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- PDB-9pzm: Augmin V junction with NEDD1 (WD) -

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Basic information

Entry
Database: PDB / ID: 9pzm
TitleAugmin V junction with NEDD1 (WD)
Components
  • (AUGMIN subunit ...) x 6
  • Protein NEDD1
KeywordsPLANT PROTEIN / Microtubule nucleator
Function / homology
Function and homology information


gamma-tubulin complex binding / regulation of phragmoplast microtubule organization / megagametogenesis / microgametogenesis / cell plate assembly / cytokinesis by cell plate formation / phragmoplast microtubule organization / HAUS complex / embryo sac development / regulation of microtubule nucleation ...gamma-tubulin complex binding / regulation of phragmoplast microtubule organization / megagametogenesis / microgametogenesis / cell plate assembly / cytokinesis by cell plate formation / phragmoplast microtubule organization / HAUS complex / embryo sac development / regulation of microtubule nucleation / microtubule minus-end binding / phragmoplast / pollen development / microtubule organizing center organization / kinetochore microtubule / microtubule nucleation / positive regulation of cytokinesis / microtubule organizing center / spindle assembly / regulation of mitotic spindle organization / spindle microtubule / kinetochore / microtubule cytoskeleton organization / spindle / nuclear envelope / mitotic cell cycle / microtubule / cell division / nucleus
Similarity search - Function
Protein NEDD1 / QWRF family / Plant AUGMIN subunit 7 / QWRF family / Plant nuclear matrix protein 1 (NMP1) / AUGMIN subunit 5, plant / HAUS augmin-like complex subunit 2 / HAUS augmin-like complex subunit 2 / HAUS augmin-like complex subunit 7-like / HAUS augmin-like complex subunit 6 ...Protein NEDD1 / QWRF family / Plant AUGMIN subunit 7 / QWRF family / Plant nuclear matrix protein 1 (NMP1) / AUGMIN subunit 5, plant / HAUS augmin-like complex subunit 2 / HAUS augmin-like complex subunit 2 / HAUS augmin-like complex subunit 7-like / HAUS augmin-like complex subunit 6 / HAUS augmin-like complex subunit 6, N-terminal / HAUS augmin-like complex subunit 5 / HAUS augmin-like complex subunit 6 N-terminus / 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 / WD domain, G-beta repeat / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Protein NEDD1 / AUGMIN subunit 2 / AUGMIN subunit 3 / AUGMIN subunit 7 / AUGMIN subunit 6 / AUGMIN subunit 5 / AUGMIN subunit 8
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8 Å
AuthorsAshaduzzaman, M. / Al-Bassam, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Augmin(top) with NEDD1 (wd40)
Authors: Ashaduzzaman, M. / Al-Bassam, J.
History
DepositionAug 11, 2025Deposition site: RCSB / Processing site: RCSB
SupersessionJan 7, 2026ID: 9NBI
Revision 1.0Jan 7, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 7, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 7, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 7, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 7, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 7, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: AUGMIN subunit 2
C: AUGMIN subunit 3
E: AUGMIN subunit 5
F: AUGMIN subunit 6
G: AUGMIN subunit 7
H: AUGMIN subunit 8
I: Protein NEDD1


Theoretical massNumber of molelcules
Total (without water)299,6637
Polymers299,6637
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

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AUGMIN subunit ... , 6 types, 6 molecules BCEFGH

#1: Protein AUGMIN subunit 2


Mass: 16952.092 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AUG2, At2g32980, T21L14.8 / Production host: Escherichia coli (E. coli) / References: UniProt: O48767
#2: Protein AUGMIN subunit 3


Mass: 69809.453 Da / Num. of mol.: 1
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
#3: Protein AUGMIN subunit 5


Mass: 87230.984 Da / Num. of mol.: 1
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 6


Mass: 36708.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AUG6, At5g40740, MNF13.29 / Production host: Escherichia coli (E. coli) / References: UniProt: Q94BP7
#5: Protein AUGMIN subunit 7


Mass: 37046.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AUG7, At5g17620, K10A8.100 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0WTP1
#6: Protein AUGMIN subunit 8 / QWRF motif-containing protein 8 / ROP1 enhancer 2


Mass: 18658.330 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AUG8, QWRF8, REN2, At4g30710, T10C21.60 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SUH5

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Protein , 1 types, 1 molecules I

#7: Protein Protein NEDD1 / Neural precursor cell expressed developmentally down-regulated protein 1 homolog / Protein GCP-WD


Mass: 33256.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: NEDD1, GCP-WD, At5g05970, K18J17.16 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: B3H5K9

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Details

Has protein modificationN

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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 NEDD1 complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: 2500 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 0.8 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21_5207model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49000 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 379.77 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00314331
ELECTRON MICROSCOPYf_angle_d0.708519367
ELECTRON MICROSCOPYf_chiral_restr0.04342187
ELECTRON MICROSCOPYf_plane_restr0.00532516
ELECTRON MICROSCOPYf_dihedral_angle_d5.77781937

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