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- PDB-8at3: Structure of the augmin holocomplex in open conformation -

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Basic information

Entry
Database: PDB / ID: 8at3
TitleStructure of the augmin holocomplex in open conformation
Components
  • (HAUS augmin like complex subunit ...) x 4
  • (HAUS augmin-like complex subunit ...) x 4
KeywordsCELL CYCLE / Microtubule / Branching / Nucleation
Function / homology
Function and homology information


HAUS complex / mitotic spindle microtubule / centrosome cycle / spindle assembly / spindle / spindle pole / microtubule / cell division / centrosome / cytoplasm
Similarity search - Function
HAUS augmin-like complex subunit 2, metazoa / HAUS augmin-like complex subunit 6 / HAUS augmin-like complex subunit 6, N-terminal / HAUS augmin-like complex subunit 2 / HAUS augmin-like complex subunit 7-like / HAUS augmin-like complex subunit 6 N-terminus / HAUS augmin-like complex subunit 2 / HAUS augmin-like complex subunit 4, metazoa / HAUS complex subunit 5, metazoa / HAUS augmin-like complex subunit 1 ...HAUS augmin-like complex subunit 2, metazoa / HAUS augmin-like complex subunit 6 / HAUS augmin-like complex subunit 6, N-terminal / HAUS augmin-like complex subunit 2 / HAUS augmin-like complex subunit 7-like / HAUS augmin-like complex subunit 6 N-terminus / HAUS augmin-like complex subunit 2 / 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 / HAUS augmin like complex subunit 6 L homeolog / HAUS augmin like complex subunit 7 S homeolog / HAUS augmin-like complex subunit 8 / LOC495502 protein / HAUS augmin like complex subunit 4 L homeolog / HAUS augmin-like complex subunit 3 / HAUS augmin like complex subunit 2 L homeolog
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodELECTRON MICROSCOPY / single particle reconstruction / negative staining / Resolution: 33 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 1.1Oct 12, 2022Group: Database references / Category: citation / citation_author
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.identifier_ORCID / _citation_author.name
Revision 1.2Dec 13, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HAUS augmin-like complex subunit 1
B: HAUS augmin-like complex subunit 3
C: HAUS augmin like complex subunit 4 L homeolog
D: HAUS augmin-like complex subunit 5
E: HAUS augmin like complex subunit 2 L homeolog
F: HAUS augmin like complex subunit 6 L homeolog
G: HAUS augmin like complex subunit 7 S homeolog
H: HAUS augmin-like complex subunit 8


Theoretical massNumber of molelcules
Total (without water)435,9348
Polymers435,9348
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area109080 Å2
ΔGint-964 kcal/mol
Surface area174440 Å2
MethodPISA

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Components

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HAUS augmin-like complex subunit ... , 4 types, 4 molecules ABDH

#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
#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
#8: Protein HAUS augmin-like complex subunit 8 / HEC1/NDC80-interacting centrosome-associated protein 1 / Sarcoma antigen NY-SAR-48 homolog


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
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: Q0IHJ3

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HAUS augmin like complex subunit ... , 4 types, 4 molecules CEFG

#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
#5: Protein HAUS augmin like complex subunit 2 L homeolog / MGC82377 protein


Mass: 25135.715 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
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: Q6INL9
#6: Protein HAUS augmin like complex subunit 6 L homeolog / LOC100036802 protein


Mass: 110863.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: haus6.L, haus6, LOC100036802
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: A0JPI0
#7: Protein HAUS augmin like complex subunit 7 S homeolog / LOC100158301 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
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: B1H1T5

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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 octameric holocomplex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.435 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: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: NO
EM stainingType: NEGATIVE / Material: Uranyl Acetate
Specimen supportGrid material: COPPER/PALLADIUM / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil

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Electron microscopy imaging

Experimental equipment
Model: Talos L120C / Image courtesy: FEI Company
MicroscopyModel: TFS TALOS L120C
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 2000 nm
Image recordingElectron dose: 101.8 e/Å2 / Film or detector model: FEI CETA (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 583

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Processing

EM software
IDNameVersionCategory
2EPU2.9image acquisition
4Gctf1.06CTF correction
7UCSF Chimera1.13model fitting
9RELION3.1initial Euler assignment
10RELION3.1final Euler assignment
11RELION3.1classification
12RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 80837
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11969 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL

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