9NA9 | pdb_00009na9

Augmin1345-Extended-Tripod


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Cryo-EM structures of the Plant Augmin reveal its intertwined coiled-coil assembly, antiparallel dimerization and NEDD1 binding mechanisms.

Ashaduzzaman, M.Taheri, A.Lee, Y.J.Tang, Y.Guo, F.Fried, S.D.Liu, B.Al-Bassam, J.

(2025) bioRxiv 

  • DOI: https://doi.org/10.1101/2025.02.25.640204
  • Primary Citation of Related Structures:  
    9NA8, 9NA9, 9NBA, 9NBB, 9NBD, 9NBI

  • PubMed Abstract: 

    Microtubule (MT) branch nucleation is fundamental for building parallel MT networks in eukaryotic cells. In plants and metazoans, MT branch nucleation requires Augmin and NEDD1 proteins which bind along MTs and then recruit and activate the gamma-tubulin ring complex (γ-TuRC). Augmin is a fork-shaped assembly composed of eight coiled-coil subunits, while NEDD1 is a WD40 β-propellor protein that bridges across MTs, Augmin, and γ-TuRC during MT branch nucleation. Here, we reconstitute hetero-tetrameric and hetero-octameric Arabidopsis thaliana Augmin assemblies, resolve their subunit interactions using crosslinking mass spectrometry and determine 3.7 to 7.3-Å cryo-EM structures for the V-junction and extended regions of Augmin. These structures allowed us to generate a complete de novo plant Augmin model that reveals the long-range multi coiled-coil interfaces that stabilize its 40-nm hetero-octameric fork-shaped organization. We discovered the dual calponin homology (CH) domain forming its MT binding site at the end of its V-junction undertake open and closed conformations. We determined a 12-Å dimeric Augmin cryo-EM structure revealing Augmin undergoes anti-parallel dimerization through two conserved surfaces along Augmin's extended region. We reconstituted the NEDD1 WD40 β-propellor with Augmin revealing it directly binds on top its V-junction and enhances Augmin dimerization. Our studies suggest that cooperativity between the Augmin dual CH domains and NEDD1 WD40 binding site may regulate Augmin V-junction dual binding to MT lattices. This unique V-shaped dual binding and organization anchors Augmins along MTs generating a platform to recruit γ-TuRC and activate branched MT nucleation.


  • Organizational Affiliation
    • Department of Molecular Cellular Biology, University of California, Davis, CA, USA.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AUGMIN subunit 1298Arabidopsis thalianaMutation(s): 0 
Gene Names: AUG1At2g41350F13H10.10
UniProt
Find proteins for F4IK01 (Arabidopsis thaliana)
Explore F4IK01 
Go to UniProtKB:  F4IK01
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UniProt GroupF4IK01
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
AUGMIN subunit 4B [auth D]423Arabidopsis thalianaMutation(s): 0 
Gene Names: AUG4At1g50710F17J6.23F4M15.6
UniProt
Find proteins for Q8GYM3 (Arabidopsis thaliana)
Explore Q8GYM3 
Go to UniProtKB:  Q8GYM3
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UniProt GroupQ8GYM3
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
AUGMIN subunit 5,Green fluorescent proteinC [auth E]1,040Arabidopsis thalianaAequorea victoria
This entity is chimeric
Mutation(s): 0 
Gene Names: AUG5At5g38880K15E6.9GFP
UniProt
Find proteins for Q9FMB4 (Arabidopsis thaliana)
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UniProt GroupQ9FMB4
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
AUGMIN subunit 3D [auth C]617Arabidopsis thalianaMutation(s): 0 
Gene Names: AUG3At5g48520MJE7.16
UniProt
Find proteins for Q0WQE7 (Arabidopsis thaliana)
Explore Q0WQE7 
Go to UniProtKB:  Q0WQE7
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UniProt GroupQ0WQE7
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesNIH-5R01GM110283

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-26
    Type: Initial release