3U06 | pdb_00003u06

Crystal structure of the kinesin-14 NcdG347D

PDB DOI: https://doi.org/10.2210/pdb3U06/pdb

Classification: MOTOR PROTEIN
Organism(s): Drosophila melanogaster
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2011-09-28 Released: 2012-03-07
Deposition Author(s): Liu, H.-L., Pemble IV, C.W., Endow, S.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.250 (Depositor), 0.246 (DCC)
R-Value Work:
0.216 (Depositor), 0.217 (DCC)
R-Value Observed:
0.217 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Neck-motor interactions trigger rotation of the kinesin stalk.

Liu, H.L., Pemble Iv, C.W., Endow, S.A.

(2012) Sci Rep 2: 236-236

PubMed: 22355749 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/srep00236
Primary Citation Related Structures:
3U06

PubMed Abstract:
Rotation of the coiled-coil stalk of the kinesin-14 motors is thought to drive displacements or steps by the motor along microtubules, but the structural changes that trigger stalk rotation and the nucleotide state in which it occurs are not certain. Here we report a kinesin-14 neck mutant that releases ADP more slowly than wild type and shows weaker microtubule affinity, consistent with defective stalk rotation. Unexpectedly, crystal structures show the stalk fully rotated - neck-motor interactions destabilize the stalk, causing it to rotate and ADP to be released, and alter motor affinity for microtubules. A new structural pathway accounts for the coupling of stalk rotation - the force-producing stroke - to changes in motor affinity for nucleotide and microtubules. Sequential disruption of salt bridges that stabilize the unrotated stalk could cause the stalk to initiate and complete rotation in different nucleotide states.

Organizational Affiliation

Department of Cell Biology, Duke University Medical Center, Durham, NC 27710 USA.

Macromolecule Content

Total Structure Weight: 94.92 kDa
Atom Count: 5,836
Modeled Residue Count: 703
Deposited Residue Count: 824
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein claret segregational	A, B	412	Drosophila melanogaster	Mutation(s): 1 Gene Names: CA(ND), CG7831, ncd, non-claret disjunctional EC: 3.6.4
UniProt
Find proteins for P20480 (Drosophila melanogaster) Explore P20480 Go to UniProtKB: P20480
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P20480
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain I [auth B]	C [auth A], I [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B]	E [auth A], F [auth A], G [auth A], H [auth A], J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.250 (Depositor), 0.246 (DCC)
R-Value Work: 0.216 (Depositor), 0.217 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 160.539	α = 90
b = 67.094	β = 98.91
c = 94.369	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-03-07

Deposition Author(s):

Liu, H.-L.

Pemble IV, C.W.

Endow, S.A.

Revision History (Full details and data files)

Version 1.0: 2012-03-07
Type: Initial release
Version 1.1: 2014-11-12
Changes: Structure summary
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2024-02-28
Changes: Data collection, Database references, Derived calculations