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- PDB-9rpd: D. melanogaster Augmin TII N-clamp (GST-fusion) bound to a microt... -

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Basic information

Entry
Database: PDB / ID: 9rpd
TitleD. melanogaster Augmin TII N-clamp (GST-fusion) bound to a microtubule, well-defined subset of particles
Components
  • Augmin complex subunit dgt4
  • Augmin complex subunit dgt6
  • Augmin complex subunit msd5,Green fluorescent protein,Glutathione S-transferase class-mu 26 kDa isozyme
  • Tubulin alpha-1A chain
  • Tubulin beta chain
KeywordsCELL CYCLE / augmin / N-clamp / TII / microtubule / branching / nucleation / HAUS / HAUS augmin-like complex subunit / HAUS6 / HAUS7 / HAUS2 / HAUS8 / Dgt6 / Msd5 / Dgt4 / Msd1 / Drosophila melanogaster / complex / CH domain / calponin homology domain / MAP / cell division
Function / homology
Function and homology information


mitotic spindle-templated microtubule nucleation / HAUS complex / mitotic spindle microtubule / motile cilium / regulation of mitotic nuclear division / glutathione transferase / centrosome duplication / glutathione transferase activity / mitotic spindle assembly / glutathione metabolic process ...mitotic spindle-templated microtubule nucleation / HAUS complex / mitotic spindle microtubule / motile cilium / regulation of mitotic nuclear division / glutathione transferase / centrosome duplication / glutathione transferase activity / mitotic spindle assembly / glutathione metabolic process / bioluminescence / mitotic spindle organization / generation of precursor metabolites and energy / kinetochore / structural constituent of cytoskeleton / microtubule cytoskeleton organization / spindle / neuron migration / spindle pole / mitotic cell cycle / protein-macromolecule adaptor activity / microtubule binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / hydrolase activity / cell division / GTPase activity / centrosome / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
HAUS augmin-like complex subunit 6 / HAUS augmin-like complex subunit 6, N-terminal / HAUS augmin-like complex subunit 6 N-terminus / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. ...HAUS augmin-like complex subunit 6 / HAUS augmin-like complex subunit 6, N-terminal / HAUS augmin-like complex subunit 6 N-terminus / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Green fluorescent protein, GFP / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Green fluorescent protein-related / Green fluorescent protein / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Green fluorescent protein / 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 / Thioredoxin-like superfamily
Similarity search - Domain/homology
Tubulin alpha-1A chain / Tubulin beta chain / Glutathione S-transferase class-mu 26 kDa isozyme / Green fluorescent protein / Augmin complex subunit dgt6 / Augmin complex subunit msd5 / Augmin complex subunit dgt4
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Aequorea victoria (jellyfish)
Schistosoma japonicum (invertebrata)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsWuertz, M. / Vermeulen, B.J.A. / Tonon, G. / Pfeffer, S.
Funding support Germany, 9items
OrganizationGrant numberCountry
German Research Foundation (DFG)Sch Baden-Wuerttemberg Germany
German Research Foundation (DFG)INST 35/1314-1 FUGG Germany
German Research Foundation (DFG)INST 35/1503-1 FUGG Germany
German Research Foundation (DFG)INST 35/1134-1 FUGG Germany
German Research Foundation (DFG)DFG Schi 295/4-4 Germany
German Research Foundation (DFG)SCHI 295/11-1 Germany
German Research Foundation (DFG)SCHI 295/9-1 Germany
German Research Foundation (DFG)DFG PF 963/1-4 Germany
German Research Foundation (DFG)DFG PF 963/4-1 Germany
CitationJournal: Nat Commun / Year: 2025
Title: Conserved function of the HAUS6 calponin homology domain in anchoring augmin for microtubule branching.
Authors: Martin Würtz / Giulia Tonon / Bram J A Vermeulen / Maja Zezlina / Qi Gao / Annett Neuner / Angelika Seidl / Melanie König / Maximilian Harkenthal / Sebastian Eustermann / Sylvia Erhardt / ...Authors: Martin Würtz / Giulia Tonon / Bram J A Vermeulen / Maja Zezlina / Qi Gao / Annett Neuner / Angelika Seidl / Melanie König / Maximilian Harkenthal / Sebastian Eustermann / Sylvia Erhardt / Fabio Lolicato / Elmar Schiebel / Stefan Pfeffer /
Abstract: Branching microtubule nucleation is a key mechanism for mitotic and meiotic spindle assembly and requires the hetero-octameric augmin complex. Augmin recruits the major microtubule nucleator, the γ- ...Branching microtubule nucleation is a key mechanism for mitotic and meiotic spindle assembly and requires the hetero-octameric augmin complex. Augmin recruits the major microtubule nucleator, the γ-tubulin ring complex, to pre-existing microtubules to direct the formation of new microtubules in a defined orientation. Although recent structural work has provided key insights into the structural organization of augmin, molecular details of its interaction with microtubules remain elusive. Here, we identify the minimal conserved microtubule-binding unit of augmin across species and demonstrate that stable microtubule anchoring is predominantly mediated via the calponin homology (CH) domain in Dgt6/HAUS6. Comparative sequence and functional analyses in vitro and in vivo reveal a highly conserved functional role of the HAUS6 CH domain in microtubule binding. Using cryo-electron microscopy and molecular dynamics simulations in combination with AlphaFold structure predictions, we show that the D. melanogaster Dgt6/HAUS6 CH domain binds microtubules at the inter-protofilament groove between two adjacent β-tubulin subunits and thereby orients augmin on microtubules. Altogether, our findings reveal how augmin binds microtubules to pre-determine the branching angle during microtubule nucleation and facilitate the rapid assembly of complex microtubule networks.
History
DepositionJun 24, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: Augmin complex subunit dgt4
J: Augmin complex subunit dgt6
K: Augmin complex subunit msd5,Green fluorescent protein,Glutathione S-transferase class-mu 26 kDa isozyme
B: Tubulin beta chain
D: Tubulin beta chain
A: Tubulin alpha-1A chain
C: Tubulin alpha-1A chain
G: Tubulin alpha-1A chain
E: Tubulin alpha-1A chain


Theoretical massNumber of molelcules
Total (without water)421,4919
Polymers421,4919
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Augmin complex subunit dgt4 / Dim gamma-tubulin 4


Mass: 12246.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: dgt4, CG4865 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9W4M8
#2: Protein Augmin complex subunit dgt6 / Dim gamma-tubulin 6


Mass: 32382.451 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: dgt6, CG11881 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9VAP2
#3: Protein Augmin complex subunit msd5,Green fluorescent protein,Glutathione S-transferase class-mu 26 kDa isozyme / Mitotic spindle density protein 5 / GST 26 / Sj26 antigen / SjGST


Mass: 76561.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly), (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Schistosoma japonicum (invertebrata)
Gene: msd5, dgt7, CG2213, GFP / Production host: Escherichia coli (E. coli)
References: UniProt: Q9W0G6, UniProt: P42212, UniProt: P08515, glutathione transferase
#4: Protein Tubulin beta chain / Beta-tubulin


Mass: 49907.770 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P02554
#5: Protein
Tubulin alpha-1A chain


Mass: 50121.266 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P02550
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Microtubule decorated with D. melanogaster N-clampCOMPLEXall0MULTIPLE SOURCES
2Heterotetrameric Augmin TII N-clamp complexCOMPLEX1RECOMBINANT
3MicrotubuleORGANELLE OR CELLULAR COMPONENT1NATURAL
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
31NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDOrgan
21Drosophila melanogaster (fruit fly)7227
32Drosophila melanogaster (fruit fly)7227
43Sus scrofa (pig)9823Brain
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Escherichia coli (E. coli)562BL21
32Escherichia coli (E. coli)562BL21
43Escherichia coli (E. coli)562BL21
Buffer solutionpH: 6.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 40.4 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1crYOLO1.8particle selection
13RELION53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 117870 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT

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