSPKK A

UniProtKB: Probable histone H2A.7

+
Macromolecule #2: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 16.474459 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MAPRAEKKPA EKKPAAEKPV EEKSKAEKAP AEKKPKAGKK LPKEAGAGGD KKKKMKKKSV ETYKIYIFKV LKQVHPDIGI SSKAMGIMN SFINDIFEKL ASESSKLARY NKKPTITSRE IQTAVRLVLP GELAKHAVSE GTKAVTKFTS S

UniProtKB: Histone H2B

+
Macromolecule #3: Histone H3.3

MacromoleculeName: Histone H3.3 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 15.440144 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PTTGGVKKPH RYRPGTVALR EIRKYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSHA VLALQEAAEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3.3

+
Macromolecule #4: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

+
Macromolecule #5: ATP-dependent DNA helicase DDM1

MacromoleculeName: ATP-dependent DNA helicase DDM1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 86.757758 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MVSLRSRKVI PASEMVSDGK TEKDASGDSP TSVLNEEENC EEKSVTVVEE EILLAKNGDS SLISEAMAQE EEQLLKLRED EEKANNAGS AVAPNLNETQ FTKLDELLTQ TQLYSEFLLE KMEDITINGI ESESQKAEPE KTGRGRKRKA ASQYNNTKAK R AVAAMISR ...String:
MVSLRSRKVI PASEMVSDGK TEKDASGDSP TSVLNEEENC EEKSVTVVEE EILLAKNGDS SLISEAMAQE EEQLLKLRED EEKANNAGS AVAPNLNETQ FTKLDELLTQ TQLYSEFLLE KMEDITINGI ESESQKAEPE KTGRGRKRKA ASQYNNTKAK R AVAAMISR SKEDGETINS DLTEEETVIK LQNELCPLLT GGQLKSYQLK GVKWLISLWQ NGLNGILADQ MGLGKTIQTI GF LSHLKGN GLDGPYLVIA PLSTLSNWFN EIARFTPSIN AIIYHGDKNQ RDELRRKHMP KTVGPKFPIV ITSYEVAMND AKR ILRHYP WKYVVIDEGH RLKNHKCKLL RELKHLKMDN KLLLTGTPLQ NNLSELWSLL NFILPDIFTS HDEFESWFDF SEKN KNEAT KEEEEKRRAQ VVSKLHGILR PFILRRMKCD VELSLPRKKE IIMYATMTDH QKKFQEHLVN NTLEAHLGEN AIRGQ GWKG KLNNLVIQLR KNCNHPDLLQ GQIDGSYLYP PVEEIVGQCG KFRLLERLLV RLFANNHKVL IFSQWTKLLD IMDYYF SEK GFEVCRIDGS VKLDERRRQI KDFSDEKSSC SIFLLSTRAG GLGINLTAAD TCILYDSDWN PQMDLQAMDR CHRIGQT KP VHVYRLSTAQ SIETRVLKRA YSKLKLEHVV IGQGQFHQER AKSSTPLEEE DILALLKEDE TAEDKLIQTD ISDADLDR L LDRSDLTITA PGETQAAEAF PVKGPGWEVV LPSSGGMLSS LNS

UniProtKB: ATP-dependent DNA helicase DDM1

+
Macromolecule #6: DNA (sense strand)

MacromoleculeName: DNA (sense strand) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 45.105727 KDa
SequenceString: (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA) (DG) (DA)(DC)(DA)(DG)(DC)(DT) ...String:
(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA) (DG) (DA)(DC)(DA)(DG)(DC)(DT)(DC)(DT) (DA)(DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT) (DA)(DA) (DA)(DC)(DG)(DC)(DA)(DC)(DG) (DT)(DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT) (DC)(DC)(DC) (DC)(DC)(DG)(DC)(DG)(DT) (DT)(DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC) (DA)(DA)(DG)(DG) (DG)(DG)(DA)(DT)(DT) (DA)(DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT) (DC)(DT)(DC)(DC)(DA) (DG)(DG)(DC)(DA) (DC)(DG)(DT)(DG)(DT)(DC)(DA)(DC)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DC) (DA)(DT)(DC) (DC)(DT)(DG)(DT)

+
Macromolecule #7: DNA (antisense strand)

MacromoleculeName: DNA (antisense strand) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 45.64407 KDa
SequenceString: (DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DG)(DT)(DG)(DA)(DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG) (DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG) (DA) (DG)(DT)(DA)(DA)(DT)(DC) ...String:
(DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DG)(DT)(DG)(DA)(DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG) (DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG) (DA) (DG)(DT)(DA)(DA)(DT)(DC)(DC)(DC) (DC)(DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT) (DA)(DA) (DA)(DA)(DC)(DG)(DC)(DG)(DG) (DG)(DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DC) (DG)(DT)(DA) (DC)(DG)(DT)(DG)(DC)(DG) (DT)(DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG)(DT) (DG)(DC)(DT)(DA) (DG)(DA)(DG)(DC)(DT) (DG)(DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC)(DC) (DA)(DA)(DT)(DT)(DG) (DA)(DG)(DC)(DG) (DG)(DC)(DC)(DT)(DC)(DG)(DG)(DC)(DA)(DC) (DC)(DG)(DG)(DG)(DA)(DT) (DT)(DC)(DT) (DC)(DC)(DA)(DG)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.35 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
2.0 mMC4H11NO3Tris
10.0 mMC8H18N2O4SHEPES
50.0 mMNaClSodium chloridesodium chloride
2.0 mMMgCl2magnesium chloride
1.0 mMC10H12N5O12P3SATP-gamma-S
GridModel: Quantifoil R0.6/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 70 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 42.0 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 298 K / Instrument: LEICA EM GP / Details: Blotted for 2.5 seconds before plunging..
DetailsDDM1 and reconstituted nucleosomes were reconstituted in a 4:1 molar ratio. Crosslinking with 0.05% glutaraldehyde was performed for 15 minutes followed by quenching with 2 mM Tris, pH 8.0. ATP-gamma-S and MgCl2 were added at 1 and 2 mM, respectively.

-
Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 8165 / Average exposure time: 4.8 sec. / Average electron dose: 71.2 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 3788872
Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.0.2+210831)
Final 3D classificationNumber classes: 4 / Avg.num./class: 141299 / Software - Name: cryoSPARC (ver. 3.0.2+210831)
Details: Iterative rounds of 2D classification, 3D classification, and subselection were made. The last round of 3D classification had 4 classes of which 1 was chosen for further refinement and final reconstruction.
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.0.2+210831)
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.0.2+210831) / Number images used: 215066
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

6uxw

chain_id: A, source_name: PDB, initial_model_type: experimental model

6uxw

chain_id: B, source_name: PDB, initial_model_type: experimental model

6uxw

chain_id: C, source_name: PDB, initial_model_type: experimental model

6uxw

chain_id: D, source_name: PDB, initial_model_type: experimental model

6uxw

chain_id: E, source_name: PDB, initial_model_type: experimental model

6uxw

chain_id: F, source_name: PDB, initial_model_type: experimental model

6uxw

chain_id: G, source_name: PDB, initial_model_type: experimental model

6uxw

chain_id: H, source_name: PDB, initial_model_type: experimental model

6uxw

chain_id: I, source_name: PDB, initial_model_type: experimental model

6uxw

chain_id: J, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Overall B value: 57.8 / Target criteria: Correlation coefficient
Output model

PDB-7ux9:
Arabidopsis DDM1 bound to nucleosome (H2A.W, H2B, H3.3, H4, with 147 bp DNA)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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

-
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

Read more