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- EMDB-46488: C1 reconstruction of augmin T-II bonsai on the microtubule -

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Basic information

Entry
Database: EMDB / ID: EMD-46488
TitleC1 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: TUBA1
      • Protein or peptide: TUBB2
    • Complex: augmin T-II bonsai
      • Protein or peptide: HAUS6.L
      • Protein or peptide: HAUS7.S
      • Protein or peptide: HAUS8.L
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: 3.83 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: 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_46488.png

Downloads & links

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Map

FileDownload / File: emd_46488.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.)
1.43 Å/pix.
x 400 pix.
= 570.4 Å		1.43 Å/pix.
x 400 pix.
= 570.4 Å		1.43 Å/pix.
x 400 pix.
= 570.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.426 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.128
Minimum - Maximum-0.24773565 - 0.6826258
Average (Standard dev.)0.0031290553 (±0.04722343)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 570.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_46488_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_46488_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_46488_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: TUBA1
      • Protein or peptide: TUBB2
    • Complex: augmin T-II bonsai
      • Protein or peptide: HAUS6.L
      • Protein or peptide: HAUS7.S
      • Protein or peptide: HAUS8.L

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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: all / 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: TUBA1

MacromoleculeName: TUBA1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle) / Organ: BRAIN
SequenceString: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHPE QLITGKEDAA NNYARGHYTI GKEIIDLVLD RIRKLADQCT GLQGFLVFHS FGGGTGSGFT SLLMERLSVD YGKKSKLEFS ...String:
MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHPE QLITGKEDAA NNYARGHYTI GKEIIDLVLD RIRKLADQCT GLQGFLVFHS FGGGTGSGFT SLLMERLSVD YGKKSKLEFS IYPAPQVSTA VVEPYNSILT THTTLEHSDC AFMVDNEAIY DICRRNLDIE RPTYTNLNRL ISQIVSSITA SLRFDGALNV DLTEFQTNLV PYPRIHFPLA TYAPVISAEK AYHEQLSVAE ITNACFEPAN QMVKCDPRHG KYMACCLLYR GDVVPKDVNA AIATIKTKRS IQFVDWCPTG FKVGINYQPP TVVPGGDLAK VQRAVCMLSN TTAIAEAWAR LDHKFDLMYA KRAFVHWYVG EGMEEGEFSE AREDMAALEK DYEEVGVDSV EGEGEEEGEE Y

UniProtKB: Tubulin alpha-1B chain

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Macromolecule #2: TUBB2

MacromoleculeName: TUBB2 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle) / Organ: BRAIN
SequenceString: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEATGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDNF VFGQSGAGNN WAKGHYTEGA ELVDSVLDVV RKESESCDCL QGFQLTHSLG GGTGSGMGTL LISKIREEYP DRIMNTFSVM ...String:
MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEATGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDNF VFGQSGAGNN WAKGHYTEGA ELVDSVLDVV RKESESCDCL QGFQLTHSLG GGTGSGMGTL LISKIREEYP DRIMNTFSVM PSPKVSDTVV EPYNATLSVH QLVENTDETY CIDNEALYDI CFRTLKLTTP TYGDLNHLVS ATMSGVTTCL RFPGQLNADL RKLAVNMVPF PRLHFFMPGF APLTSRGSQQ YRALTVPELT QQMFDSKNMM AACDPRHGRY LTVAAIFRGR MSMKEVDEQM LNVQNKNSSY FVEWIPNNVK TAVCDIPPRG LKMSATFIGN STAIQELFKR ISEQFTAMFR RKAFLHWYTG EGMDEMEFTE AESNMNDLVS EYQQYQDATA DEQGEFEEEE GEDEA

UniProtKB: Tubulin beta-2B chain

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Macromolecule #3: HAUS6.L

MacromoleculeName: HAUS6.L / type: protein_or_peptide / ID: 3 / Details: N-terminal 6xHis / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MGSSHHHHHH SGRENLYFQG SMQSGSRPHL AWQREHMWLA LQGLGFESGA EAANAGKTLV HVTFGVNMFD KPNKDAFYVV FHFLFGKLDN VRCKEVFRYC WPPLDKKRDA EFRKACCEWL KKISDEVGAG FPQVVASIFL SPGGPKFVHL LYHFARYVML QHIKRDADAG ...String:
MGSSHHHHHH SGRENLYFQG SMQSGSRPHL AWQREHMWLA LQGLGFESGA EAANAGKTLV HVTFGVNMFD KPNKDAFYVV FHFLFGKLDN VRCKEVFRYC WPPLDKKRDA EFRKACCEWL KKISDEVGAG FPQVVASIFL SPGGPKFVHL LYHFARYVML QHIKRDADAG NVFISEALQS KIQDPQKALA RNKLARQKYL KVLQKENLVI EEYQRKAQLL IKQIRDMRSE HVALQNQQKL AEKVDRKISD KDENIQKTRC MWNTIMQMLK EMEKEVDVVD AVVRGNIDQ

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

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Macromolecule #4: HAUS7.S

MacromoleculeName: HAUS7.S / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MADPWSHPQF EKGGTGGKEL GAAVELYERL QMLSCPCLEG VYLTDPQSIY ELLCTPSSHR LDILQWLCSR IYPPVQEQLS SLKESQTDTK VKEIAKLCFD LMLCHFDDLD LIRGHASPFK QISFIGQLLD VIQYPDTISS NVILESLSHS TEKNVVTCIR ENEELLKELF ...String:
MADPWSHPQF EKGGTGGKEL GAAVELYERL QMLSCPCLEG VYLTDPQSIY ELLCTPSSHR LDILQWLCSR IYPPVQEQLS SLKESQTDTK VKEIAKLCFD LMLCHFDDLD LIRGHASPFK QISFIGQLLD VIQYPDTISS NVILESLSHS TEKNVVTCIR ENEELLKELF SSPHFQATLS PECNPWPADF KPLLNAEESL QKRATQSSKG KDMSNSVEAL LEISSSLKAL KEECVDLCSS VTDGDKVIQS LRLALTDFHQ LTIAFNQIYA NEFQWSHPQF EK

UniProtKB: HAUS augmin like complex subunit 7 S homeolog

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Macromolecule #5: HAUS8.L

MacromoleculeName: HAUS8.L / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MRSMSEAGVA PIEDGSQNSS GGSSGDAALK KSKGGAKVVK SRYMQIGRSK VSKNSLANTT VCSGGKVPER GSGGTPTRRS LAPHKAKITA AVPLPALDGS IFTKEDLQST LLDGHRIARP DLDLSVINDR TLQKITPRPV VTSEQKKPKR DTTPVNLVPE DMVEMIESQT ...String:
MRSMSEAGVA PIEDGSQNSS GGSSGDAALK KSKGGAKVVK SRYMQIGRSK VSKNSLANTT VCSGGKVPER GSGGTPTRRS LAPHKAKITA AVPLPALDGS IFTKEDLQST LLDGHRIARP DLDLSVINDR TLQKITPRPV VTSEQKKPKR DTTPVNLVPE DMVEMIESQT LLLTYLTIKM QKNLFRLEEK AERNLLLVND QKDQLQETIH MMKRDLTLLQ REERLRDLIE KQDEVLTPVV TSKDPFKDNY TTFATALDST

UniProtKB: HAUS augmin-like complex subunit 8

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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

MicroscopeFEI TITAN 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: 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: 3.83 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 136352
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

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