+Open data
-Basic information
Entry | Database: PDB / ID: 7xhn | ||||||
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Title | Structure of human inner kinetochore CCAN-DNA complex | ||||||
Components |
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Keywords | CELL CYCLE | ||||||
Function / homology | Function and homology information positive regulation of protein localization to kinetochore / Mis6-Sim4 complex / FANCM-MHF complex / centromere complex assembly / kinetochore organization / metaphase chromosome alignment / spindle attachment to meiosis I kinetochore / Fanconi anaemia nuclear complex / inner kinetochore / kinetochore binding ...positive regulation of protein localization to kinetochore / Mis6-Sim4 complex / FANCM-MHF complex / centromere complex assembly / kinetochore organization / metaphase chromosome alignment / spindle attachment to meiosis I kinetochore / Fanconi anaemia nuclear complex / inner kinetochore / kinetochore binding / centromeric DNA binding / sex differentiation / CENP-A containing chromatin assembly / resolution of meiotic recombination intermediates / chordate embryonic development / negative regulation of epithelial cell apoptotic process / attachment of mitotic spindle microtubules to kinetochore / kinetochore assembly / condensed chromosome, centromeric region / replication fork processing / mitotic sister chromatid segregation / chromosome, centromeric region / centriolar satellite / chromosome organization / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / pericentric heterochromatin / interstrand cross-link repair / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Deposition of new CENPA-containing nucleosomes at the centromere / Resolution of Sister Chromatid Cohesion / NRIF signals cell death from the nucleus / mitotic spindle organization / positive regulation of protein ubiquitination / chromosome segregation / positive regulation of epithelial cell proliferation / RHO GTPases Activate Formins / Fanconi Anemia Pathway / PKR-mediated signaling / kinetochore / nuclear matrix / Separation of Sister Chromatids / actin cytoskeleton / mitotic cell cycle / chromosome / midbody / nuclear body / cell adhesion / protein heterodimerization activity / cell division / DNA repair / apoptotic process / DNA damage response / chromatin binding / chromatin / nucleolus / regulation of DNA-templated transcription / signal transduction / DNA binding / nucleoplasm / membrane / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.71 Å | ||||||
Authors | Sun, L.F. / Tian, T. / Wang, C.L. / Yang, Z.S. / Zang, J.Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Cell Discov / Year: 2022 Title: Structural insights into human CCAN complex assembled onto DNA. Authors: Tian Tian / Lili Chen / Zhen Dou / Zhisen Yang / Xinjiao Gao / Xiao Yuan / Chengliang Wang / Ran Liu / Zuojun Shen / Ping Gui / Maikun Teng / Xianlei Meng / Donald L Hill / Lin Li / Xuan ...Authors: Tian Tian / Lili Chen / Zhen Dou / Zhisen Yang / Xinjiao Gao / Xiao Yuan / Chengliang Wang / Ran Liu / Zuojun Shen / Ping Gui / Maikun Teng / Xianlei Meng / Donald L Hill / Lin Li / Xuan Zhang / Xing Liu / Linfeng Sun / Jianye Zang / Xuebiao Yao / Abstract: In mitosis, accurate chromosome segregation depends on kinetochores that connect centromeric chromatin to spindle microtubules. The centromeres of budding yeast, which are relatively simple, are ...In mitosis, accurate chromosome segregation depends on kinetochores that connect centromeric chromatin to spindle microtubules. The centromeres of budding yeast, which are relatively simple, are connected to individual microtubules via a kinetochore constitutive centromere associated network (CCAN). However, the complex centromeres of human chromosomes comprise millions of DNA base pairs and attach to multiple microtubules. Here, by use of cryo-electron microscopy and functional analyses, we reveal the molecular basis of how human CCAN interacts with duplex DNA and facilitates accurate chromosome segregation. The overall structure relates to the cooperative interactions and interdependency of the constituent sub-complexes of the CCAN. The duplex DNA is topologically entrapped by human CCAN. Further, CENP-N does not bind to the RG-loop of CENP-A but to DNA in the CCAN complex. The DNA binding activity is essential for CENP-LN localization to centromere and chromosome segregation during mitosis. Thus, these analyses provide new insights into mechanisms of action underlying kinetochore assembly and function in mitosis. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xhn.cif.gz | 602.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xhn.ent.gz | 443.4 KB | Display | PDB format |
PDBx/mmJSON format | 7xhn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xh/7xhn ftp://data.pdbj.org/pub/pdb/validation_reports/xh/7xhn | HTTPS FTP |
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-Related structure data
Related structure data | 33196MC 7xhoC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Centromere protein ... , 15 types, 17 molecules oOHIKLMNPSTXCcQUR
#1: Protein | Mass: 33830.637 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CENPO / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: Q9BU64 #2: Protein | | Mass: 29349.811 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CENPH / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: Q9H3R5 #3: Protein | | Mass: 86820.188 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CENPI / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: Q92674 #4: Protein | | Mass: 31696.070 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CENPK / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: Q9BS16 #5: Protein | | Mass: 39039.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CENPL / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8N0S6 #6: Protein | | Mass: 19761.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CENPM / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9NSP4 #7: Protein | | Mass: 40438.418 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CENPN / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96H22 #8: Protein | | Mass: 33210.949 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CENPP / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: Q6IPU0 #9: Protein | | Mass: 15917.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CENPS / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8N2Z9 #10: Protein | | Mass: 60502.613 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CENPT / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96BT3 #12: Protein | | Mass: 8972.415 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CENPX / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A8MT69 #15: Protein | Mass: 107022.273 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CENPC / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q03188 #16: Protein | | Mass: 31477.244 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CENPQ / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: Q7L2Z9 #17: Protein | | Mass: 47609.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CENPU / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: Q71F23 #18: Protein | | Mass: 20228.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CENPR / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: Q13352 |
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-Protein , 1 types, 1 molecules W
#11: Protein | Mass: 10087.236 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q5EE01 |
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-DNA chain , 2 types, 2 molecules GJ
#13: DNA chain | Mass: 7685.937 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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#14: DNA chain | Mass: 7676.923 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: CCAN-DNA / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: DIFFRACTION / Nominal defocus max: 2700 nm / Nominal defocus min: 1700 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.71 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 79777 / Symmetry type: POINT | ||||||||||||||||||||||||
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