9PZM | pdb_00009pzm

Augmin V junction with NEDD1 (WD)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Cryo-EM structures of plant Augmin reveal coiled-coil assembly, antiparallel dimerization, and NEDD1 binding.

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

(2025) Nat Commun 16: 11440-11440

  • DOI: https://doi.org/10.1038/s41467-025-66332-4
  • Primary Citation Related Structures: 
    9PZM

  • PubMed Abstract: 

    Microtubule (MT) branch nucleation requires Augmin and NEDD1 proteins, which recruit and activate the gamma-tubulin ring complex (γ-TuRC). Augmin is a fork-shaped assembly of eight coiled-coil subunits, while NEDD1 is a β-propeller protein bridging MTs, Augmin, and γ-TuRC. We reconstitute Arabidopsis thaliana Augmin assemblies and determine 3.7-7.3-Å cryo-EM structures of its V-junction and extended regions using crosslinking mass spectrometry. These structures reveal a complete plant Augmin model showing multi-coiled-coil interfaces stabilizing its 40-nm hetero-octameric fork architecture. The dual calponin homology (CH) domains at the V-junction terminus adopt open and closed conformations for MT binding. A 12-Å cryo-EM structure shows Augmin undergoes anti-parallel dimerization through conserved surfaces on its extended region. We determine the NEDD1 β-propeller structure with Augmin, revealing direct binding inside the V-junction that enhances dimerization. Direct coupling and evolutionary analyses identify co-varying residue pairs validating the eight-subunit model and NEDD1 interface. Cooperativity between dual CH domains and NEDD1 binding may regulate V-junction binding to MT lattices. This V-shaped dual binding anchors Augmin along MTs, creating platforms for γ-TuRC recruitment and branched MT nucleation.


  • Organizational Affiliation
    • Department of Molecular Cellular Biology, University of California, Davis, CA, USA. mashaduzzaman@ucdavis.edu.

Macromolecule Content 

  • Total Structure Weight: 299.66 kDa 
  • Atom Count: 14,092 
  • Modeled Residue Count: 1,785 
  • Deposited Residue Count: 2,678 
  • Unique protein chains: 7

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
AUGMIN subunit 2A [auth B]152Arabidopsis thalianaMutation(s): 0 
Gene Names: AUG2At2g32980T21L14.8
UniProt
Find proteins for O48767 (Arabidopsis thaliana)
Explore O48767 
Go to UniProtKB:  O48767
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UniProt GroupO48767
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
AUGMIN subunit 3B [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
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
AUGMIN subunit 5C [auth E]777Arabidopsis thalianaMutation(s): 0 
Gene Names: AUG5At5g38880K15E6.9
UniProt
Find proteins for Q9FMB4 (Arabidopsis thaliana)
Explore Q9FMB4 
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UniProt GroupQ9FMB4
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
AUGMIN subunit 6D [auth F]328Arabidopsis thalianaMutation(s): 0 
Gene Names: AUG6At5g40740MNF13.29
UniProt
Find proteins for Q94BP7 (Arabidopsis thaliana)
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UniProt GroupQ94BP7
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
AUGMIN subunit 7E [auth G]329Arabidopsis thalianaMutation(s): 0 
Gene Names: AUG7At5g17620K10A8.100
UniProt
Find proteins for Q0WTP1 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
AUGMIN subunit 8F [auth H]165Arabidopsis thalianaMutation(s): 0 
Gene Names: AUG8QWRF8REN2At4g30710T10C21.60
UniProt
Find proteins for Q9SUH5 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein NEDD1G [auth I]310Arabidopsis thalianaMutation(s): 0 
Gene Names: NEDD1GCP-WDAt5g05970K18J17.16
UniProt
Find proteins for B3H5K9 (Arabidopsis thaliana)
Explore B3H5K9 
Go to UniProtKB:  B3H5K9
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UniProt GroupB3H5K9
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2026-01-07
    Type: Initial release
  • Version 1.1: 2026-07-22
    Changes: Data collection, Database references