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Yorodumi- EMDB-11552: Entire Human Top2a - Interface between ATPase and DNA-binding/cle... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11552 | ||||||||||||
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Title | Entire Human Top2a - Interface between ATPase and DNA-binding/cleavage domains | ||||||||||||
Map data | |||||||||||||
Sample |
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Function / homology | Function and homology information negative regulation of DNA duplex unwinding / positive regulation of single stranded viral RNA replication via double stranded DNA intermediate / sister chromatid segregation / apoptotic chromosome condensation / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / resolution of meiotic recombination intermediates / female meiotic nuclear division / DNA ligation / embryonic cleavage / Transcription of E2F targets under negative control by DREAM complex ...negative regulation of DNA duplex unwinding / positive regulation of single stranded viral RNA replication via double stranded DNA intermediate / sister chromatid segregation / apoptotic chromosome condensation / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / resolution of meiotic recombination intermediates / female meiotic nuclear division / DNA ligation / embryonic cleavage / Transcription of E2F targets under negative control by DREAM complex / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA binding, bending / DNA topological change / SUMOylation of DNA replication proteins / chromosome, centromeric region / ATP-dependent activity, acting on DNA / hematopoietic progenitor cell differentiation / condensed chromosome / ubiquitin binding / male germ cell nucleus / chromosome segregation / protein kinase C binding / regulation of circadian rhythm / rhythmic process / positive regulation of apoptotic process / ribonucleoprotein complex / protein heterodimerization activity / DNA damage response / chromatin binding / nucleolus / magnesium ion binding / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / nucleoplasm / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.6 Å | ||||||||||||
Authors | Vanden Broeck A / Lamour V | ||||||||||||
Funding support | France, 3 items
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Citation | Journal: Nat Commun / Year: 2021 Title: Structural basis for allosteric regulation of Human Topoisomerase IIα. Authors: Arnaud Vanden Broeck / Christophe Lotz / Robert Drillien / Léa Haas / Claire Bedez / Valérie Lamour / Abstract: The human type IIA topoisomerases (Top2) are essential enzymes that regulate DNA topology and chromosome organization. The Topo IIα isoform is a prime target for antineoplastic compounds used in ...The human type IIA topoisomerases (Top2) are essential enzymes that regulate DNA topology and chromosome organization. The Topo IIα isoform is a prime target for antineoplastic compounds used in cancer therapy that form ternary cleavage complexes with the DNA. Despite extensive studies, structural information on this large dimeric assembly is limited to the catalytic domains, hindering the exploration of allosteric mechanism governing the enzyme activities and the contribution of its non-conserved C-terminal domain (CTD). Herein we present cryo-EM structures of the entire human Topo IIα nucleoprotein complex in different conformations solved at subnanometer resolutions (3.6-7.4 Å). Our data unveils the molecular determinants that fine tune the allosteric connections between the ATPase domain and the DNA binding/cleavage domain. Strikingly, the reconstruction of the DNA-binding/cleavage domain uncovers a linker leading to the CTD, which plays a critical role in modulating the enzyme's activities and opens perspective for the analysis of post-translational modifications. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11552.map.gz | 8.4 MB | EMDB map data format | |
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Header (meta data) | emd-11552-v30.xml emd-11552.xml | 13.7 KB 13.7 KB | Display Display | EMDB header |
Images | emd_11552.png | 43.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11552 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11552 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11552.map.gz / Format: CCP4 / Size: 98.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Etoposide-bound Entire Human Top2a
Entire | Name: Etoposide-bound Entire Human Top2a |
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Components |
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-Supramolecule #1: Etoposide-bound Entire Human Top2a
Supramolecule | Name: Etoposide-bound Entire Human Top2a / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Vaccinia virus Ankara / Recombinant cell: BHK21 |
Molecular weight | Theoretical: 280 KDa |
-Macromolecule #1: Human Top2a
Macromolecule | Name: Human Top2a / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Vaccinia virus Ankara |
Sequence | String: MEVSPLQPVN ENMQVNKIKK NEDAKKRLSV ERIYQKKTQL EHILLRPDTY IGSVELVTQQ MWVYDEDVG INYREVTFVP GLYKIFDEIL VNAADNKQRD PKMSCIRVTI DPENNLISIW N NGKGIPVV EHKVEKMYVP ALIFGQLLTS SNYDDDEKKV TGGRNGYGAK ...String: MEVSPLQPVN ENMQVNKIKK NEDAKKRLSV ERIYQKKTQL EHILLRPDTY IGSVELVTQQ MWVYDEDVG INYREVTFVP GLYKIFDEIL VNAADNKQRD PKMSCIRVTI DPENNLISIW N NGKGIPVV EHKVEKMYVP ALIFGQLLTS SNYDDDEKKV TGGRNGYGAK LCNIFSTKFT VE TASREYK KMFKQTWMDN MGRAGEMELK PFNGEDYTCI TFQPDLSKFK MQSLDKDIVA LMV RRAYDI AGSTKDVKVF LNGNKLPVKG FRSYVDMYLK DKLDETGNSL KVIHEQVNHR WEVC LTMSE KGFQQISFVN SIATSKGGRH VDYVADQIVT KLVDVVKKKN KGGVAVKAHQ VKNHM WIFV NALIENPTFD SQTKENMTLQ PKSFGSTCQL SEKFIKAAIG CGIVESILNW VKFKAQ VQL NKKCSAVKHN RIKGIPKLDD ANDAGGRNST ECTLILTEGD SAKTLAVSGL GVVGRDK YG VFPLRGKILN VREASHKQIM ENAEINNIIK IVGLQYKKNY EDEDSLKTLR YGKIMIMT D QDQDGSHIKG LLINFIHHNW PSLLRHRFLE EFITPIVKVS KNKQEMAFYS LPEFEEWKS STPNHKKWKV KYYKGLGTST SKEAKEYFAD MKRHRIQFKY SGPEDDAAIS LAFSKKQIDD RKEWLTNFM EDRRQRKLLG LPEDYLYGQT TTYLTYNDFI NKELILFSNS DNERSIPSMV D GLKPGQRK VLFTCFKRND KREVKVAQLA GSVAEMSSYH HGEMSLMMTI INLAQNFVGS NN LNLLQPI GQFGTRLHGG KDSASPRYIF TMLSSLARLL FPPKDDHTLK FLYDDNQRVE PEW YIPIIP MVLINGAEGI GTGWSCKIPN FDVREIVNNI RRLMDGEEPL PMLPSYKNFK GTIE ELAPN QYVISGEVAI LNSTTIEISE LPVRTWTQTY KEQVLEPMLN GTEKTPPLIT DYREY HTDT TVKFVVKMTE EKLAEAERVG LHKVFKLQTS LTCNSMVLFD HVGCLKKYDT VLDILR DFF ELRLKYYGLR KEWLLGMLGA ESAKLNNQAR FILEKIDGKI IIENKPKKEL IKVLIQR GY DSDPVKAWKE AQQKVPDEEE NEESDNEKET EKSDSVTDSG PTFNYLLDMP LWYLTKEK K DELCRLRNEK EQELDTLKRK SPSDLWKEDL ATFIEELEAV EAKEKQDEQV GLPGKGGKA KGKKTQMAEV LPSPRGQRVI PRITIEMKAE AEKKNKKKIK NENTEGSPQE DGVELEGLKQ RLEKKQKRE PGTKTKKQTT LAFKPIKKGK KRNPWSDSES DRSSDESNFD VPPRETEPRR A ATKTKFTM DLDSDEDFSD FDEKTDDEDF VPSDASPPKT KTSPKLSNKE LKPQKSVVSD LE ADDVKGS VPLSSSPPAT HFPDETEITN PVPKKNVTVK KTAAKSQSST STTGAKKRAA PKG TKRDPA LNSGVSQKPD PAKTKNRRKR KPSTSDDSDS NFEKIVSKAV TSKKSKGESD DFHM DFDSA VAPRAKSVRA KKPIKYLEES DEDDLF |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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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 / Cs: 0.01 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000 |
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 1908092 |
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CTF correction | Software: (Name: Gctf, RELION, cryoSPARC) |
Startup model | Type of model: INSILICO MODEL In silico model: An ab initio model was reconstructed using cryoSPARC |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC |
Final 3D classification | Software - Name: RELION |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 36610 |