+
Open data
-
Basic information
Entry | ![]() | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of DDM1-nucleosome complex | ||||||||||||||||||||||||||||||||||||||||||
![]() | Cryo-EM map of DDM1-nucleosome complex | ||||||||||||||||||||||||||||||||||||||||||
![]() |
| ||||||||||||||||||||||||||||||||||||||||||
![]() | Chromatin / Epigenetics / Histon variant / chromatin remodeler / NUCLEAR PROTEIN | ||||||||||||||||||||||||||||||||||||||||||
Function / homology | ![]() DNA-mediated transformation / retrotransposition / chloroplast thylakoid / chromocenter / : / response to water deprivation / plasmodesma / plant-type vacuole / DNA methylation-dependent heterochromatin formation / thylakoid ...DNA-mediated transformation / retrotransposition / chloroplast thylakoid / chromocenter / : / response to water deprivation / plasmodesma / plant-type vacuole / DNA methylation-dependent heterochromatin formation / thylakoid / ATP-dependent chromatin remodeler activity / plastid / chloroplast stroma / heterochromatin / pericentric heterochromatin / heterochromatin formation / heterochromatin organization / epigenetic regulation of gene expression / DNA helicase activity / chloroplast / structural constituent of chromatin / peroxisome / nucleosome / nucleosome assembly / DNA helicase / chromatin remodeling / protein heterodimerization activity / chromatin binding / nucleolus / ATP hydrolysis activity / DNA binding / extracellular region / ATP binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||||||||||||||||||||||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.71 Å | ||||||||||||||||||||||||||||||||||||||||||
![]() | Osakabe A / Takizawa Y / Horikoshi N / Hatazawa S / Berger F / Kurumizaka H / Kakutani T | ||||||||||||||||||||||||||||||||||||||||||
Funding support | ![]() ![]()
| ||||||||||||||||||||||||||||||||||||||||||
![]() | ![]() Title: Molecular and structural basis of the chromatin remodeling activity by Arabidopsis DDM1 Authors: Takizawa Y / Horikoshi N / Hatazawa S / Negishi L / Sato S / Berger F / Kakutani T / Kurumizaka H / Osakabe A | ||||||||||||||||||||||||||||||||||||||||||
History |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 4.5 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 27.3 KB 27.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 7.2 KB | Display | ![]() |
Images | ![]() | 103.2 KB | ||
Filedesc metadata | ![]() | 7.3 KB | ||
Others | ![]() ![]() ![]() | 27.2 MB 23.4 MB 23.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 864.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 864.4 KB | Display | |
Data in XML | ![]() | 12.7 KB | Display | |
Data in CIF | ![]() | 17.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8j90MC ![]() 8j91C ![]() 8j92C M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Cryo-EM map of DDM1-nucleosome complex | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Additional map: Cryo-EM map of DDM1-nucleosome complex post-processed by DeepEMhancer
File | emd_36083_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Cryo-EM map of DDM1-nucleosome complex post-processed by DeepEMhancer | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_36083_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_36083_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : DDM1-nucleosome complex
Entire | Name: DDM1-nucleosome complex |
---|---|
Components |
|
-Supramolecule #1: DDM1-nucleosome complex
Supramolecule | Name: DDM1-nucleosome complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7 |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 300 KDa |
-Macromolecule #1: Histone H3.1
Macromolecule | Name: Histone H3.1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 15.583246 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GSHMARTKQT ARKSTGGKAP RKQLATKAAR KSAPATGGVK KPHRFRPGTV ALREIRKYQK STELLIRKLP FQRLVREIAQ DFKTDLRFQ SSAVAALQEA AEAYLVGLFE DTNLCAIHAK RVTIMPKDIQ LARRIRGERA UniProtKB: Histone H3.1 |
-Macromolecule #2: Histone H4
Macromolecule | Name: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 11.718744 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GSHMSGRGKG GKGLGKGGAK RHRKVLRDNI QGITKPAIRR LARRGGVKRI SGLIYEETRG VLKIFLENVI RDAVTYTEHA RRKTVTAMD VVYALKRQGR TLYGFGG UniProtKB: Histone H4 |
-Macromolecule #3: HTA6
Macromolecule | Name: HTA6 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 16.280221 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GSHMESTGKV KKAFGGRKPP GAPKTKSVSK SMKAGLQFPV GRITRFLKKG RYAQRLGGGA PVYMAAVLEY LAAEVLELAG NAARDNKKS RIIPRHLLLA IRNDEELGKL LSGVTIAHGG VLPNINSVLL PKKSATKPAE EKATKSPVKS PKKA UniProtKB: Probable histone H2A.7 |
-Macromolecule #4: HTB9
Macromolecule | Name: HTB9 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 16.756738 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GSHMAPRAEK KPAEKKPAAE KPVEEKSKAE KAPAEKKPKA GKKLPKEAGA GGDKKKKMKK KSVETYKIYI FKVLKQVHPD IGISSKAMG IMNSFINDIF EKLASESSKL ARYNKKPTIT SREIQTAVRL VLPGELAKHA VSEGTKAVTK FTSS UniProtKB: Histone H2B.6 |
-Macromolecule #7: ATP-dependent DNA helicase DDM1
Macromolecule | Name: ATP-dependent DNA helicase DDM1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 87.050062 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GPHMVSLRSR KVIPASEMVS DGKTEKDASG DSPTSVLNEE ENCEEKSVTV VEEEILLAKN GDSSLISEAM AQEEEQLLKL REDEEKANN AGSAVAPNLN ETQFTKLDEL LTQTQLYSEF LLEKMEDITI NGIESESQKA EPEKTGRGRK RKAASQYNNT K AKRAVAAM ...String: GPHMVSLRSR KVIPASEMVS DGKTEKDASG DSPTSVLNEE ENCEEKSVTV VEEEILLAKN GDSSLISEAM AQEEEQLLKL REDEEKANN AGSAVAPNLN ETQFTKLDEL LTQTQLYSEF LLEKMEDITI NGIESESQKA EPEKTGRGRK RKAASQYNNT K AKRAVAAM ISRSKEDGET INSDLTEEET VIKLQNELCP LLTGGQLKSY QLKGVKWLIS LWQNGLNGIL ADQMGLGKTI QT IGFLSHL KGNGLDGPYL VIAPLSTLSN WFNEIARFTP SINAIIYHGD KNQRDELRRK HMPKTVGPKF PIVITSYEVA MND AKRILR HYPWKYVVID EGHRLKNHKC KLLRELKHLK MDNKLLLTGT PLQNNLSELW SLLNFILPDI FTSHDEFESW FDFS EKNKN EATKEEEEKR RAQVVSKLHG ILRPFILRRM KCDVELSLPR KKEIIMYATM TDHQKKFQEH LVNNTLEAHL GENAI RGQG WKGKLNNLVI QLRKNCNHPD LLQGQIDGSY LYPPVEEIVG QCGKFRLLER LLVRLFANNH KVLIFSQWTK LLDIMD YYF SEKGFEVCRI DGSVKLDERR RQIKDFSDEK SSCSIFLLST RAGGLGINLT AADTCILYDS DWNPQMDLQA MDRCHRI GQ TKPVHVYRLS TAQSIETRVL KRAYSKLKLE HVVIGQGQFH QERAKSSTPL EEEDILALLK EDETAEDKLI QTDISDAD L DRLLDRSDLT ITAPGETQAA EAFPVKGPGW EVVLPSSGGM LSSLNS UniProtKB: ATP-dependent DNA helicase DDM1 |
-Macromolecule #5: DNA (169-MER)
Macromolecule | Name: DNA (169-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA |
---|---|
Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 51.922059 KDa |
Sequence | String: (DA)(DT)(DC)(DG)(DG)(DA)(DC)(DC)(DC)(DT) (DA)(DT)(DC)(DG)(DC)(DG)(DA)(DG)(DC)(DC) (DA)(DG)(DG)(DC)(DC)(DT)(DG)(DA)(DG) (DA)(DA)(DT)(DC)(DC)(DG)(DG)(DT)(DG)(DC) (DC) (DG)(DA)(DG)(DG)(DC)(DC) ...String: (DA)(DT)(DC)(DG)(DG)(DA)(DC)(DC)(DC)(DT) (DA)(DT)(DC)(DG)(DC)(DG)(DA)(DG)(DC)(DC) (DA)(DG)(DG)(DC)(DC)(DT)(DG)(DA)(DG) (DA)(DA)(DT)(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) (DG)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DC) (DA)(DT)(DC)(DC)(DG)(DA)(DT) |
-Macromolecule #6: DNA (169-MER)
Macromolecule | Name: DNA (169-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA |
---|---|
Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 52.424352 KDa |
Sequence | String: (DA)(DT)(DC)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DC)(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)(DT)(DC)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DC)(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)(DA)(DT)(DT) (DC)(DT)(DC) (DA)(DG)(DG)(DC)(DC)(DT)(DG)(DG)(DC)(DT) (DC)(DG)(DC)(DG)(DA)(DT)(DA) (DG)(DG) (DG)(DT)(DC)(DC)(DG)(DA)(DT) |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 7.5 |
---|---|
Grid | Model: Quantifoil / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 25.0 µm / Nominal defocus min: 10.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |