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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: To Be Published / Year: 2025
Title: Structural insights into the augmin-microtubule interaction reveal a conserved function of the HAUS6 CH domain in orienting augmin on microtubules
Authors: Wuertz, M. / Tonon, G. / Vermeulen, B.J.A. / Gao, Q. / Zezlina, M. / Neuner, A. / Seidl, A. / Koenig, M. / Harkenthal, M. / Eustermann, S. / Erhardt, S. / Lolicato, F. / Schiebel, E. / Pfeffer, S.
History
DepositionJun 24, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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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