+Open data
-Basic information
Entry | Database: PDB / ID: 8fck | ||||||||||||
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Title | Structure of the vertebrate augmin complex | ||||||||||||
Components |
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Keywords | CELL CYCLE / microtubule / branching microtubule nucleation / spindle assembly | ||||||||||||
Function / homology | Function and homology information HAUS complex / microtubule minus-end binding / mitotic spindle microtubule / microtubule nucleation / centrosome cycle / spindle assembly / spindle pole / spindle / serine-type endopeptidase inhibitor activity / microtubule binding ...HAUS complex / microtubule minus-end binding / mitotic spindle microtubule / microtubule nucleation / centrosome cycle / spindle assembly / spindle pole / spindle / serine-type endopeptidase inhibitor activity / microtubule binding / microtubule / cell division / centrosome / extracellular space / metal ion binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Xenopus laevis (African clawed frog) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.88 Å | ||||||||||||
Authors | Travis, S.M. / Huang, W. / Zhang, R. / Petry, S. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Nat Commun / Year: 2023 Title: Integrated model of the vertebrate augmin complex. Authors: Sophie M Travis / Brian P Mahon / Wei Huang / Meisheng Ma / Michael J Rale / Jodi Kraus / Derek J Taylor / Rui Zhang / Sabine Petry / Abstract: Accurate segregation of chromosomes is required to maintain genome integrity during cell division. This feat is accomplished by the microtubule-based spindle. To build a spindle rapidly and with high ...Accurate segregation of chromosomes is required to maintain genome integrity during cell division. This feat is accomplished by the microtubule-based spindle. To build a spindle rapidly and with high fidelity, cells take advantage of branching microtubule nucleation, which rapidly amplifies microtubules during cell division. Branching microtubule nucleation relies on the hetero-octameric augmin complex, but lack of structure information about augmin has hindered understanding how it promotes branching. In this work, we combine cryo-electron microscopy, protein structural prediction, and visualization of fused bulky tags via negative stain electron microscopy to identify the location and orientation of each subunit within the augmin structure. Evolutionary analysis shows that augmin's structure is highly conserved across eukaryotes, and that augmin contains a previously unidentified microtubule binding site. Thus, our findings provide insight into the mechanism of branching microtubule nucleation. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fck.cif.gz | 562.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fck.ent.gz | 453.3 KB | Display | PDB format |
PDBx/mmJSON format | 8fck.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fck_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8fck_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8fck_validation.xml.gz | 93 KB | Display | |
Data in CIF | 8fck_validation.cif.gz | 144.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fc/8fck ftp://data.pdbj.org/pub/pdb/validation_reports/fc/8fck | HTTPS FTP |
-Related structure data
Related structure data | 28981MC 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
-HAUS augmin-like complex subunit ... , 4 types, 4 molecules ABDH
#1: Protein | Mass: 32655.621 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: haus1.L / Plasmid: pFASTBAC / Cell (production host): Epithelial / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / Tissue (production host): Ovary / References: UniProt: A0A8J1L9M8 |
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#2: Protein | Mass: 68112.250 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: haus3 / Plasmid: pFASTBAC / Cell (production host): Epithelial / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / Tissue (production host): Ovary / References: UniProt: Q6DCY9 |
#4: Protein | Mass: 77357.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: haus5.L / Plasmid: pFASTBAC / Cell (production host): Epithelial / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / Tissue (production host): Ovary / References: UniProt: A0A1L8FPI2 |
#8: Protein | Mass: 41144.852 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: haus8, hice1 / Plasmid: pFASTBAC / Cell (production host): Epithelial / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / Tissue (production host): Ovary / References: UniProt: Q0IHJ3 |
-HAUS augmin like complex subunit ... , 4 types, 4 molecules CEFG
#3: Protein | Mass: 41256.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: haus4.L, haus4, MGC115689 / Plasmid: pFASTBAC / Cell (production host): Epithelial / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / Tissue (production host): Ovary / References: UniProt: Q4V7I1 |
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#5: Protein | Mass: 53505.473 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: haus2.L, cep27, haus2, MGC82377, GFP / Plasmid: pFASTBAC / Cell (production host): Epithelial / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / Tissue (production host): Ovary / References: UniProt: Q6INL9, UniProt: P42212 |
#6: Protein | Mass: 50927.965 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: haus6.L / Plasmid: pFASTBAC / Cell (production host): Epithelial / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / Tissue (production host): Ovary / References: UniProt: A0JPI0 |
#7: Protein | Mass: 39379.605 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: haus7.S, haus7, LOC100158301, uchl5ip, uip1 / Plasmid: pFASTBAC / Cell (production host): Epithelial / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / Tissue (production host): Ovary / References: UniProt: B1H1T5 |
-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: Augmin / Type: COMPLEX / Details: Peak octameric fraction following gel filtration / Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||||||||||
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Molecular weight | Value: 0.403 MDa / Experimental value: NO | ||||||||||||||||||||||||||||
Source (natural) | Organism: Xenopus laevis (African clawed frog) / Cellular location: cytoplasm / Organelle: mitotic spindle | ||||||||||||||||||||||||||||
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) / Strain: Sf9 / Plasmid: pFASTBAC | ||||||||||||||||||||||||||||
Buffer solution | pH: 7.7 | ||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.06 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / 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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 64000 X / Nominal defocus max: 39903 nm / Nominal defocus min: 10105 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 66 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2350 |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2046060 Details: Template picks, trained on evenly-spaced templates from ab initio model | |||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 6.88 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 114000 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient | |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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