4UBF | pdb_00004ubf

HsMCAK motor domain complex

PDB DOI: https://doi.org/10.2210/pdb4UBF/pdb

Classification: CELL CYCLE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2014-08-12 Released: 2015-05-06
Deposition Author(s): Welburn, J.P.I., Talapatra, S.K.
Funding Organization(s): Cancer Research UK

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.286 (Depositor), 0.308 (DCC)
R-Value Work:
0.264 (Depositor)
R-Value Observed:
0.265 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

The C-terminal region of the motor protein MCAK controls its structure and activity through a conformational switch.

Talapatra, S.K., Harker, B., Welburn, J.P.

(2015) Elife 4

PubMed: 25915621 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.7554/eLife.06421
Primary Citation Related Structures:
4UBF

PubMed Abstract:
The precise regulation of microtubule dynamics is essential during cell division. The kinesin-13 motor protein MCAK is a potent microtubule depolymerase. The divergent non-motor regions flanking the ATPase domain are critical in regulating its targeting and activity. However, the molecular basis for the function of the non-motor regions within the context of full-length MCAK is unknown. Here, we determine the structure of MCAK motor domain bound to its regulatory C-terminus. Our analysis reveals that the MCAK C-terminus binds to two motor domains in solution and is displaced allosterically upon microtubule binding, which allows its robust accumulation at microtubule ends. These results demonstrate that MCAK undergoes long-range conformational changes involving its C-terminus during the soluble to microtubule-bound transition and that the C-terminus-motor interaction represents a structural intermediate in the MCAK catalytic cycle. Together, our work reveals intrinsic molecular mechanisms underlying the regulation of kinesin-13 activity.

Organizational Affiliation

Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom.

Macromolecule Content

Total Structure Weight: 176.44 kDa
Atom Count: 9,707
Modeled Residue Count: 1,279
Deposited Residue Count: 1,560
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kinesin-like protein KIF2C	A, B, C, D	387	Homo sapiens	Mutation(s): 0 Gene Names: KIF2C, KNSL6
UniProt & NIH Common Fund Data Resources
Find proteins for Q99661 (Homo sapiens) Explore Q99661 Go to UniProtKB: Q99661
PHAROS: Q99661 GTEx: ENSG00000142945
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q99661
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Kinesin-like protein KIF2C	E [auth P]	12	Homo sapiens	Mutation(s): 0 Gene Names: KIF2C, KNSL6
UniProt & NIH Common Fund Data Resources
Find proteins for Q99661 (Homo sapiens) Explore Q99661 Go to UniProtKB: Q99661
PHAROS: Q99661 GTEx: ENSG00000142945
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q99661
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain P [auth D] SDF format, chain M [auth C] SDF format, chain I [auth B] MOL2 format, chain G [auth A] MOL2 format, chain P [auth D] MOL2 format, chain M [auth C] MOL2 format, chain I [auth B] mmCIF format, chain G [auth A] mmCIF format, chain P [auth D] mmCIF format, chain M [auth C] mmCIF format, chain I [auth B]	G [auth A], I [auth B], M [auth C], P [auth D]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain P [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain O [auth D] SDF format, chain L [auth C] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth D] MOL2 format, chain L [auth C] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth D] mmCIF format, chain L [auth C]	F [auth A] H [auth A] J [auth B] K [auth B] L [auth C] F [auth A], H [auth A], J [auth B], K [auth B], L [auth C], N [auth C], O [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain N [auth C] Focus chain O [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain N [auth C] Focus chain O [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.286 (Depositor), 0.308 (DCC)
R-Value Work: 0.264 (Depositor)
R-Value Observed: 0.265 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.306	α = 90
b = 245.644	β = 95.84
c = 79.399	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2015-05-06

Deposition Author(s):

Welburn, J.P.I.

Talapatra, S.K.

Funding Organization	Location	Grant Number
Cancer Research UK	United Kingdom	543WJW_R42094

Revision History (Full details and data files)

Version 1.0: 2015-05-06
Type: Initial release
Version 1.1: 2017-08-30
Changes: Author supporting evidence
Version 1.2: 2018-06-06
Changes: Data collection, Database references
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Refinement description