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- PDB-9nbd: AUGMIN Dimer -

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Basic information

Entry
Database: PDB / ID: 9nbd
TitleAUGMIN Dimer
Components
  • AUGMIN subunit 1
  • AUGMIN subunit 3
  • AUGMIN subunit 4
  • AUGMIN subunit 5
KeywordsPLANT PROTEIN / Augmin1345-Dimer
Function / homology
Function and homology information


phragmoplast microtubule organization / HAUS complex / phragmoplast / microtubule minus-end binding / spindle assembly / spindle microtubule / spindle / microtubule / cell division / nucleus
Similarity search - Function
AUGMIN subunit 5, plant / HAUS augmin-like complex subunit 1 / HAUS augmin-like complex subunit 4 / HAUS augmin-like complex subunit 4 / HAUS augmin-like complex subunit 5 / HAUS augmin-like complex subunit 5 / HAUS augmin-like complex subunit 3 / HAUS augmin-like complex subunit 3, N-terminal / HAUS augmin-like complex subunit 3
Similarity search - Domain/homology
AUGMIN subunit 1 / AUGMIN subunit 3 / AUGMIN subunit 4 / AUGMIN subunit 5
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.1 Å
AuthorsAshaduzzaman, M. / Al-Bassam, J. / Taheri, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)5R01 GM110283 United States
CitationJournal: bioRxiv / Year: 2025
Title: Cryo-EM structures of the Plant Augmin reveal its intertwined coiled-coil assembly, antiparallel dimerization and NEDD1 binding mechanisms.
Authors: Md Ashaduzzaman / Aryan Taheri / Yuh-Ru Julie Lee / Yuqi Tang / Fei Guo / Stephen D Fried / Bo Liu / Jawdat Al-Bassam /
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 ...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.
History
DepositionFeb 13, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AUGMIN subunit 1
D: AUGMIN subunit 4
E: AUGMIN subunit 5
C: AUGMIN subunit 3
M: AUGMIN subunit 1
N: AUGMIN subunit 4
O: AUGMIN subunit 5
P: AUGMIN subunit 3


Theoretical massNumber of molelcules
Total (without water)470,9988
Polymers470,9988
Non-polymers00
Water00
1


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

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Components

#1: Protein AUGMIN subunit 1


Mass: 33537.996 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AUG1, At2g41350, F13H10.10 / Production host: Escherichia coli (E. coli) / References: UniProt: F4IK01
#2: Protein AUGMIN subunit 4


Mass: 47825.855 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AUG4, At1g50710, F17J6.23, F4M15.6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8GYM3
#3: Protein AUGMIN subunit 5


Mass: 84325.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AUG5, At5g38880, K15E6.9 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FMB4
#4: Protein AUGMIN subunit 3


Mass: 69809.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AUG3, At5g48520, MJE7.16 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0WQE7
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Augmin Dimer / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.99 MDa / Experimental value: YES
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Buffer componentConc.: 50 mM / Name: HEPES
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 293 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21_5207 / Category: model refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 8.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6578 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 1900.42 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00322900
ELECTRON MICROSCOPYf_angle_d0.749330961
ELECTRON MICROSCOPYf_chiral_restr0.04443512
ELECTRON MICROSCOPYf_plane_restr0.00514065
ELECTRON MICROSCOPYf_dihedral_angle_d6.50053141

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