7WRG | pdb_00007wrg

Crystal structure of full-length kinesin-3 KLP-6

• PDB DOI: https://doi.org/10.2210/pdb7WRG/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Caenorhabditis elegans
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2022-01-26 Released: 2022-08-10 
• Deposition Author(s): Wang, W.J., Ren, J.Q., Song, W.Y., Feng, W.
• Funding Organization(s): Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.16 Å
• R-Value Free: 
  0.263 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Models: experimental

Literature

The architecture of kinesin-3 KLP-6 reveals a multilevel-lockdown mechanism for autoinhibition.

Wang, W., Ren, J., Song, W., Zhang, Y., Feng, W.

(2022) Nat Commun 13: 4281-4281

• PubMed: 35879313 
• DOI: https://doi.org/10.1038/s41467-022-32048-y
• Primary Citation Related Structures: 
  7WRG


• PubMed Abstract: 
  

  Autoinhibition of kinesin-3 ensures the proper spatiotemporal control of the motor activity for intracellular transport, but the underlying mechanism remains elusive. Here, we determine the full-length structure of kinesin-3 KLP-6 in a compact self-folded state. Unexpectedly, all the internal coiled-coil segments and domains in KLP-6 cooperate to successively lock down the neck and motor domains. The first coiled-coil segment is melted into several short helices that work with the motor domain to restrain the entire neck domain. The second coiled-coil segment associates with its neighboring FHA and MBS domains and integrates with the tail MATH domain to form a supramodule that synergistically wraps around the motor domain to trap the nucleotide and hinder the microtubule binding. This multilevel-lockdown mechanism for autoinhibition could be applicable to other kinesin-3 motors.

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Organizational Affiliation: 
• National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, 100101, Beijing, China.
College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China.
Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, 100101, Beijing, China.
National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, 100101, Beijing, China. [e-mail].
College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: light scattering

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 215.55 kDa 
• Atom Count: 12,589 
• Modeled Residue Count: 1,595 
• Deposited Residue Count: 1,920 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kinesin-like protein	A, B	960	Caenorhabditis elegans	Mutation(s): 0  Gene Names: klp-6, CELE_R144.1, R144.1
UniProt
Find proteins for G5EFQ4 (Caenorhabditis elegans) Explore G5EFQ4  Go to UniProtKB:  G5EFQ4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	C [auth A], E [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.16 Å
• R-Value Free:  0.263 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.138	α = 90
b = 68.816	β = 92.75
c = 253.216	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-08-10 
Deposition Author(s): Wang, W.J., Ren, J.Q., Song, W.Y., Feng, W.

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Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	--

Revision History  

• Version 1.0: 2022-08-10
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description