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Yorodumi- EMDB-42774: Structure of Heterochromatin Protein 1 (HP1) alpha in complex wit... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-42774 | |||||||||
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Title | Structure of Heterochromatin Protein 1 (HP1) alpha in complex with an H2A.Z nucleosome | |||||||||
Map data | primary map, consensus refinement with mask | |||||||||
Sample |
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Keywords | heterochromatin / nucleosome / chromatin / GENE REGULATION / STRUCTURAL PROTEIN | |||||||||
Function / homology | Function and homology information chromocenter / histone methyltransferase complex / Transcriptional Regulation by E2F6 / site of DNA damage / histone deacetylase complex / RNA polymerase II core promoter sequence-specific DNA binding / heterochromatin / pericentric heterochromatin / ribonucleoprotein complex binding / nucleosomal DNA binding ...chromocenter / histone methyltransferase complex / Transcriptional Regulation by E2F6 / site of DNA damage / histone deacetylase complex / RNA polymerase II core promoter sequence-specific DNA binding / heterochromatin / pericentric heterochromatin / ribonucleoprotein complex binding / nucleosomal DNA binding / transcription repressor complex / methylated histone binding / Regulation of endogenous retroelements by KRAB-ZFP proteins / SUMOylation of chromatin organization proteins / cellular response to estradiol stimulus / euchromatin / heterochromatin formation / kinetochore / histone deacetylase binding / cellular response to insulin stimulus / structural constituent of chromatin / nucleosome / nucleosome assembly / nuclear envelope / chromatin organization / protein-macromolecule adaptor activity / Factors involved in megakaryocyte development and platelet production / DNA-binding transcription factor binding / chromosome, telomeric region / ribonucleoprotein complex / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding / protein-containing complex binding / nucleolus / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / identical protein binding / nucleus Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) / Homo sapiens (human) / Xenopus laevis (African clawed frog) / Mus musculus (house mouse) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.3 Å | |||||||||
Authors | Tan D / Sokolova V | |||||||||
Funding support | United States, 2 items
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Citation | Journal: To Be Published Title: Structure of human HP1 in complex with H2A.Z nucleosome Authors: Tan D / Sokolova V | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_42774.map.gz | 49.5 MB | EMDB map data format | |
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Header (meta data) | emd-42774-v30.xml emd-42774.xml | 24.1 KB 24.1 KB | Display Display | EMDB header |
Images | emd_42774.png | 55.2 KB | ||
Filedesc metadata | emd-42774.cif.gz | 6.9 KB | ||
Others | emd_42774_half_map_1.map.gz emd_42774_half_map_2.map.gz | 49.8 MB 49.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-42774 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42774 | HTTPS FTP |
-Validation report
Summary document | emd_42774_validation.pdf.gz | 846.3 KB | Display | EMDB validaton report |
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Full document | emd_42774_full_validation.pdf.gz | 845.8 KB | Display | |
Data in XML | emd_42774_validation.xml.gz | 12 KB | Display | |
Data in CIF | emd_42774_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42774 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42774 | HTTPS FTP |
-Related structure data
Related structure data | 8uxqMC C: citing same article (ref.) M: atomic model generated by this map |
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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_42774.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | primary map, consensus refinement with mask | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : HP1alpha dimer bound to H2A.Z nucleosome
Entire | Name: HP1alpha dimer bound to H2A.Z nucleosome |
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Components |
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-Supramolecule #1: HP1alpha dimer bound to H2A.Z nucleosome
Supramolecule | Name: HP1alpha dimer bound to H2A.Z nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 288 KDa |
-Macromolecule #1: Chromobox protein homolog 5
Macromolecule | Name: Chromobox protein homolog 5 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 22.651398 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GSPEFGKKTK RTADSSSSED EEEYVVEKVL DRRVVKGQVE YLLKWKGFSE EHNTWEPEKN LDCPELISEF MKKYKKMKEG ENNKPREKS ESNKRKSNFS NSADDIKSKK KREQSNDIAR GFERGLEPEK IIGATDSCGD LMFLMKWKDT DEADLVLAKE A NVKCPQIV ...String: GSPEFGKKTK RTADSSSSED EEEYVVEKVL DRRVVKGQVE YLLKWKGFSE EHNTWEPEKN LDCPELISEF MKKYKKMKEG ENNKPREKS ESNKRKSNFS NSADDIKSKK KREQSNDIAR GFERGLEPEK IIGATDSCGD LMFLMKWKDT DEADLVLAKE A NVKCPQIV IAFYEERLTW HAYPEDAENK EKETAKS UniProtKB: Chromobox protein homolog 5 |
-Macromolecule #2: Histone H3.2
Macromolecule | Name: Histone H3.2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Molecular weight | Theoretical: 15.30393 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEASEAY LVALFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA UniProtKB: Histone H3.2 |
-Macromolecule #3: Histone H4
Macromolecule | Name: Histone H4 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Molecular weight | Theoretical: 11.263231 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYA LKRQGRTLYG FGG UniProtKB: Histone H4 |
-Macromolecule #4: Histone H2A.Z
Macromolecule | Name: Histone H2A.Z / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 13.450601 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: AGGKAGKDSG KAKTKAVSRS QRAGLQFPVG RIHRHLKSRT TSHGRVGATA AVYSAAILEY LTAEVLELAG NASKDLKVKR ITPRHLQLA IRGDEELDSL IKATIAGGGV IPHIHKSLIG KKGQQKTV UniProtKB: Histone H2A.Z |
-Macromolecule #5: Histone H2B 1.1
Macromolecule | Name: Histone H2B 1.1 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Molecular weight | Theoretical: 13.848097 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: PEPAKSAPAP KKGSKKAVTK TQKKDGKKRR KTRKESYAIY VYKVLKQVHP DTGISSKAMS IMNSFVNDVF ERIAGEASRL AHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSAK UniProtKB: Histone H2B 1.1 |
-Macromolecule #6: DNA Widom601 (208bp) strand1
Macromolecule | Name: DNA Widom601 (208bp) strand1 / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 64.456039 KDa |
Sequence | String: (DA)(DC)(DT)(DC)(DC)(DG)(DG)(DC)(DA)(DA) (DG)(DG)(DT)(DC)(DG)(DC)(DT)(DG)(DT)(DT) (DC)(DA)(DA)(DT)(DA)(DC)(DA)(DT)(DG) (DC)(DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT) (DA) (DT)(DA)(DT)(DA)(DT)(DC) ...String: (DA)(DC)(DT)(DC)(DC)(DG)(DG)(DC)(DA)(DA) (DG)(DG)(DT)(DC)(DG)(DC)(DT)(DG)(DT)(DT) (DC)(DA)(DA)(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)(DC)(DG)(DT)(DA)(DT)(DA) (DG)(DG)(DG)(DT)(DC)(DC)(DA)(DT)(DC) (DA)(DC)(DA)(DT)(DA)(DA)(DG)(DT) |
-Macromolecule #7: DNA Widom601 (208bp) strand2
Macromolecule | Name: DNA Widom601 (208bp) strand2 / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 63.988711 KDa |
Sequence | String: (DA)(DC)(DT)(DT)(DA)(DT)(DG)(DT)(DG)(DA) (DT)(DG)(DG)(DA)(DC)(DC)(DC)(DT)(DA)(DT) (DA)(DC)(DG)(DC)(DG)(DG)(DC)(DC)(DG) (DC)(DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA) (DT) (DC)(DC)(DC)(DG)(DG)(DT) ...String: (DA)(DC)(DT)(DT)(DA)(DT)(DG)(DT)(DG)(DA) (DT)(DG)(DG)(DA)(DC)(DC)(DC)(DT)(DA)(DT) (DA)(DC)(DG)(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)(DT)(DT)(DG)(DA)(DA)(DC) (DA)(DG)(DC)(DG)(DA)(DC)(DC)(DT)(DT) (DG)(DC)(DC)(DG)(DG)(DA)(DG)(DT) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 39.2 K / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated magnification: 81000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.25 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |