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

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Basic information

Entry
Database: PDB / ID: 9d2b
TitleSymmetry-expanded reconstruction of augmin T-II bonsai on the microtubule
Components
  • (HAUS augmin like complex subunit ...) x 2
  • HAUS augmin-like complex subunit 8
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
KeywordsCELL CYCLE / Microtubule / augmin / CH / spindle
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
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GUANOSINE-5'-TRIPHOSPHATE / 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 speciesXenopus laevis (African clawed frog)
Bos taurus (domestic cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.08 Å
AuthorsTravis, S.M. / Zhang, R.
Funding support United States, 4items
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, S.M. / Kraus, J. / McManus, C.T. / Golden, J. / Zhang, R. / Petry, S.
History
DepositionAug 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Tubulin alpha-1B chain
B: Tubulin beta-2B chain
A: Tubulin alpha-1B chain
F: HAUS augmin like complex subunit 6 L homeolog isoform X1
G: HAUS augmin like complex subunit 7 S homeolog
H: HAUS augmin-like complex subunit 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)246,20312
Polymers244,5636
Non-polymers1,6406
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 3 types, 4 molecules CABH

#1: Protein Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


Mass: 50204.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: BRAIN / References: UniProt: P81947
#2: Protein Tubulin beta-2B chain


Mass: 49999.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: BRAIN / References: UniProt: Q6B856
#5: Protein HAUS augmin-like complex subunit 8 / HEC1/NDC80-interacting centrosome-associated protein 1 / Sarcoma antigen NY-SAR-48 homolog


Mass: 28742.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: haus8, hice1 / Plasmid: pETDuet-1 / Details (production host): MCS2 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Rosetta2 (DE3) / References: UniProt: Q0IHJ3

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HAUS augmin like complex subunit ... , 2 types, 2 molecules FG

#3: Protein HAUS augmin like complex subunit 6 L homeolog isoform X1


Mass: 33562.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: haus6.L, haus6 / Plasmid: pETDuet-1 / Details (production host): MCS1 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Rosetta2 (DE3) / References: UniProt: A0A8J1MAE8
#4: Protein HAUS augmin like complex subunit 7 S homeolog / LOC100158301 protein


Mass: 31848.111 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: haus7.S, haus7, LOC100158301, uchl5ip, uip1 / Plasmid: pRSFDuet-1 / Details (production host): MCS2 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Rosetta2 (DE3) / References: UniProt: B1H1T5

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Non-polymers , 3 types, 6 molecules

#6: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-G2P / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-CPP, energy-carrying molecule analogue*YM

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Augmin T-II bonsai on the microtubuleCOMPLEXComplex of augmin bound to the microtubule#1-#50MULTIPLE SOURCES
2GMPCPP microtubuleCOMPLEXbovine tubulin polymerized in the presence of GMPCPP#1-#21NATURAL
3augmin T-II bonsaiCOMPLEXtrimeric fragment of Xenopus laevis augmin#3-#51RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
11345 kDa/nmNO
21188 kDa/nmNO
310.092 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDOrgan
32Bos taurus (domestic cattle)9913BRAIN
43Xenopus laevis (African clawed frog)8355
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21 Rosetta 2 (DE3) / Plasmid: pETDuet1/pRSFDuet-1
Buffer solutionpH: 6.8
Buffer component
IDConc.NameFormulaBuffer-ID
10.08 MPIPES1
21 mMEGTA1
31 mMmagnesium chlorideMgCl21
40.05 % v/vTween-201
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 20 uM tubulin, 10 uM augmin T-II bonsai
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 85 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 2000 nm / Cs: 0.1 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 4.1 sec. / Electron dose: 15 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2088
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARCparticle selectioncryoSPARC filament tracer was used to automatically select particle images from templates
2EPUimage acquisition
4CTFFINDCTF correction
7UCSF Chimera6.8model fittingChimera fit_in_map was used for initial rigid body fitting
9cryoSPARCinitial Euler assignmentcryoSPARC heterogeneous refinement was used to assign initial angles
10FREALIGN13final Euler assignmentFREALIGN was used for seam search
12cryoSPARC3D reconstruction
13Coot0.9.8.93model refinementCOOT was used for manual refitting and initial real space refinement
14PHENIX1.17.1-3660model refinementPhenix real space refinement was used for subsequent real space refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 177242
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1772567 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 36.83 / Protocol: FLEXIBLE FIT / Space: REAL
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeChain-IDInitial refinement model-ID
16DPU

6dpu

A6DPUA1
26DPU

6dpu

B6DPUB1
38FCK

8fck

F8FCKF2
48FCK

8fck

G8FCKG2
58FCK

8fck

H8FCKH2
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 36.63 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.010512341
ELECTRON MICROSCOPYf_angle_d0.729716746
ELECTRON MICROSCOPYf_chiral_restr0.04951834
ELECTRON MICROSCOPYf_plane_restr0.00552165
ELECTRON MICROSCOPYf_dihedral_angle_d12.86171692

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