6PEN | pdb_00006pen

Structure of Spastin Hexamer (whole model) in complex with substrate peptide


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6PEN

This is version 1.4 of the entry. See complete history

Literature

Structure of spastin bound to a glutamate-rich peptide implies a hand-over-hand mechanism of substrate translocation.

Han, H.Schubert, H.L.McCullough, J.Monroe, N.Purdy, M.D.Yeager, M.Sundquist, W.I.Hill, C.P.

(2020) J Biological Chem 295: 435-443

  • DOI: https://doi.org/10.1074/jbc.AC119.009890
  • Primary Citation Related Structures: 
    6PEK, 6PEN

  • PubMed Abstract: 

    Many members of the AAA+ ATPase family function as hexamers that unfold their protein substrates. These AAA unfoldases include spastin, which plays a critical role in the architecture of eukaryotic cells by driving the remodeling and severing of microtubules, which are cytoskeletal polymers of tubulin subunits. Here, we demonstrate that a human spastin binds weakly to unmodified peptides from the C-terminal segment of human tubulin α1A/B. A peptide comprising alternating glutamate and tyrosine residues binds more tightly, which is consistent with the known importance of glutamylation for spastin microtubule severing activity. A cryo-EM structure of the spastin-peptide complex at 4.2 Å resolution revealed an asymmetric hexamer in which five spastin subunits adopt a helical, spiral staircase configuration that binds the peptide within the central pore, whereas the sixth subunit of the hexamer is displaced from the peptide/substrate, as if transitioning from one end of the helix to the other. This configuration differs from a recently published structure of spastin from Drosophila melanogaster , which forms a six-subunit spiral without a transitioning subunit. Our structure resembles other recently reported AAA unfoldases, including the meiotic clade relative Vps4, and supports a model in which spastin utilizes a hand-over-hand mechanism of tubulin translocation and microtubule remodeling.


  • Organizational Affiliation
    • Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112.

Macromolecule Content 

  • Total Structure Weight: 330.97 kDa 
  • Atom Count: 12,675 
  • Modeled Residue Count: 1,722 
  • Deposited Residue Count: 2,998 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Spastin
A,
B,
C,
D,
E,
G [auth F]
498Homo sapiensMutation(s): 0 
Gene Names: SPASTADPSPFSP2KIAA1083SPG4
EC: 5.6.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBP0 (Homo sapiens)
Explore Q9UBP0 
Go to UniProtKB:  Q9UBP0
PHAROS:  Q9UBP0
GTEx:  ENSG00000021574 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UBP0
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
EYEYEYEYEYF [auth G]10synthetic constructMutation(s): 0 

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP

Query on ADP



Download:Ideal Coordinates CCD File
H [auth A],
K [auth B],
N [auth C],
Q [auth D],
T [auth E]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
BEF

Query on BEF



Download:Ideal Coordinates CCD File
I [auth A],
L [auth B],
O [auth C],
R [auth D]
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
MG

Query on MG



Download:Ideal Coordinates CCD File
J [auth A],
M [auth B],
P [auth C],
S [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesRO1 GM112080

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-04
    Type: Initial release
  • Version 1.1: 2019-12-11
    Changes: Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.3: 2020-01-22
    Changes: Database references
  • Version 1.4: 2024-03-13
    Changes: Data collection, Database references, Derived calculations