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- PDB-3edl: Kinesin13-Microtubule Ring complex -

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Basic information

Entry
Database: PDB / ID: 3edl
TitleKinesin13-Microtubule Ring complex
Components
  • (Tubulin alpha-1A ...) x 2
  • Beta tubulin
  • Kinesin-like protein KIF2C
KeywordsSTRUCTURAL PROTEIN / Kinesin / Kinesin13 / Kin-I / M-Kinesin / Microtubule / Tubulin / depolymerization
Function / homology
Function and homology information


regulation of chromosome segregation / metaphase chromosome alignment / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / establishment or maintenance of microtubule cytoskeleton polarity / Kinesins / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / RHO GTPases Activate Formins / COPI-dependent Golgi-to-ER retrograde traffic ...regulation of chromosome segregation / metaphase chromosome alignment / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / establishment or maintenance of microtubule cytoskeleton polarity / Kinesins / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / RHO GTPases Activate Formins / COPI-dependent Golgi-to-ER retrograde traffic / Separation of Sister Chromatids / microtubule plus-end / attachment of mitotic spindle microtubules to kinetochore / MHC class II antigen presentation / microtubule plus-end binding / microtubule depolymerization / kinesin complex / microtubule motor activity / mitotic metaphase chromosome alignment / microtubule-based movement / chromosome, centromeric region / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / spindle / microtubule cytoskeleton organization / kinetochore / microtubule cytoskeleton / mitotic cell cycle / microtubule binding / microtubule / hydrolase activity / cell division / GTPase activity / centrosome / GTP binding / ATP hydrolysis activity / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin ...Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Chem-CN2 / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / TAXOL / Tubulin alpha-1A chain / Tubulin beta chain / Tubulin alpha-1D chain / Kinesin-like protein KIF2C
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Bos taurus (cattle)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 28 Å
AuthorsTan, D. / Rice, W.J. / Sosa, H.
CitationJournal: Structure / Year: 2008
Title: Structure of the kinesin13-microtubule ring complex.
Authors: Dongyan Tan / William J Rice / Hernando Sosa /
Abstract: To investigate the mechanism of kinesin13-induced microtubule depolymerization, we have calculated a three-dimensional (3D) map of the kinesin13-microtubule ring complex, using cryo-electron ...To investigate the mechanism of kinesin13-induced microtubule depolymerization, we have calculated a three-dimensional (3D) map of the kinesin13-microtubule ring complex, using cryo-electron microscopy (cryo-EM) and image analysis. An atomic model of the complex was produced by docking the crystal structures of tubulin and a kinesin13 motor domain (MD) into the 3D map. The model reveals a snapshot of the depolymerization mechanism by providing a 3D view of the complex formed between the kinesin13 MD and a curved tubulin protofilament (pf). It suggests that contacts mediated by kinesin13 class-specific residues in the putative microtubule-binding site stabilize intra-dimer tubulin curvature. In addition, a tubulin-binding site on the kinesin13 MD was identified. Mutations at this class-conserved site selectively disrupt the formation of microtubule-associated ring complexes.
History
DepositionSep 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 18, 2018Group: Author supporting evidence / Data collection
Category: em_image_scans / em_single_particle_entity / em_software
Item: _em_software.image_processing_id
Revision 1.3Jun 24, 2020Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / entity_src_nat / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.pdbx_beg_seq_num ..._entity.pdbx_description / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_seq_type
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: Tubulin alpha-1A chain
B: Beta tubulin
D: Kinesin-like protein KIF2C
F: Tubulin alpha-1A chain
G: Beta tubulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,02116
Polymers237,1595
Non-polymers3,86311
Water1,928107
1
A: Tubulin alpha-1A chain
B: Beta tubulin
D: Kinesin-like protein KIF2C
F: Tubulin alpha-1A chain
G: Beta tubulin
hetero molecules
x 33


Theoretical massNumber of molelcules
Total (without water)7,953,707528
Polymers7,826,238165
Non-polymers127,469363
Water1,18966
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
helical symmetry operation32
2


  • Idetical with deposited unit
  • helical asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • helical asymmetric unit, std helical frame
TypeNameSymmetry operationNumber
transform to helical frame1
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 33 / Rise per n subunits: 5.506 Å / Rotation per n subunits: 168.1 °)

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Components

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Tubulin alpha-1A ... , 2 types, 2 molecules AF

#1: Protein Tubulin alpha-1A chain / / Alpha-tubulin 1 / Tubulin alpha-1 chain


Mass: 50107.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: brain / References: UniProt: P02550
#4: Protein Tubulin alpha-1A chain / / Alpha-tubulin 1 / Tubulin alpha-1 chain


Mass: 50163.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: brain / References: UniProt: P02550

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Protein , 2 types, 3 molecules BGD

#2: Protein Beta tubulin


Mass: 49907.770 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: brain / References: UniProt: P02554
#3: Protein Kinesin-like protein KIF2C / Mitotic centromere-associated kinesin / MCAK


Mass: 37072.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: DmKlp10A / Plasmid: pRSET B / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q922S8

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Non-polymers , 8 types, 118 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#8: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#9: Chemical ChemComp-TA1 / TAXOL / Paclitaxel


Mass: 853.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C47H51NO14 / Comment: medication, chemotherapy*YM
#10: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#11: Chemical ChemComp-CN2 / 2-MERCAPTO-N-[1,2,3,10-TETRAMETHOXY-9-OXO-5,6,7,9-TETRAHYDRO-BENZO[A]HEPTALEN-7-YL]ACETAMIDE


Mass: 431.502 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H25NO6S
#12: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsDBREF IS NOT PROVIDED BECAUSE THE STRUCTURES USED TO GENERATE THE MODELS WERE DERIVED FROM ...DBREF IS NOT PROVIDED BECAUSE THE STRUCTURES USED TO GENERATE THE MODELS WERE DERIVED FROM DIFFERENT SOURCE THAN THE SOURCE OF THE PROTEIN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Kinesin13-Microtubule ring complex / Type: COMPLEX
Buffer solutionpH: 6.8
Details: 80 mM Pipes, pH 6.8, 2 mM MgCl2, 1 mM EGTA, 2 mM AMP-PNP, 0.02 mM taxol
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 400 mesh Quantifoil grid R2/4
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingFilm or detector model: KODAK SO-163 FILM

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Processing

EM software
IDNameCategory
1SITUS COLORESmodel fitting
2UCSF Chimeramodel fitting
3UCSF Chimeramodel fitting
4Custom3D reconstruction
5MRC3D reconstruction
6PHOELIX3D reconstruction
7SUPRIM3D reconstruction
CTF correctionDetails: Each particle
3D reconstructionMethod: HELICAL / Resolution: 28 Å / Nominal pixel size: 2.5 Å / Details: Helical Fourier-Bessel / Symmetry type: HELICAL
Atomic model buildingSpace: REAL
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms15403 0 247 107 15757

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