3EDL | pdb_00003edl

Kinesin13-Microtubule Ring complex

PDB DOI: https://doi.org/10.2210/pdb3EDL/pdb
EM Map EMD-5027: EMDB EMDataResource

Classification: STRUCTURAL PROTEIN
Organism(s): Bos taurus, Drosophila melanogaster
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2008-09-03 Released: 2009-01-20
Deposition Author(s): Tan, D., Rice, W.J., Sosa, H.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 28.0 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Structure of the kinesin13-microtubule ring complex.

Tan, D., Rice, W.J., Sosa, H.

(2008) Structure 16: 1732-1739

PubMed: 19000825 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.str.2008.08.017
Primary Citation Related Structures:
3EDL

PubMed 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 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.

Organizational Affiliation

Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx NY, 10461, USA.

Macromolecule Content

Total Structure Weight: 241.02 kDa
Atom Count: 15,757
Modeled Residue Count: 1,979
Deposited Residue Count: 2,123
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha-1A chain	A	451	Bos taurus	Mutation(s): 0 EC: 3.6.5
UniProt
Find proteins for P81947 (Bos taurus) Explore P81947 Go to UniProtKB: P81947
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P81947
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta tubulin	B, E [auth G]	445	Bos taurus	Mutation(s): 0
UniProt
Find proteins for P02554 (Sus scrofa) Explore P02554 Go to UniProtKB: P02554
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02554
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Kinesin-like protein KIF2C	C [auth D]	331	Drosophila melanogaster	Mutation(s): 0 Gene Names: DmKlp10A
UniProt & NIH Common Fund Data Resources
Find proteins for Q922S8 (Mus musculus) Explore Q922S8 Go to UniProtKB: Q922S8
IMPC: MGI:1921054
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q922S8
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha-1A chain	D [auth F]	451	Bos taurus	Mutation(s): 0 EC: 3.6.5
UniProt
Find proteins for P81947 (Bos taurus) Explore P81947 Go to UniProtKB: P81947
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P81947
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TA1 Query on TA1 Download:Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	TAXOL C₄₇ H₅₁ N O₁₄ RCINICONZNJXQF-MZXODVADSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
GTP Query on GTP Download:Ideal Coordinates CCD File SDF format, chain N [auth F] SDF format, chain H [auth B] MOL2 format, chain N [auth F] MOL2 format, chain H [auth B] mmCIF format, chain N [auth F] mmCIF format, chain H [auth B]	H [auth B], N [auth F]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain H [auth B] Focus chain N [auth F] Interactions & Density Focus chain H [auth B] Focus chain N [auth F]
ANP Query on ANP Download:Ideal Coordinates CCD File SDF format, chain L [auth D] MOL2 format, chain L [auth D] mmCIF format, chain L [auth D]	L [auth D]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain L [auth D] Interactions & Density Focus chain L [auth D]
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain O [auth F] SDF format, chain I [auth B] MOL2 format, chain O [auth F] MOL2 format, chain I [auth B] mmCIF format, chain O [auth F] mmCIF format, chain I [auth B]	I [auth B], O [auth F]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain I [auth B] Focus chain O [auth F] Interactions & Density Focus chain I [auth B] Focus chain O [auth F]
CN2 Query on CN2 Download:Ideal Coordinates CCD File SDF format, chain P [auth G] MOL2 format, chain P [auth G] mmCIF format, chain P [auth G]	P [auth G]	2-MERCAPTO-N-[1,2,3,10-TETRAMETHOXY-9-OXO-5,6,7,9-TETRAHYDRO-BENZO[A]HEPTALEN-7-YL]ACETAMIDE C₂₂ H₂₅ N O₆ S TYDIWMTWTXFWSY-HNNXBMFYSA-N		Interactions Focus chain P [auth G] Interactions & Density Focus chain P [auth G]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain M [auth F] SDF format, chain K [auth D] SDF format, chain G [auth A] MOL2 format, chain M [auth F] MOL2 format, chain K [auth D] MOL2 format, chain G [auth A] mmCIF format, chain M [auth F] mmCIF format, chain K [auth D] mmCIF format, chain G [auth A]	G [auth A], K [auth D], M [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth D] Focus chain M [auth F] Interactions & Density Focus chain G [auth A] Focus chain K [auth D] Focus chain M [auth F]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 28.0 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

EM Software:

Task	Software Package	Version
RECONSTRUCTION	Custom
RECONSTRUCTION	MRC
RECONSTRUCTION	PHOELIX
RECONSTRUCTION	SUPRIM

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-01-20

Deposition Author(s):

Tan, D.

Rice, W.J.

Sosa, H.

Revision History (Full details and data files)

Version 1.0: 2009-01-20
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2018-07-18
Changes: Author supporting evidence, Data collection
Version 1.3: 2020-06-24
Changes: Database references, Source and taxonomy, Structure summary
Version 1.4: 2024-02-21
Changes: Data collection, Database references, Derived calculations