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- PDB-8at2: Structure of the augmin TIII subcomplex -

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Basic information

Entry
Database: PDB / ID: 8at2
TitleStructure of the augmin TIII subcomplex
Components
  • HAUS augmin like complex subunit 4 L homeolog
  • HAUS augmin-like complex subunit 1
  • HAUS augmin-like complex subunit 3
  • HAUS augmin-like complex subunit 5
KeywordsCELL CYCLE / Microtubule / Branching / Nucleation
Function / homology
Function and homology information


HAUS complex / mitotic spindle microtubule / centrosome cycle / spindle assembly / spindle / microtubule / cell division / centrosome / cytoplasm
Similarity search - Function
HAUS augmin-like complex subunit 4, metazoa / HAUS complex subunit 5, metazoa / HAUS augmin-like complex subunit 1 / HAUS augmin-like complex subunit 5 / HAUS augmin-like complex subunit 4 / HAUS augmin-like complex subunit 4 / HAUS augmin-like complex subunit 5 / HAUS augmin-like complex subunit 3 / HAUS augmin-like complex subunit 3, N-terminal / HAUS augmin-like complex subunit 3
Similarity search - Domain/homology
HAUS augmin-like complex subunit 5 / LOC495502 protein / HAUS augmin like complex subunit 4 L homeolog / HAUS augmin-like complex subunit 3
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.7 Å
AuthorsZupa, E. / Pfeffer, S.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)PF 963/1-4 Germany
German Research Foundation (DFG)Schi 295/4-4 Germany
CitationJournal: Nat Commun / Year: 2022
Title: The augmin complex architecture reveals structural insights into microtubule branching.
Authors: Erik Zupa / Martin Würtz / Annett Neuner / Thomas Hoffmann / Mandy Rettel / Anna Böhler / Bram J A Vermeulen / Sebastian Eustermann / Elmar Schiebel / Stefan Pfeffer /
Abstract: In mitosis, the augmin complex binds to spindle microtubules to recruit the γ-tubulin ring complex (γ-TuRC), the principal microtubule nucleator, for the formation of branched microtubules. Our ...In mitosis, the augmin complex binds to spindle microtubules to recruit the γ-tubulin ring complex (γ-TuRC), the principal microtubule nucleator, for the formation of branched microtubules. Our understanding of augmin-mediated microtubule branching is hampered by the lack of structural information on the augmin complex. Here, we elucidate the molecular architecture and conformational plasticity of the augmin complex using an integrative structural biology approach. The elongated structure of the augmin complex is characterised by extensive coiled-coil segments and comprises two structural elements with distinct but complementary functions in γ-TuRC and microtubule binding, linked by a flexible hinge. The augmin complex is recruited to microtubules via a composite microtubule binding site comprising a positively charged unordered extension and two calponin homology domains. Our study provides the structural basis for augmin function in branched microtubule formation, decisively fostering our understanding of spindle formation in mitosis.
History
DepositionAug 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 2.0Oct 26, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / citation ...atom_site / citation / citation_author / em_software / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_unobs_or_zero_occ_residues / pdbx_validate_peptide_omega / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_conf / struct_mon_prot_cis
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details
Description: Model completeness
Details: Removing parts of the model not covered by corresponding EM map.
Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: HAUS augmin-like complex subunit 1
C: HAUS augmin-like complex subunit 3
D: HAUS augmin like complex subunit 4 L homeolog
E: HAUS augmin-like complex subunit 5


Theoretical massNumber of molelcules
Total (without water)219,4114
Polymers219,4114
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein HAUS augmin-like complex subunit 1 / LOC495502 protein


Mass: 32684.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC495502
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: Q3B8L5
#2: Protein HAUS augmin-like complex subunit 3


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
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: Q6DCY9
#3: Protein HAUS augmin like complex subunit 4 L homeolog / MGC115689 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
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: Q4V7I1
#4: Protein HAUS augmin-like complex subunit 5


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
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: A0A1L8FPI2

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Augmin TIII subcomplex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.218 MDa / Experimental value: NO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Source (recombinant)Organism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 85 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 81000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 69 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 12615
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

SoftwareName: PHENIX / Version: 1.16_3549: / Classification: refinement
EM software
IDNameVersionCategory
2EPU2.9image acquisition
4Gctf1.06CTF correction
7UCSF Chimera1.13model fitting
9cryoSPARC3.2initial Euler assignment
10cryoSPARC3.2final Euler assignment
11cryoSPARC3.2classification
12cryoSPARC3.23D reconstruction
13NAMD2.14model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1060446
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 7.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 82776 / Algorithm: BACK PROJECTION / Num. of class averages: 5 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.03515572
ELECTRON MICROSCOPYf_angle_d3.43620931
ELECTRON MICROSCOPYf_dihedral_angle_d20.3489811
ELECTRON MICROSCOPYf_chiral_restr0.22353
ELECTRON MICROSCOPYf_plane_restr0.0242717

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