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- EMDB-49225: Augmin/V junction(closed) -

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Basic information

Entry
Database: EMDB / ID: EMD-49225
TitleAugmin/V junction(closed)
Map data
Sample
  • Complex: AUGMIN/V junction(close)
    • Protein or peptide: AUGMIN subunit 2
    • Protein or peptide: AUGMIN subunit 3
    • Protein or peptide: AUGMIN subunit 5
    • Protein or peptide: AUGMIN subunit 6
    • Protein or peptide: AUGMIN subunit 7
    • Protein or peptide: AUGMIN subunit 8
KeywordsAugmin complex / PLANT PROTEIN
Function / homology
Function and homology information


megagametogenesis / microgametogenesis / cytokinesis by cell plate formation / phragmoplast microtubule organization / HAUS complex / phragmoplast / microtubule minus-end binding / microtubule organizing center organization / microtubule nucleation / spindle assembly ...megagametogenesis / microgametogenesis / cytokinesis by cell plate formation / phragmoplast microtubule organization / HAUS complex / phragmoplast / microtubule minus-end binding / microtubule organizing center organization / microtubule nucleation / spindle assembly / spindle microtubule / microtubule cytoskeleton organization / spindle / mitotic cell cycle / microtubule / cell division / nucleus
Similarity search - Function
QWRF family / Plant AUGMIN subunit 7 / QWRF family / Plant nuclear matrix protein 1 (NMP1) / AUGMIN subunit 5, plant / HAUS augmin-like complex subunit 6 / HAUS augmin-like complex subunit 6, N-terminal / HAUS augmin-like complex subunit 2 / HAUS augmin-like complex subunit 7-like / HAUS augmin-like complex subunit 6 N-terminus ...QWRF family / Plant AUGMIN subunit 7 / QWRF family / Plant nuclear matrix protein 1 (NMP1) / AUGMIN subunit 5, plant / HAUS augmin-like complex subunit 6 / HAUS augmin-like complex subunit 6, N-terminal / HAUS augmin-like complex subunit 2 / HAUS augmin-like complex subunit 7-like / HAUS augmin-like complex subunit 6 N-terminus / HAUS augmin-like complex subunit 2 / 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 2 / AUGMIN subunit 3 / AUGMIN subunit 7 / AUGMIN subunit 6 / AUGMIN subunit 5 / AUGMIN subunit 8
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.9 Å
AuthorsAshaduzzaman M / Al-Bassam J / Taheri A
Funding support United States, 1 items
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, 2025-
Header (metadata) releaseMar 19, 2025-
Map releaseMar 19, 2025-
UpdateMar 19, 2025-
Current statusMar 19, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49225.png

Downloads & links

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Map

FileDownload / File: emd_49225.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.76 Å/pix.
x 250 pix.
= 440. Å		1.76 Å/pix.
x 250 pix.
= 440. Å		1.76 Å/pix.
x 250 pix.
= 440. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.76 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.001776573 - 1.7302915
Average (Standard dev.)0.00058896095 (±0.017529555)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 440.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_49225_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_49225_half_map_2.map
Projections & Slices
AxesZYX

Projections

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Histogram

Histogram (log scale)

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Sample components

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Entire : AUGMIN/V junction(close)

EntireName: AUGMIN/V junction(close)
Components
  • Complex: AUGMIN/V junction(close)
    • Protein or peptide: AUGMIN subunit 2
    • Protein or peptide: AUGMIN subunit 3
    • Protein or peptide: AUGMIN subunit 5
    • Protein or peptide: AUGMIN subunit 6
    • Protein or peptide: AUGMIN subunit 7
    • Protein or peptide: AUGMIN subunit 8

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Supramolecule #1: AUGMIN/V junction(close)

SupramoleculeName: AUGMIN/V junction(close) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: AUGMIN subunit 2

MacromoleculeName: AUGMIN subunit 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 33.057941 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSMGGDTTWV GKKPIRRIGG LSDALSIASD LGFAVAPPPS QEELQSFASS NGERGDDLIR VLRELSVVQR KIADLQVELQ GRKDDKNVA HLTHVGEMQK KIETLSRITQ ILKDVIQNKD RIIARLQQPY SLDCIPVEAE YQKQFSELLM KAASDYGALT A SVSDFQWS ...String:
MSMGGDTTWV GKKPIRRIGG LSDALSIASD LGFAVAPPPS QEELQSFASS NGERGDDLIR VLRELSVVQR KIADLQVELQ GRKDDKNVA HLTHVGEMQK KIETLSRITQ ILKDVIQNKD RIIARLQQPY SLDCIPVEAE YQKQFSELLM KAASDYGALT A SVSDFQWS QNFKEPPSVW GEMLRPIPVA LASCTRFFEA MSAMRESFAT LQELRVGNSA VSLPTTPGGN EMTHRDSDCV TP PQGRIES SFDDLAVHKT RRQNNDQNEE EEEEEEEEDG NNNGNRRLSW PPSVKKSSV

UniProtKB: AUGMIN subunit 2

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Macromolecule #2: AUGMIN subunit 3

MacromoleculeName: AUGMIN subunit 3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 69.809453 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSSARLCSLV AELGYEGAGK LDPDSFEWPF QYDDARPILD WICSSLRPSN VLSLAELSLY EQFQRDGKLL EGDDLDQAYD SISAFSSRR NNQEAVFGAE ESIKEVRDAT LAHKAEALEL QRQLRRLQTQ YDLLTGQSSA LIQGRRARVA ATSAVSGQIT A IEDSLSAR ...String:
MSSARLCSLV AELGYEGAGK LDPDSFEWPF QYDDARPILD WICSSLRPSN VLSLAELSLY EQFQRDGKLL EGDDLDQAYD SISAFSSRR NNQEAVFGAE ESIKEVRDAT LAHKAEALEL QRQLRRLQTQ YDLLTGQSSA LIQGRRARVA ATSAVSGQIT A IEDSLSAR NLQMNGVLGR LASTSQELAH YHSGEEDGIY LAYSDFHAYL AGDSACTKEL NQWFAKQLDT GPYRLVAEEG KS KCSWVSL DDTSNMLRDL EKSQHQRVAE LQRLRSIFGT SERQWIEAQV ENAKQQAILL TLKSQVTSVE AHIHFDLHSL RRK HADLVE EISTLYQKEE KLLSETIPEL CWELAQLQDT YILQGDYDLK VMRQELYISK QKVFINHLVN QLARHQFLKL ACQL EKKNM LGAFSLLKVI ESELQGYLSA TRSRVGRCSA LIQAASDVQE QGAVDDRDSF LHGVRDLLSI HSNTQAGLST YVSAP AIIQ QIVALQSDLS SLQSDLENSL PDDRNRCINE LCTHIQNLQQ LLFASSTTAQ PILTPWPLMK ELDEMGKINS KLSTAV EEV TLEHRNKREI VKHHAKDVEL QRRVFVDFFC NPERLRNQVR ELNALVRARQ ASSS

UniProtKB: AUGMIN subunit 3

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Macromolecule #3: AUGMIN subunit 5

MacromoleculeName: AUGMIN subunit 5 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 84.325758 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MQSLSSSAPT PEAILEWLQK EMGYRQLGPY NGSSKSHVPS IDAIRKICRG NMIPIWNFLI NRVKSEKTVE RIRRNITVHG GSSNASIGS SVNPGKEESK SKGRRKDKTV TGESSSYAED REAALQEREL AAKEVERLRN IVRRQRKDLK ARMLEVSREE A ERKRMLDE ...String:
MQSLSSSAPT PEAILEWLQK EMGYRQLGPY NGSSKSHVPS IDAIRKICRG NMIPIWNFLI NRVKSEKTVE RIRRNITVHG GSSNASIGS SVNPGKEESK SKGRRKDKTV TGESSSYAED REAALQEREL AAKEVERLRN IVRRQRKDLK ARMLEVSREE A ERKRMLDE RANYRHKQAL LEAYDQQCDE ATRIFAEYHK RLQVYVNQAN DAQRSVNSSN EVLSSLSANS EREAVYSTVK GT KSADDVI LMETTRERNI RIVCDLLASR MIERIRNSFP AYEGNGICSL PELETAKLGF EYDGEITDEM KTVIVNSLRG PPL LLQAIA AYTLRIKTLI SREMEKIDVR ADAEMLRYKF ENNRVTDNSS SDVSSPSNNQ LLERQKAHVQ QFLATEDALN KAAE ARDLC HKFINRLHGS ADTATHSFVG GTTQSGSNLR QFELDVWGKE REAAGLRASL NTLLSEIQRL NKLCAERKEA EDSLK KKWK KIEEFDARRS ELETIYTTLL KANMDAVAFW NQQPLAAREY ASATVIPASE VVVDISNSAK DFIEKEVSAF FQSPDN SLY MLPATPQGLA RDPSAIPSIC RISAALQYPA GLEGSDASLA SVLESLEFCL RVRGSEACVL EDLAKAIDLV HIRQDLV ES GHSLLDHAFR AQQKYERTTN YCLDLASEQE NTISDQWLPE LRTAVQNAQA SSEHCKYVRG LLDEWWEQPA STVVDWVT V DGQSVAAWQN HVKQLLAFYD KESLRT

UniProtKB: AUGMIN subunit 5

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Macromolecule #4: AUGMIN subunit 6

MacromoleculeName: AUGMIN subunit 6 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 43.303605 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTMDREKERE LELESAMYTN CLLLGLDPNV IGLGASNGTP RVGLFRHSNP KLGEQLLYFI LSSLRGPAQS SKDFDKVWPI FDSAQSRDF RKVVQAIISE LESQGALPRS NSRVSSLATC CGPRFVELLW QLSLHALREV HRRTFPADVA SNPLPSSLTD V SFSHAATL ...String:
MTMDREKERE LELESAMYTN CLLLGLDPNV IGLGASNGTP RVGLFRHSNP KLGEQLLYFI LSSLRGPAQS SKDFDKVWPI FDSAQSRDF RKVVQAIISE LESQGALPRS NSRVSSLATC CGPRFVELLW QLSLHALREV HRRTFPADVA SNPLPSSLTD V SFSHAATL LPVTKARIVL ERRRFLKNAE TAVQRQAMWS NLAHEMTAEF RGLCAEEAYL QQELEKLNDL RNKVKQEGEV WD DLVSSSS QNSHLVSKAT RLWDSIMARK GQHEVLASGP IEDLIAHREH RYRISGSALL AAMDQSSQVP RAELLSAHSD DSA SLADDK ELSDGSYTNM HDHSLVDSFE TASSQASDET LSRVDDRGGK INQTVDVAEV IRRWTHALQR I

UniProtKB: AUGMIN subunit 6

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Macromolecule #5: AUGMIN subunit 7

MacromoleculeName: AUGMIN subunit 7 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 37.046961 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAAKQMEEIQ KKLRLLSYPR ANAPAQSLLF AGMERYALLE WLFFKLLGDK SPFSQQNLQG DAGVRDEETV RIQYLAEIAK FLGITPTVD IEAIQGHGTY EDRMEMLRNI VDLVEASLFS DNQEWSIDEQ VAKDIQLIDA IAERQSLIFS EECKLFPADV Q IQSIYPLP ...String:
MAAKQMEEIQ KKLRLLSYPR ANAPAQSLLF AGMERYALLE WLFFKLLGDK SPFSQQNLQG DAGVRDEETV RIQYLAEIAK FLGITPTVD IEAIQGHGTY EDRMEMLRNI VDLVEASLFS DNQEWSIDEQ VAKDIQLIDA IAERQSLIFS EECKLFPADV Q IQSIYPLP DVSELETKLS EQAKILSNLQ QKVDDLAAKH AYNPDEEYTE VESQLRARLE SFLETARAFN TIYTKEIRPW TH MMEVPQL HGFGPAANRL LEAYNMLLKF LGNLKNLRDS HAALSIGSSG TVAGEPSSVT RIVSDCEAAL TVLNRDLGIL SAS IAREQG ERL

UniProtKB: AUGMIN subunit 7

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Macromolecule #6: AUGMIN subunit 8

MacromoleculeName: AUGMIN subunit 8 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 31.372709 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKSSEDQVDP RLIDGKGSGR PSTPPSRGIS PSRIRQTTTS TQSSTTTSVL SFITDVKKGK KASYIEDVHQ LRLLHNRYLQ WRFAIARAE SVMYIQRLTS EETLFNVWHA ISELQDHVTR QRIGLQQLKL EIKLNSLLND QMVSLEDWAT LERDHVSSLV G AISDLEAN ...String:
MKSSEDQVDP RLIDGKGSGR PSTPPSRGIS PSRIRQTTTS TQSSTTTSVL SFITDVKKGK KASYIEDVHQ LRLLHNRYLQ WRFAIARAE SVMYIQRLTS EETLFNVWHA ISELQDHVTR QRIGLQQLKL EIKLNSLLND QMVSLEDWAT LERDHVSSLV G AISDLEAN TLRLPATGGT KADTESLKAA MSSALDVMQA MGSSIWSLLS KVEEMNIMVT ELAVVVTKES SMQGKCEDLL AS TAIMQIE ECSLRTHLIQ TRREEGEDAE TPPPLLPLSK FPWP

UniProtKB: AUGMIN subunit 8

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
SoftwareName: SerialEM
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm

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Image processing

Startup modelType of model: OTHER / Details: abinitio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 18243
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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