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- PDB-5mjs: S. pombe microtubule copolymerized with GTP and Mal3-143 -

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Basic information

Entry
Database: PDB / ID: 5mjs
TitleS. pombe microtubule copolymerized with GTP and Mal3-143
Components
  • Microtubule integrity protein mal3
  • Tubulin alpha-1 chain
  • Tubulin beta chain
KeywordsSTRUCTURAL PROTEIN / Schizosaccharomyces pombe microtubules
Function / homology
Function and homology information


mitotic spindle pole body duplication / dynein-driven meiotic oscillatory nuclear movement / post-anaphase array microtubule end / Platelet degranulation / nuclear migration involved in conjugation with cellular fusion / cortical microtubule / nuclear migration by microtubule mediated pushing forces / cell cortex of cell tip / karyogamy involved in conjugation with cellular fusion / mitotic spindle astral microtubule ...mitotic spindle pole body duplication / dynein-driven meiotic oscillatory nuclear movement / post-anaphase array microtubule end / Platelet degranulation / nuclear migration involved in conjugation with cellular fusion / cortical microtubule / nuclear migration by microtubule mediated pushing forces / cell cortex of cell tip / karyogamy involved in conjugation with cellular fusion / mitotic spindle astral microtubule / nuclear division / mitotic spindle midzone / mitotic spindle pole body / mitotic spindle elongation / protein localization to microtubule / nuclear microtubule / astral microtubule / microtubule plus-end / cytoskeletal anchor activity / attachment of mitotic spindle microtubules to kinetochore / microtubule plus-end binding / microtubule lateral binding / spindle midzone / intracellular distribution of mitochondria / ATPase activator activity / microtubule organizing center / regulation of microtubule polymerization or depolymerization / spindle assembly / cytoplasmic microtubule / cytoplasmic microtubule organization / spindle microtubule / molecular condensate scaffold activity / structural constituent of cytoskeleton / microtubule cytoskeleton organization / spindle / mitotic cell cycle / microtubule cytoskeleton / microtubule binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / hydrolase activity / cell division / response to antibiotic / GTPase activity / GTP binding / metal ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
EB1, C-terminal / Microtubule-associated protein RP/EB / EB1, C-terminal domain superfamily / EB1-C terminal (EB1-C) domain profile. / EB1-like C-terminal motif / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Alpha tubulin ...EB1, C-terminal / Microtubule-associated protein RP/EB / EB1, C-terminal domain superfamily / EB1-C terminal (EB1-C) domain profile. / EB1-like C-terminal motif / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / 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
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin alpha-1 chain / Tubulin beta chain / Microtubule integrity protein mal3
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å
Authorsvon Loeffelholz, O. / Moores, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/L00190X/1 United Kingdom
CitationJournal: Nat Commun / Year: 2017
Title: Nucleotide- and Mal3-dependent changes in fission yeast microtubules suggest a structural plasticity view of dynamics.
Authors: Ottilie von Loeffelholz / Neil A Venables / Douglas Robert Drummond / Miho Katsuki / Robert Cross / Carolyn A Moores /
Abstract: Using cryo-electron microscopy, we characterize the architecture of microtubules assembled from Schizosaccharomyces pombe tubulin, in the presence and absence of their regulatory partner Mal3. Cryo- ...Using cryo-electron microscopy, we characterize the architecture of microtubules assembled from Schizosaccharomyces pombe tubulin, in the presence and absence of their regulatory partner Mal3. Cryo-electron tomography reveals that microtubules assembled from S. pombe tubulin have predominantly B-lattice interprotofilament contacts, with protofilaments skewed around the microtubule axis. Copolymerization with Mal3 favors 13 protofilament microtubules with reduced protofilament skew, indicating that Mal3 adjusts interprotofilament interfaces. A 4.6-Å resolution structure of microtubule-bound Mal3 shows that Mal3 makes a distinctive footprint on the S. pombe microtubule lattice and that unlike mammalian microtubules, S. pombe microtubules do not show the longitudinal lattice compaction associated with EB protein binding and GTP hydrolysis. Our results firmly support a structural plasticity view of microtubule dynamics in which microtubule lattice conformation is sensitive to a variety of effectors and differently so for different tubulins.
History
DepositionDec 1, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB
Revision 1.2Mar 19, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update

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Structure visualization

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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Tubulin beta chain
D: Microtubule integrity protein mal3
E: Tubulin alpha-1 chain
F: Tubulin alpha-1 chain
G: Tubulin alpha-1 chain
H: Tubulin alpha-1 chain
J: Tubulin beta chain
B: Tubulin beta chain
C: Tubulin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)408,55417
Polymers404,6889
Non-polymers3,8668
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34660 Å2
ΔGint-121 kcal/mol
Surface area135090 Å2
MethodPISA

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Components

#1: Protein
Tubulin beta chain / Beta-tubulin


Mass: 47191.031 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: nda3, alp12, SPBC26H8.07c / Production host: Schizosaccharomyces pombe (fission yeast) / References: UniProt: P05219
#2: Protein Microtubule integrity protein mal3


Mass: 16668.900 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: mal3, SPAC18G6.15 / Production host: Escherichia coli (E. coli) / References: UniProt: Q10113
#3: Protein
Tubulin alpha-1 chain


Mass: 49813.832 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: nda2, SPBC16A3.15c / Production host: Schizosaccharomyces pombe (fission yeast) / References: UniProt: P04688
#4: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C10H15N5O11P2
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Production host: Schizosaccharomyces pombe (fission yeast) / Comment: GDP, energy-carrying molecule*YM
#5: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O14P3
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Production host: Schizosaccharomyces pombe (fission yeast) / Comment: GTP, energy-carrying molecule*YM
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Microtubule decorated with Mal3 / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Source (recombinant)Organism: Schizosaccharomyces pombe (fission yeast)
Buffer solutionpH: 6.5
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 30 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM software
IDNameVersionCategory
2FREALIGN8image acquisition
4CTFFIND3CTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10SPIDER14.18initial Euler assignment
11FREALIGN8final Euler assignment
13FREALIGN83D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12763 / Symmetry type: POINT
Atomic model buildingProtocol: BACKBONE TRACE / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0128752
ELECTRON MICROSCOPYf_angle_d1.13139006
ELECTRON MICROSCOPYf_dihedral_angle_d8.58817073
ELECTRON MICROSCOPYf_chiral_restr0.0694200
ELECTRON MICROSCOPYf_plane_restr0.0095117

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