5WCB | pdb_00005wcb

Katanin hexamer in the ring conformation

• PDB DOI: https://doi.org/10.2210/pdb5WCB/pdb
• EM Map EMD-8796: EMDB EMDataResource

• Classification: MOTOR PROTEIN
• Organism(s): Caenorhabditis elegans
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-06-29 Released: 2017-08-09 
• Deposition Author(s): Zehr, E.A., Szyk, A., Piszczek, G., Szczesna, E., Zuo, X., Roll-Mecak, A.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 6.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Katanin spiral and ring structures shed light on power stroke for microtubule severing.

Zehr, E., Szyk, A., Piszczek, G., Szczesna, E., Zuo, X., Roll-Mecak, A.

(2017) Nat Struct Mol Biol 24: 717-725

• PubMed: 28783150 
• DOI: https://doi.org/10.1038/nsmb.3448
• Primary Citation Related Structures: 
  5WC0, 5WC1, 5WCB


• PubMed Abstract: 
  

  Microtubule-severing enzymes katanin, spastin and fidgetin are AAA ATPases important for the biogenesis and maintenance of complex microtubule arrays in axons, spindles and cilia. Because of a lack of known 3D structures for these enzymes, their mechanism of action has remained poorly understood. Here we report the X-ray crystal structure of the monomeric AAA katanin module from Caenorhabditis elegans and cryo-EM reconstructions of the hexamer in two conformations. The structures reveal an unexpected asymmetric arrangement of the AAA domains mediated by structural elements unique to microtubule-severing enzymes and critical for their function. The reconstructions show that katanin cycles between open spiral and closed ring conformations, depending on the ATP occupancy of a gating protomer that tenses or relaxes interprotomer interfaces. Cycling of the hexamer between these conformations would provide the power stroke for microtubule severing.

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Organizational Affiliation: 
• Cell Biology and Biophysics Unit, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, Bethesda, Maryland, USA.
Biophysics Core, National Heart, Lung and Blood Institute, Bethesda, Maryland, USA.
X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois, USA.
Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, Maryland, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: SAXS

Macromolecule Content 

• Total Structure Weight: 313.35 kDa 
• Atom Count: 11,395 
• Modeled Residue Count: 1,662 
• Deposited Residue Count: 2,832 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Meiotic spindle formation protein mei-1	A, B, C, D, E, F	472	Caenorhabditis elegans	Mutation(s): 1  Gene Names: mei-1, T01G9.5 EC: 3.6.4.3 (PDB Primary Data), 5.6.1.1 (UniProt)
UniProt
Find proteins for P34808 (Caenorhabditis elegans) Explore P34808  Go to UniProtKB:  P34808

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	G [auth B], H [auth C], I [auth D], J [auth E], K [auth F]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 6.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION	1.4

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-09 
Deposition Author(s): Zehr, E.A., Szyk, A., Piszczek, G., Szczesna, E., Zuo, X., Roll-Mecak, A.

Revision History  

• Version 1.0: 2017-08-09
  Type: Initial release
  
• Version 1.1: 2017-08-23
  Changes: Database references
• Version 1.2: 2017-09-20
  Changes: Data collection, Database references
• Version 1.3: 2019-11-06
  Changes: Data collection, Other, Structure summary
• Version 1.4: 2024-03-13
  Changes: Data collection, Database references
• Version 1.5: 2025-05-21
  Changes: Data collection, Structure summary