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- EMDB-46489: Symmetry-expanded reconstruction of augmin T-II bonsai on the mic... -

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Basic information

Entry
Database: EMDB / ID: EMD-46489
TitleSymmetry-expanded reconstruction of augmin T-II bonsai on the microtubule
Map data
Sample
  • Complex: Augmin T-II bonsai on the microtubule
    • Complex: GMPCPP 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 isoform X1
      • 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: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
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 / cytosol / cytoplasm
Similarity search - Function
HAUS augmin-like complex subunit 6 / HAUS augmin-like complex subunit 6, N-terminal / HAUS augmin-like complex subunit 7-like / HAUS augmin-like complex subunit 6 N-terminus / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal ...HAUS augmin-like complex subunit 6 / HAUS augmin-like complex subunit 6, N-terminal / HAUS augmin-like complex subunit 7-like / HAUS augmin-like complex subunit 6 N-terminus / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / 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 isoform X1 / 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: 3.08 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: To Be Published
Title: How augmin establishes the angle of the microtubule branch site
Authors: Travis SM / Kraus J / McManus CT / Golden J / Zhang R / Petry S
History
DepositionAug 8, 2024-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46489.png

Downloads & links

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Map

FileDownload / File: emd_46489.map.gz / Format: CCP4 / Size: 255.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.41 Å/pix.
x 406 pix.
= 570.836 Å		1.41 Å/pix.
x 406 pix.
= 570.836 Å		1.41 Å/pix.
x 406 pix.
= 570.836 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.406 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.121
Minimum - Maximum-0.74149936 - 1.4458637
Average (Standard dev.)0.002991524 (±0.032906726)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions406406406
Spacing406406406
CellA=B=C: 570.836 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_46489_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened map

Fileemd_46489_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_46489_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_46489_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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: GMPCPP 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 isoform X1
      • 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: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER

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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: GMPCPP microtubule

SupramoleculeName: GMPCPP microtubule / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Details: bovine tubulin polymerized in the presence of GMPCPP
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 isoform X1

MacromoleculeName: HAUS augmin like complex subunit 6 L homeolog isoform X1
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 isoform X1

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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: 31.848111 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MADPWSHPQF EKGGTGGKEL GAAVELYERL QMLSCPCLEG VYLTDPQSIY ELLCTPSSHR LDILQWLCSR IYPPVQEQLS SLKESQTDT KVKEIAKLCF DLMLCHFDDL DLIRGHASPF KQISFIGQLL DVIQYPDTIS SNVILESLSH STEKNVVTCI R ENEELLKE ...String:
MADPWSHPQF EKGGTGGKEL GAAVELYERL QMLSCPCLEG VYLTDPQSIY ELLCTPSSHR LDILQWLCSR IYPPVQEQLS SLKESQTDT KVKEIAKLCF DLMLCHFDDL DLIRGHASPF KQISFIGQLL DVIQYPDTIS SNVILESLSH STEKNVVTCI R ENEELLKE LFSSPHFQAT LSPECNPWPA DFKPLLNAEE SLQKRATQSS KGKDMSNSVE ALLEISSSLK ALKEECVDLC SS VTDGDKV IQSLRLALTD FHQLTIAFNQ IYANEFQWSH PQFEK

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: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER

MacromoleculeName: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / type: ligand / ID: 8 / Number of copies: 1 / Formula: G2P
Molecular weightTheoretical: 521.208 Da
Chemical component information

ChemComp-G2P:
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GMP-CPP, energy-carrying molecule analogue*YM

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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 R1.2/1.3 / 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

MicroscopeFEI TITAN KRIOS
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: 2088 / Average exposure time: 4.1 sec. / Average electron dose: 15.0 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: 177242
CTF correctionSoftware - Name: CTFFIND / Type: 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: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1772567
Initial angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC
Software - details: cryoSPARC heterogeneous refinement was used to assign initial angles
Final angle assignmentType: NOT APPLICABLE / Software - Name: FREALIGN (ver. 13) / Software - details: FREALIGN was used for seam search
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: FLEXIBLE FIT / Overall B value: 36.83
Output model

PDB-9d2b:
Symmetry-expanded reconstruction of augmin T-II bonsai on the microtubule

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