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- PDB-9olh: Symmetry-expanded reconstruction of augmin T-II bonsai on the GTP... -

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Basic information

Entry
Database: PDB / ID: 9olh
TitleSymmetry-expanded reconstruction of augmin T-II bonsai on the GTPgammaS microtubule
Components
  • (HAUS augmin like complex subunit ...) x 2
  • HAUS augmin-like complex subunit 8
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
KeywordsCELL CYCLE / Microtubule / augmin / CH / spindle
Function / homology
Function and homology information


HAUS complex / microtubule minus-end binding / microtubule organizing center organization / mitotic spindle microtubule / positive regulation of axon guidance / centrosome cycle / microtubule-based process / spindle assembly / cytoplasmic microtubule / cellular response to interleukin-4 ...HAUS complex / microtubule minus-end binding / microtubule organizing center organization / mitotic spindle microtubule / positive regulation of axon guidance / centrosome cycle / microtubule-based process / spindle assembly / cytoplasmic microtubule / cellular response to interleukin-4 / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / spindle pole / mitotic cell cycle / double-stranded RNA binding / microtubule cytoskeleton / microtubule binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / cilium / protein heterodimerization activity / cell division / GTPase activity / ubiquitin protein ligase binding / centrosome / GTP binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
HAUS augmin-like complex subunit 7-like / HAUS augmin-like complex subunit 6 / HAUS augmin-like complex subunit 6, N-terminal / HAUS augmin-like complex subunit 6 N-terminus / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal ...HAUS augmin-like complex subunit 7-like / HAUS augmin-like complex subunit 6 / HAUS augmin-like complex subunit 6, N-terminal / HAUS augmin-like complex subunit 6 N-terminus / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
Similarity search - Domain/homology
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / HAUS augmin like complex subunit 6 L homeolog / HAUS augmin like complex subunit 7 S homeolog / Tubulin alpha-1B chain / HAUS augmin-like complex subunit 8 / Tubulin beta-2B chain
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Bos taurus (domestic cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.83 Å
AuthorsTravis, S.M. / Zhang, R.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32 GM142149 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99 GM152794 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01 GM138854 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01 GM141100 United States
CitationJournal: Nat Commun / Year: 2025
Title: How augmin establishes the angle of the microtubule branch site.
Authors: Sophie M Travis / Jodi Kraus / Collin T McManus / Kiana Golden / Rui Zhang / Sabine Petry /
Abstract: How microtubules (MTs) are generated in the proper orientation is essential to understanding how the cytoskeleton organizes a cell and MT-dependent events such as cell division. In the spindle, most ...How microtubules (MTs) are generated in the proper orientation is essential to understanding how the cytoskeleton organizes a cell and MT-dependent events such as cell division. In the spindle, most MTs are generated through the branching MT nucleation pathway. In this pathway, new MTs are nucleated from the side of existing MTs and oriented at a shallow angle by the branching factor augmin, ensuring that both MTs have the same polarity. Yet, how augmin binds MTs and sets the branch angle has remained unclear. Here, we report the cryo-electron microscopy structure of an augmin subcomplex on the MT. This structure resembles that of NDC80 bound to the MT, with the conserved CH domain of augmin's Haus6 subunit directly proximal to the MT lattice. We find that the Haus6 CH domain is a bona fide MT binding site that increases augmin's affinity for the MT and helps establish branch angle. A second binding site, located in the disordered N-terminus of Haus8, also establishes branch angle,. Thus, we find that augmin regulates MT branching using two domains, each tuned to modulate MT affinity and MT branch angle. This work expands our mechanistic understanding of branching MT nucleation and thus spindle formation.
History
DepositionMay 12, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tubulin alpha-1B chain
B: Tubulin beta-2B chain
C: Tubulin alpha-1B chain
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,92512
Polymers242,2666
Non-polymers1,6596
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 3 types, 4 molecules ACBH

#1: Protein Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


Mass: 50204.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: BRAIN / References: UniProt: P81947
#2: Protein Tubulin beta-2B chain


Mass: 49999.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: Brain / References: UniProt: Q6B856
#5: Protein HAUS augmin-like complex subunit 8 / HEC1/NDC80-interacting centrosome-associated protein 1 / Sarcoma antigen NY-SAR-48 homolog


Mass: 28742.902 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: pETDuet1 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Rosetta 2 (DE3) / References: UniProt: Q0IHJ3

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HAUS augmin like complex subunit ... , 2 types, 2 molecules FG

#3: Protein HAUS augmin like complex subunit 6 L homeolog / LOC100036802 protein


Mass: 33562.742 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 / Plasmid: pETDuet1 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Rosetta 2 (DE3) / References: UniProt: A0JPI0
#4: Protein HAUS augmin like complex subunit 7 S homeolog / LOC100158301 protein


Mass: 29551.631 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: pRSFDuet1 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Rosetta 2 (DE3) / References: UniProt: B1H1T5

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Non-polymers , 3 types, 6 molecules

#6: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3S

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Augmin T-II bonsai on the microtubuleCOMPLEXComplex of augmin bound to the microtubule#1-#50MULTIPLE SOURCES
2GTPgammaS microtubuleCOMPLEXbovine tubulin polymerized in the presence of GTPgammaS#1-#21NATURAL
3augmin T-II bonsaiCOMPLEXtrimeric fragment of Xenopus laevis augmin#3-#51RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
11345 kDa/nmNO
21188 kDa/nmNO
310.092 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDOrgan
32Bos taurus (domestic cattle)9913BRAIN
43Xenopus laevis (African clawed frog)8355
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21 Rosetta 2 (DE3) / Plasmid: pETDuet1/pRSFDuet-1
Buffer solutionpH: 6.8
Buffer component
IDConc.NameFormulaBuffer-ID
10.08 MPIPES1
21 mMEGTA1
31 mMmagnesium chlorideMgCl21
40.05 % v/vTween-201
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 20 uM tubulin, 10 uM augmin T-II bonsai
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: LEICA EM GP / 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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 2000 nm / Cs: 0.1 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 4.1 sec. / Electron dose: 20 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5012
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 20 eV
Image scansWidth: 4096 / Height: 4096

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Processing

EM softwareName: PHENIX / Version: 1.21.1_5286 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 17021
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 99011 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeChain-IDInitial refinement model-ID
16DPU

6dpu

A6DPUA1
26DPU

6dpu

B6DPUB1
38FCK

8fck

F8FCKF2
48FCK

8fck

G8FCKG2
58FCK

8fck

H8FCKH2

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