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- EMDB-70593: Symmetry-expanded reconstruction of augmin T-II bonsai on the GTP... -

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Basic information

Entry
Database: EMDB / ID: EMD-70593
TitleSymmetry-expanded reconstruction of augmin T-II bonsai on the GTPgammaS microtubule
Map data
Sample
  • Complex: Augmin T-II bonsai on the microtubule
    • Complex: GTPgammaS microtubule
      • Protein or peptide: Tubulin alpha-1B chain
      • Protein or peptide: Tubulin beta-2B chain
    • Complex: augmin T-II bonsai
      • Protein or peptide: HAUS augmin like complex subunit 6 L homeolog
      • Protein or peptide: HAUS augmin like complex subunit 7 S homeolog
      • Protein or peptide: HAUS augmin-like complex subunit 8
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
KeywordsMicrotubule / augmin / CH / spindle / CELL CYCLE
Function / homology
Function and homology information


HAUS complex / microtubule minus-end binding / microtubule organizing center organization / mitotic spindle microtubule / positive regulation of axon guidance / centrosome cycle / microtubule-based process / spindle assembly / cytoplasmic microtubule / cellular response to interleukin-4 ...HAUS complex / microtubule minus-end binding / microtubule organizing center organization / mitotic spindle microtubule / positive regulation of axon guidance / centrosome cycle / microtubule-based process / spindle assembly / cytoplasmic microtubule / cellular response to interleukin-4 / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / spindle pole / mitotic cell cycle / double-stranded RNA binding / microtubule cytoskeleton / microtubule binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / cilium / protein heterodimerization activity / cell division / GTPase activity / ubiquitin protein ligase binding / centrosome / GTP binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
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 6 N-terminus / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal ...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 6 N-terminus / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
Similarity search - Domain/homology
HAUS augmin like complex subunit 6 L homeolog / HAUS augmin like complex subunit 7 S homeolog / Tubulin alpha-1B chain / HAUS augmin-like complex subunit 8 / Tubulin beta-2B chain
Similarity search - Component
Biological speciesBos taurus (domestic cattle) / Xenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.83 Å
AuthorsTravis SM / Zhang R
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32 GM142149 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99 GM152794 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01 GM138854 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01 GM141100 United States
CitationJournal: Nat Commun / Year: 2025
Title: How augmin establishes the angle of the microtubule branch site.
Authors: Sophie M Travis / Jodi Kraus / Collin T McManus / Kiana Golden / Rui Zhang / Sabine Petry /
Abstract: How microtubules (MTs) are generated in the proper orientation is essential to understanding how the cytoskeleton organizes a cell and MT-dependent events such as cell division. In the spindle, most ...How microtubules (MTs) are generated in the proper orientation is essential to understanding how the cytoskeleton organizes a cell and MT-dependent events such as cell division. In the spindle, most MTs are generated through the branching MT nucleation pathway. In this pathway, new MTs are nucleated from the side of existing MTs and oriented at a shallow angle by the branching factor augmin, ensuring that both MTs have the same polarity. Yet, how augmin binds MTs and sets the branch angle has remained unclear. Here, we report the cryo-electron microscopy structure of an augmin subcomplex on the MT. This structure resembles that of NDC80 bound to the MT, with the conserved CH domain of augmin's Haus6 subunit directly proximal to the MT lattice. We find that the Haus6 CH domain is a bona fide MT binding site that increases augmin's affinity for the MT and helps establish branch angle. A second binding site, located in the disordered N-terminus of Haus8, also establishes branch angle,. Thus, we find that augmin regulates MT branching using two domains, each tuned to modulate MT affinity and MT branch angle. This work expands our mechanistic understanding of branching MT nucleation and thus spindle formation.
History
DepositionMay 12, 2025-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70593.png

Downloads & links

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Map

FileDownload / File: emd_70593.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 540 pix.
= 601.56 Å		1.11 Å/pix.
x 540 pix.
= 601.56 Å		1.11 Å/pix.
x 540 pix.
= 601.56 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.114 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0615
Minimum - Maximum-0.1742363 - 0.56622547
Average (Standard dev.)0.005040041 (±0.04182381)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions540540540
Spacing540540540
CellA=B=C: 601.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70593_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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Additional map: Local-filtered map

Fileemd_70593_additional_1.map
AnnotationLocal-filtered map
Projections & Slices
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Half map: #2

Fileemd_70593_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_70593_half_map_2.map
Projections & Slices
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Sample components

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Entire : Augmin T-II bonsai on the microtubule

EntireName: Augmin T-II bonsai on the microtubule
Components
  • Complex: Augmin T-II bonsai on the microtubule
    • Complex: GTPgammaS microtubule
      • Protein or peptide: Tubulin alpha-1B chain
      • Protein or peptide: Tubulin beta-2B chain
    • Complex: augmin T-II bonsai
      • Protein or peptide: HAUS augmin like complex subunit 6 L homeolog
      • Protein or peptide: HAUS augmin like complex subunit 7 S homeolog
      • Protein or peptide: HAUS augmin-like complex subunit 8
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE

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Supramolecule #1: Augmin T-II bonsai on the microtubule

SupramoleculeName: Augmin T-II bonsai on the microtubule / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 / Details: Complex of augmin bound to the microtubule
Molecular weightTheoretical: 92 KDa

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Supramolecule #2: GTPgammaS microtubule

SupramoleculeName: GTPgammaS microtubule / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Details: bovine tubulin polymerized in the presence of GTPgammaS
Source (natural)Organism: Bos taurus (domestic cattle) / Organ: BRAIN

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Supramolecule #3: augmin T-II bonsai

SupramoleculeName: augmin T-II bonsai / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#5 / Details: trimeric fragment of Xenopus laevis augmin
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Macromolecule #1: Tubulin alpha-1B chain

MacromoleculeName: Tubulin alpha-1B chain / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle) / Organ: BRAIN
Molecular weightTheoretical: 50.204445 KDa
SequenceString: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFLVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE ...String:
MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFLVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE FSIYPAPQVS TAVVEPYNSI LTTHTTLEHS DCAFMVDNEA IYDICRRNLD IERPTYTNLN RLISQIVSSI TA SLRFDGA LNVDLTEFQT NLVPYPRIHF PLATYAPVIS AEKAYHEQLS VAEITNACFE PANQMVKCDP RHGKYMACCL LYR GDVVPK DVNAAIATIK TKRSIQFVDW CPTGFKVGIN YQPPTVVPGG DLAKVQRAVC MLSNTTAIAE AWARLDHKFD LMYA KRAFV HWYVGEGMEE GEFSEAREDM AALEKDYEEV GVDSVEGEGE EEGEEY

UniProtKB: Tubulin alpha-1B chain

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Macromolecule #2: Tubulin beta-2B chain

MacromoleculeName: Tubulin beta-2B chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle) / Organ: Brain
Molecular weightTheoretical: 49.999887 KDa
SequenceString: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEATGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKESESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS ...String:
MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEATGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKESESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS VMPSPKVSDT VVEPYNATLS VHQLVENTDE TYCIDNEALY DICFRTLKLT TPTYGDLNHL VSATMSGVTT CL RFPGQLN ADLRKLAVNM VPFPRLHFFM PGFAPLTSRG SQQYRALTVP ELTQQMFDSK NMMAACDPRH GRYLTVAAIF RGR MSMKEV DEQMLNVQNK NSSYFVEWIP NNVKTAVCDI PPRGLKMSAT FIGNSTAIQE LFKRISEQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY QDATADEQGE FEEEEGEDEA

UniProtKB: Tubulin beta-2B chain

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Macromolecule #3: HAUS augmin like complex subunit 6 L homeolog

MacromoleculeName: HAUS augmin like complex subunit 6 L homeolog / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 33.562742 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MGSSHHHHHH SGRENLYFQG SMQSGSRPHL AWQREHMWLA LQGLGFESGA EAANAGKTLV HVTFGVNMFD KPNKDAFYVV FHFLFGKLD NVRCKEVFRY CWPPLDKKRD AEFRKACCEW LKKISDEVGA GFPQVVASIF LSPGGPKFVH LLYHFARYVM L QHIKRDAD ...String:
MGSSHHHHHH SGRENLYFQG SMQSGSRPHL AWQREHMWLA LQGLGFESGA EAANAGKTLV HVTFGVNMFD KPNKDAFYVV FHFLFGKLD NVRCKEVFRY CWPPLDKKRD AEFRKACCEW LKKISDEVGA GFPQVVASIF LSPGGPKFVH LLYHFARYVM L QHIKRDAD AGNVFISEAL QSKIQDPQKA LARNKLARQK YLKVLQKENL VIEEYQRKAQ LLIKQIRDMR SEHVALQNQQ KL AEKVDRK ISDKDENIQK TRCMWNTIMQ MLKEMEKEVD VVDAVVRGNI DQ

UniProtKB: HAUS augmin like complex subunit 6 L homeolog

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Macromolecule #4: HAUS augmin like complex subunit 7 S homeolog

MacromoleculeName: HAUS augmin like complex subunit 7 S homeolog / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 29.551631 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MAGGTGGKEL GAAVELYERL QMLSCPCLEG VYLTDPQSIY ELLCTPSSHR LDILQWLCSR IYPPVQEQLS SLKESQTDTK VKEIAKLCF DLMLCHFDDL DLIRGHASPF KQISFIGQLL DVIQYPDTIS SNVILESLSH STEKNVVTCI RENEELLKEL F SSPHFQAT ...String:
MAGGTGGKEL GAAVELYERL QMLSCPCLEG VYLTDPQSIY ELLCTPSSHR LDILQWLCSR IYPPVQEQLS SLKESQTDTK VKEIAKLCF DLMLCHFDDL DLIRGHASPF KQISFIGQLL DVIQYPDTIS SNVILESLSH STEKNVVTCI RENEELLKEL F SSPHFQAT LSPECNPWPA DFKPLLNAEE SLQKRATQSS KGKDMSNSVE ALLEISSSLK ALKEECVDLC SSVTDGDKVI QS LRLALTD FHQLTIAFNQ IYANEFQ

UniProtKB: HAUS augmin like complex subunit 7 S homeolog

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Macromolecule #5: HAUS augmin-like complex subunit 8

MacromoleculeName: HAUS augmin-like complex subunit 8 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 28.742902 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MRSMSEAGVA PIEDGSQNSS GGSSGDAALK KSKGGAKVVK SRYMQIGRSK VSKNSLANTT VCSGGKVPER GSGGTPTRRS LAPHKAKIT AAVPLPALDG SIFTKEDLQS TLLDGHRIAR PDLDLSVIND RTLQKITPRP VVTSEQKKPK RDTTPVNLVP E DMVEMIES ...String:
MRSMSEAGVA PIEDGSQNSS GGSSGDAALK KSKGGAKVVK SRYMQIGRSK VSKNSLANTT VCSGGKVPER GSGGTPTRRS LAPHKAKIT AAVPLPALDG SIFTKEDLQS TLLDGHRIAR PDLDLSVIND RTLQKITPRP VVTSEQKKPK RDTTPVNLVP E DMVEMIES QTLLLTYLTI KMQKNLFRLE EKAERNLLLV NDQKDQLQET IHMMKRDLTL LQREERLRDL IEKQDEVLTP VV TSKDPFK DNYTTFATAL DST

UniProtKB: HAUS augmin-like complex subunit 8

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Macromolecule #6: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 2 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

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Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #8: 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE

MacromoleculeName: 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / type: ligand / ID: 8 / Number of copies: 1 / Formula: GSP
Molecular weightTheoretical: 539.246 Da
Chemical component information

ChemComp-GSP:
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 6.8
Component:
ConcentrationNameFormula
0.08 MPIPES
1.0 mMEGTA
1.0 mMmagnesium chlorideMgCl2
0.05 % v/vTween-20
GridModel: Quantifoil / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 10 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.037 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 298 K / Instrument: LEICA EM GP
Details20 uM tubulin, 10 uM augmin T-II bonsai

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 5012 / Average exposure time: 4.1 sec. / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.1 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 17021
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: Both 13-protofilament and 14-protofilament reference models were given, as detailed in Valdez et al 2023 DOI: 10.1101/2023.12.18.571906
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.83 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 99011
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6dpu

chain_id: A, source_name: PDB, initial_model_type: experimental model

6dpu

chain_id: B, source_name: PDB, initial_model_type: experimental model

8fck

chain_id: F, source_name: PDB, initial_model_type: experimental model

8fck

chain_id: G, source_name: PDB, initial_model_type: experimental model

8fck

chain_id: H, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9olh:
Symmetry-expanded reconstruction of augmin T-II bonsai on the GTPgammaS microtubule

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