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- EMDB-49183: Augmin1345-Extended-Tripod -

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Basic information

Entry
Database: EMDB / ID: EMD-49183
TitleAugmin1345-Extended-Tripod
Map data
Sample
  • Complex: Augmin tetramer complex tripod
    • Protein or peptide: AUGMIN subunit 1
    • Protein or peptide: AUGMIN subunit 4
    • Protein or peptide: AUGMIN subunit 5,Green fluorescent protein
    • Protein or peptide: AUGMIN subunit 3
KeywordsAugmin1345-extended-Tripod / PLANT PROTEIN
Function / homology
Function and homology information


phragmoplast microtubule organization / HAUS complex / phragmoplast / microtubule minus-end binding / spindle assembly / bioluminescence / generation of precursor metabolites and energy / spindle microtubule / spindle / microtubule ...phragmoplast microtubule organization / HAUS complex / phragmoplast / microtubule minus-end binding / spindle assembly / bioluminescence / generation of precursor metabolites and energy / 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 / Green fluorescent protein, GFP ...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 / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
AUGMIN subunit 1 / Green fluorescent protein / AUGMIN subunit 3 / AUGMIN subunit 4 / AUGMIN subunit 5
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress) / Aequorea victoria (jellyfish)
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)NIH-5R01GM110283 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 11, 2025-
Header (metadata) releaseMar 26, 2025-
Map releaseMar 26, 2025-
UpdateMar 26, 2025-
Current statusMar 26, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49183.png

Downloads & links

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Map

FileDownload / File: emd_49183.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 400 pix.
= 352. Å		0.88 Å/pix.
x 400 pix.
= 352. Å		0.88 Å/pix.
x 400 pix.
= 352. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.0005209652 - 2.184774
Average (Standard dev.)0.00057787425 (±0.018655399)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 352.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_49183_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_49183_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Augmin tetramer complex tripod

EntireName: Augmin tetramer complex tripod
Components
  • Complex: Augmin tetramer complex tripod
    • Protein or peptide: AUGMIN subunit 1
    • Protein or peptide: AUGMIN subunit 4
    • Protein or peptide: AUGMIN subunit 5,Green fluorescent protein
    • Protein or peptide: AUGMIN subunit 3

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Supramolecule #1: Augmin tetramer complex tripod

SupramoleculeName: Augmin tetramer complex tripod / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 310 KDa

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Macromolecule #1: AUGMIN subunit 1

MacromoleculeName: AUGMIN subunit 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 33.537996 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSDVTGDLAA VSEAKGGSDA ARISEVKAWL TSQFEAVGKE VPNFEYTHRS ITHLYNLATA SQAKSQAATI VANDFRLKAS EYRAQAARI REILESAGMS QESLPSNVVS SAQVLANVAN LLNIRDTELS SFLVAMGDIS LRKTGVEEKR AKAQKESNAL L DYTRKAIQ ...String:
MSDVTGDLAA VSEAKGGSDA ARISEVKAWL TSQFEAVGKE VPNFEYTHRS ITHLYNLATA SQAKSQAATI VANDFRLKAS EYRAQAARI REILESAGMS QESLPSNVVS SAQVLANVAN LLNIRDTELS SFLVAMGDIS LRKTGVEEKR AKAQKESNAL L DYTRKAIQ RLTYLKKILA QLEDDVVPCE SQMENWKTNL EVMAVKEEQY IQQYKKYEML LNRVGYTPKI SHRELVEMAE HR KELDKMT KPVLDTLRSY QDLPPDKALA ALAIEDKKRQ FTAAEKYLEE VLQSALETND E

UniProtKB: AUGMIN subunit 1

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Macromolecule #2: AUGMIN subunit 4

MacromoleculeName: AUGMIN subunit 4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 47.825855 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MVKALQGAAQ NLPADVNQLI DQLERHCLAP DGSLVTKSVY SDLQLAREEM SRERLRYLEA MAIYCEAVAM VEEYQQAISV ANHGGIRDV QGLYPQLGLK NSPQVYETLE HRLVVAEAAQ KLRLPLISDG GEIHEEEIEK WSILSRSSLD SASTSFTISS T SNSVNYAN ...String:
MVKALQGAAQ NLPADVNQLI DQLERHCLAP DGSLVTKSVY SDLQLAREEM SRERLRYLEA MAIYCEAVAM VEEYQQAISV ANHGGIRDV QGLYPQLGLK NSPQVYETLE HRLVVAEAAQ KLRLPLISDG GEIHEEEIEK WSILSRSSLD SASTSFTISS T SNSVNYAN SSANSVAGGI SLSAVDTDVV GGVPNRFLGI TPAYLSYVQL QNTISMDMAD YQMFLAREIE GRLKEKCDKL AD AIVDDTD SSTGNRNSSA RLPERVKFII EEIERDEAAL REDLYSADRK FAEYYNVLEQ ILGVLIKLVK DLKLEHQHKY NEM QKTWLC KRCETMNAKL RVLENVLLLE TYTPDSISAL HNIRNYLVEA TEEASAAYNK AVTRLREYQG VDPHFDTIAR QYHD IVKKL ENMQWTIHQV EMDLKSHD

UniProtKB: AUGMIN subunit 4

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Macromolecule #3: AUGMIN subunit 5,Green fluorescent protein

MacromoleculeName: AUGMIN subunit 5,Green fluorescent protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Aequorea victoria (jellyfish)
Molecular weightTheoretical: 116.629992 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 SDVSSPLSYQ FNGNGKIGTD THFQGSNNQL LERQ KAHVQ QFLATEDALN KAAEARDLCH KFINRLHGSA DTATHSFVGG TTQSGSNLRQ FELDVWGKER EAAGLRASLN TLLSE IQRL NKLCAERKEA EDSLKKKWKK IEEFDARRSE LETIYTTLLK ANMDAVAFWN QQPLAAREYA SATVIPASEV VVDISN SAK DFIEKEVSAF FQSPDNSLYM LPATPQGLLE SMGANGSTGP EAVAYAEKNA ALLTARAGAR DPSAIPSICR ISAALQY PA GLEGSDASLA SVLESLEFCL RVRGSEACVL EDLAKAIDLV HIRQDLVESG HSLLDHAFRA QQKYERTTNY CLDLASEQ E NTISDQWLPE LRTAVQNAQA SSEHCKYVRG LLDEWWEQPA STVVDWVTVD GQSVAAWQNH VKQLLAFYDK ESLRTGAGA GMVSKGEELF TGVVPILVEL DGDVNGHKFS VSGEGEGDAT YGKLTLKFIC TTGKLPVPWP TLVTTFTYGV QCFSRYPDHM KQHDFFKSA MPEGYVQERT IFFKDDGNYK TRAEVKFEGD TLVNRIELKG IDFKEDGNIL GHKLEYNYNS HNVYIMADKQ K NGIKVNFK IRHNIEDGSV QLADHYQQNT PIGDGPVLLP DNHYLSTQSA LSKDPNEKRD HMVLLEFVTA AGITHGMDEL YK

UniProtKB: AUGMIN subunit 5, Green fluorescent protein

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Macromolecule #4: AUGMIN subunit 3

MacromoleculeName: AUGMIN subunit 3 / type: protein_or_peptide / ID: 4 / 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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5 / Component - Concentration: 50.0 mM / Component - Name: HEPES
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293 K / Instrument: LEICA EM GP

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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: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 5.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 72002
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 10 / Avg.num./class: 12900 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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