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Yorodumi- EMDB-33521: Cryo-EM structure of Fft3-nucleosome complex with Fft3 bound to S... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33521 | |||||||||
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Title | Cryo-EM structure of Fft3-nucleosome complex with Fft3 bound to SHL+3 position of the nucleosome | |||||||||
Map data | ||||||||||
Sample |
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Keywords | DNA binding / remodeler / nucleosome / Fft3-nucleosome complex / DNA BINDING PROTEIN | |||||||||
Function / homology | Function and homology information attachment of telomeric heterochromatin to nuclear envelope / ATP-dependent H3-H4 histone complex chaperone activity / E3 ubiquitin ligases ubiquitinate target proteins / polytene chromosome band / HATs acetylate histones / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Ub-specific processing proteases / larval somatic muscle development / histone chaperone activity / polytene chromosome ...attachment of telomeric heterochromatin to nuclear envelope / ATP-dependent H3-H4 histone complex chaperone activity / E3 ubiquitin ligases ubiquitinate target proteins / polytene chromosome band / HATs acetylate histones / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Ub-specific processing proteases / larval somatic muscle development / histone chaperone activity / polytene chromosome / transcription elongation-coupled chromatin remodeling / replication fork processing / ATP-dependent activity, acting on DNA / heterochromatin / helicase activity / nucleosome assembly / structural constituent of chromatin / nucleosome / chromosome / chromatin organization / DNA helicase / damaged DNA binding / chromatin remodeling / protein heterodimerization activity / chromatin binding / chromatin / protein-containing complex binding / ATP hydrolysis activity / DNA binding / ATP binding / nucleus Similarity search - Function | |||||||||
Biological species | Schizosaccharomyces pombe 972h- (yeast) / Drosophila melanogaster (fruit fly) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.4 Å | |||||||||
Authors | Nan Z / Tao J / Yangao H | |||||||||
Funding support | China, 1 items
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Citation | Journal: To Be Published Title: Cryo-EM structure of Fft3-nucleosome complex with Fft3 bound to SHL+3 position of the nucleosome (Class II Fft3-nucleosome complex) Authors: Nan Z / Tao J / Yangao H | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33521.map.gz | 4 MB | EMDB map data format | |
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Header (meta data) | emd-33521-v30.xml emd-33521.xml | 20.9 KB 20.9 KB | Display Display | EMDB header |
Images | emd_33521.png | 37 KB | ||
Filedesc metadata | emd-33521.cif.gz | 7 KB | ||
Others | emd_33521_half_map_1.map.gz emd_33521_half_map_2.map.gz | 11.7 MB 11.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33521 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33521 | HTTPS FTP |
-Related structure data
Related structure data | 7xygMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_33521.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_33521_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33521_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of Fft3-nucleosome complex with Fft3 bound to SHL+3 of th...
Entire | Name: Complex of Fft3-nucleosome complex with Fft3 bound to SHL+3 of the nucleosome (Class II Fft3-nucleosome complex) |
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Components |
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-Supramolecule #1: Complex of Fft3-nucleosome complex with Fft3 bound to SHL+3 of th...
Supramolecule | Name: Complex of Fft3-nucleosome complex with Fft3 bound to SHL+3 of the nucleosome (Class II Fft3-nucleosome complex) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7 |
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Source (natural) | Organism: Schizosaccharomyces pombe 972h- (yeast) |
-Macromolecule #1: Histone H3
Macromolecule | Name: Histone H3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
Molecular weight | Theoretical: 15.289904 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEASEAY LVGLFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA UniProtKB: Histone H3 |
-Macromolecule #2: Histone H4
Macromolecule | Name: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
Molecular weight | Theoretical: 11.408452 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MTGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG UniProtKB: Histone H4 |
-Macromolecule #3: Histone H2A
Macromolecule | Name: Histone H2A / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
Molecular weight | Theoretical: 13.257529 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SGRGKGGKVK GKAKSRSNRA GLQFPVGRIH RLLRKGNYAE RVGAGAPVYL AAVMEYLAAE VLELAGNAAR DNKKTRIIPR HLQLAIRND EELNKLLSGV TIAQGGVLPN IQAVLLPKKT EKKA UniProtKB: Histone H2A |
-Macromolecule #4: Histone H2B
Macromolecule | Name: Histone H2B / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
Molecular weight | Theoretical: 13.727064 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MPPKTSGKAA KKAGKAQKNI TKTDKKKKRK RKESYAIYIY KVLKQVHPDT GISSKAMSIM NSFVNDIFER IAAEASRLAH YNKRSTITS REIQTAVRLL LPGELAKHAV SEGTKAVTKY TSSK UniProtKB: Histone H2B |
-Macromolecule #7: ATP-dependent helicase fft3
Macromolecule | Name: ATP-dependent helicase fft3 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase |
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Source (natural) | Organism: Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 |
Molecular weight | Theoretical: 104.629953 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MDGKRKIEHT ADGTHYDATS NVKRKPIFPP FIADSLSEAT EKANVMGGGM NSRLQILSEM SKRVQATAPI SSLEHFKQLS DISPSFTSS ANSINQPYNY SGSLENLVPT PSAGTPSQFM DAQNPYGAVY NALSQFSETE PKMPSYMDDE EASDSLPLSL S SQSLSSQV ...String: MDGKRKIEHT ADGTHYDATS NVKRKPIFPP FIADSLSEAT EKANVMGGGM NSRLQILSEM SKRVQATAPI SSLEHFKQLS DISPSFTSS ANSINQPYNY SGSLENLVPT PSAGTPSQFM DAQNPYGAVY NALSQFSETE PKMPSYMDDE EASDSLPLSL S SQSLSSQV TNQKPAPHRL TMRERYAANN LTNGLQFTLP LSSRKTYEPE ADDDSNDDMY SDDDSNADRW ASRIDTAALK EE VLKYMNR CSTQDLADMT GCTLAEAEFM VAKRPFPDLE SALVVKQPRP VIPKGRRGRR EKTPLGPRLV GICMEIMRGY FVV DALIRQ CEQLGGKIQR GIEAWGLSNT ATSDEGETSL VNFDQMKSFG TPANSSFITT PPASFSPDIK LQDYQIIGIN WLYL LYELK LAGILADEMG LGKTCQTIAF FSLLMDKNIN GPHLVIAPAS TMENWLREFA KFCPKLKIEL YYGSQVEREE IRERI NSNK DSYNVMLTTY RLAATSKADR LFLRNQKFNV CVYDEGHYLK NRASERYRHL MSIPADFRVL LTGTPLQNNL KELISL LAF ILPHVFDYGL KSLDVIFTMK KSPESDFERA LLSEQRVSRA KMMMAPFVLR RKKSQVLDAL PKKTRIIEFC EFSEEER RR YDDFASKQSV NSLLDENVMK TNLDTNANLA KKKSTAGFVL VQLRKLADHP MLFRIHYKDD ILRQMAKAIM NEPQYKKA N ELYIFEDMQY MSDIELHNLC CKFPSINSFQ LKDEPWMDAT KVRKLKKLLT NAVENGDRVV LFSQFTQVLD ILQLVMKSL NLKFLRFDGS TQVDFRQDLI DQFYADESIN VFLLSTKAGG FGINLACANM VILYDVSFNP FDDLQAEDRA HRVGQKKEVT VYKFVVKDT IEEHIQRLAN AKIALDATLS GNAETVEAED DDD UniProtKB: ATP-dependent helicase fft3 |
-Macromolecule #5: DNA (167-MER)
Macromolecule | Name: DNA (167-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 51.783977 KDa |
Sequence | String: (DA)(DT)(DC)(DT)(DA)(DC)(DA)(DT)(DG)(DC) (DA)(DC)(DA)(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) ...String: (DA)(DT)(DC)(DT)(DA)(DC)(DA)(DT)(DG)(DC) (DA)(DC)(DA)(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)(DG)(DA)(DT)(DT)(DC)(DT) (DC)(DC)(DA)(DG)(DG)(DG)(DC) (DG)(DG) (DC)(DC)(DG)(DA)(DT) |
-Macromolecule #6: DNA (167-MER)
Macromolecule | Name: DNA (167-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 51.325676 KDa |
Sequence | String: (DA)(DT)(DC)(DG)(DG)(DC)(DC)(DG)(DC)(DC) (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) ...String: (DA)(DT)(DC)(DG)(DG)(DC)(DC)(DG)(DC)(DC) (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)(DG)(DA) (DT)(DA)(DT)(DA)(DT)(DA)(DC)(DA)(DT)(DC) (DC)(DT)(DG)(DT)(DG)(DC)(DA) (DT)(DG) (DT)(DA)(DG)(DA)(DT) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.5 µm |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 60.0 e/Å2 |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 5.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 19730 |