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- EMDB-8997: 13-pf 3-start GMPCPP-human alpha1B/beta3 microtubules decorated w... -

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Entry
Database: EMDB / ID: 8997
Title13-pf 3-start GMPCPP-human alpha1B/beta3 microtubules decorated with kinesin-1 motor domain
Map data13-PF 3-start GMPCPP-human alpha1B/beta3 microtubules decorated with kinesin-1 motor domain.
Sample13-pf 3-start GMPCPP-human alpha1B/beta3 microtubule decorated with kinesin-1 motor domain:
Tubulin beta-3 chain / Tubulin alpha-1B chain / (ligand) x 3
Function / homologyTubulin/FtsZ, GTPase domain superfamily / Tubulin/FtsZ, C-terminal domain superfamily / Beta tubulin / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, C-terminal / Beta tubulin, autoregulation binding site / Tubulin, conserved site / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin, C-terminal / Recruitment of NuMA to mitotic centrosomes ...Tubulin/FtsZ, GTPase domain superfamily / Tubulin/FtsZ, C-terminal domain superfamily / Beta tubulin / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, C-terminal / Beta tubulin, autoregulation binding site / Tubulin, conserved site / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin, C-terminal / Recruitment of NuMA to mitotic centrosomes / Tubulin/FtsZ family, GTPase domain / Tubulin / Tubulin C-terminal domain / Tubulin subunits alpha, beta, and gamma signature. / Tubulin-beta mRNA autoregulation signal. / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Gap junction assembly / MHC class II antigen presentation / Separation of Sister Chromatids / Alpha tubulin / Resolution of Sister Chromatid Cohesion / HSP90 chaperone cycle for steroid hormone receptors (SHR) / Prefoldin mediated transfer of substrate to CCT/TriC / Kinesins / Carboxyterminal post-translational modifications of tubulin / The role of GTSE1 in G2/M progression after G2 checkpoint / Mitotic Prometaphase / COPI-independent Golgi-to-ER retrograde traffic / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / RHO GTPases Activate Formins / RHO GTPases activate IQGAPs / Intraflagellar transport / Cilium Assembly / Hedgehog 'off' state / Recycling pathway of L1 / Post-chaperonin tubulin folding pathway / Formation of tubulin folding intermediates by CCT/TriC / cytoskeleton-dependent intracellular transport / cytoplasmic microtubule / cellular response to interleukin-4 / microtubule-based process / microtubule cytoskeleton organization / structural constituent of cytoskeleton / microtubule cytoskeleton / double-stranded RNA binding / axon guidance / microtubule / GTPase activity / cell division / membrane raft / myelin sheath / axon / dendrite / GTP binding / ubiquitin protein ligase binding / structural molecule activity / extracellular exosome / nucleus / cytoplasm / Tubulin alpha-1B chain / Tubulin beta-3 chain
Function and homology information
SourceHomo sapiens (human)
Methodhelical reconstruction / cryo EM / 3.5 Å resolution
AuthorsTi SC / Alushin GM / Kapoor TM
CitationJournal: Dev. Cell / Year: 2018
Title: Human β-Tubulin Isotypes Can Regulate Microtubule Protofilament Number and Stability.
Authors: Shih-Chieh Ti / Gregory M Alushin / Tarun M Kapoor
Abstract: Cell biological studies have shown that protofilament number, a fundamental feature of microtubules, can correlate with the expression of different tubulin isotypes. However, it is not known if ...Cell biological studies have shown that protofilament number, a fundamental feature of microtubules, can correlate with the expression of different tubulin isotypes. However, it is not known if tubulin isotypes directly control this basic microtubule property. Here, we report high-resolution cryo-EM reconstructions (3.5-3.65 Å) of purified human α1B/β3 and α1B/β2B microtubules and find that the β-tubulin isotype can determine protofilament number. Comparisons of atomic models of 13- and 14-protofilament microtubules reveal how tubulin subunit plasticity, manifested in "accordion-like" distributed structural changes, can accommodate distinct lattice organizations. Furthermore, compared to α1B/β3 microtubules, α1B/β2B filaments are more stable to passive disassembly and against depolymerization by MCAK or chTOG, microtubule-associated proteins with distinct mechanisms of action. Mixing tubulin isotypes in different proportions results in microtubules with protofilament numbers and stabilities intermediate to those of isotypically pure filaments. Together, our findings indicate that microtubule protofilament number and stability can be controlled through β-tubulin isotype composition.
Validation ReportPDB-ID: 6e7b

SummaryFull reportAbout validation report
DateDeposition: Jul 25, 2018 / Header (metadata) release: Oct 10, 2018 / Map release: Oct 10, 2018 / Last update: Oct 10, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6e7b
  • Surface level: 5
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6e7b
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8997.map.gz (map file in CCP4 format, 536871 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
512 pix
1 Å/pix.
= 512. Å
512 pix
1 Å/pix.
= 512. Å
512 pix
1 Å/pix.
= 512. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density
Contour Level:5.0 (by author), 5 (movie #1):
Minimum - Maximum-18.715328 - 31.460293
Average (Standard dev.)0.20372319 (1.2161404)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions512512512
Origin-256.0-256.0-256.0
Limit255.0255.0255.0
Spacing512512512
CellA=B=C: 512.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z512.000512.000512.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-256-256-256
NC/NR/NS512512512
D min/max/mean-18.71531.4600.204

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Supplemental data

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Sample components

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Entire 13-pf 3-start GMPCPP-human alpha1B/beta3 microtubule decorated wi...

EntireName: 13-pf 3-start GMPCPP-human alpha1B/beta3 microtubule decorated with kinesin-1 motor domain
Number of components: 6

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Component #1: protein, 13-pf 3-start GMPCPP-human alpha1B/beta3 microtubule dec...

ProteinName: 13-pf 3-start GMPCPP-human alpha1B/beta3 microtubule decorated with kinesin-1 motor domain
Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #2: protein, Tubulin beta-3 chain

ProteinName: Tubulin beta-3 chain / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 47.761508 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #3: protein, Tubulin alpha-1B chain

ProteinName: Tubulin alpha-1B chain / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 48.611582 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #4: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #5: ligand, PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER

LigandName: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.521208 kDa

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Component #6: ligand, GUANOSINE-5'-TRIPHOSPHATE

LigandName: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.52318 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: helical array / Method: cryo EM
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 9.474 Å / Delta phi: -27.66 deg.
Sample solutionpH: 6.8
Support filmunspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.6 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionSoftware: FREALIGN / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Refinement space: RECIPROCAL
Input PDB model: 3JAT
Output model

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