6IZR

Whole structure of a 15-stranded ParM filament from Clostridium botulinum

• PDB DOI:  https://doi.org/10.2210/pdb6IZR/pdb
• EM Map EMD-9757: EMDB EMDataResource

• Classification: PROTEIN FIBRIL
• Organism(s): Clostridium botulinum Prevot_594
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-12-20 Released: 2019-06-19 
• Deposition Author(s): Koh, F., Narita, A., Lee, L.J., Tan, Y.Z., Dandey, V.P., Tanaka, K., Popp, D., Robinson, R.C.
• Funding Organization(s): Other private, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.70 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

Literature

The structure of a 15-stranded actin-like filament from Clostridium botulinum.

Koh, F., Narita, A., Lee, L.J., Tanaka, K., Tan, Y.Z., Dandey, V.P., Popp, D., Robinson, R.C.

(2019) Nat Commun 10: 2856-2856

• PubMed: 31253774 
• DOI: https://doi.org/10.1038/s41467-019-10779-9
• Primary Citation of Related Structures:  
  6IXW, 6IZR, 6IZV


• PubMed Abstract: 
  

Microfilaments (actin) and microtubules represent the extremes in eukaryotic cytoskeleton cross-sectional dimensions, raising the question of whether filament architectures are limited by protein fold. Here, we report the cryoelectron microscopy structure of a complex filament formed from 15 protofilaments of an actin-like protein. This actin-like ParM is encoded on the large pCBH Clostridium botulinum plasmid. In cross-section, the ~26 nm diameter filament comprises a central helical protofilament surrounded by intermediate and outer layers of six and eight twisted protofilaments, respectively. Alternating polarity of the layers allows for similar lateral contacts between each layer. This filament design is stiffer than the actin filament, and has likely been selected for during evolution to move large cargos. The comparable sizes of microtubule and pCBH ParM filaments indicate that larger filament architectures are not limited by the protomer fold. Instead, function appears to have been the evolutionary driving force to produce broad, complex filaments.

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Organizational Affiliation: 

Research Institute for Interdisciplinary Science, Okayama University, Okayama, 700-8530, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 30-mer - A30 

Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Macromolecule Content

• Total Structure Weight: 1,200.35 kDa 
• Atom Count: 84,360 
• Modelled Residue Count: 10,470 
• Deposited Residue Count: 10,470 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative plasmid segregation protein ParM	A [auth 1], AA [auth t], B [auth 2], BA [auth u], C [auth A], CA [auth w], D [auth B], DA [auth x], E [auth D], F [auth E], G, H, I [auth J], J [auth K], K [auth M], L [auth N], M [auth P], N [auth Q], O [auth b], P [auth c], Q [auth e], R [auth f], S [auth h], T [auth i], U [auth k], V [auth l], W [auth n], X [auth o], Y [auth q], Z [auth r]	349	Clostridium botulinum Prevot_594	Mutation(s): 0  Gene Names: T258_3831
UniProt
Find proteins for A0A0B4W229 (Clostridium botulinum Prevot_594) Explore A0A0B4W229  Go to UniProtKB:  A0A0B4W229

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	AB [auth N], AC [auth q], CB [auth P], CC [auth r], EA [auth 1], EB [auth Q], EC [auth t], GA [auth 2], GB [auth b], GC [auth u], IA [auth A], IB [auth c], IC [auth w], KA [auth B], KB [auth e], KC [auth x], MA [auth D], MB [auth f], OA [auth E], OB [auth h], QA [auth G], QB [auth i], SA [auth H], SB [auth k], UA [auth J], UB [auth l], WA [auth K], WB [auth n], YA [auth M], YB [auth o]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG	BB [auth N], BC [auth q], DB [auth P], DC [auth r], FA [auth 1], FB [auth Q], FC [auth t], HA [auth 2], HB [auth b], HC [auth u], JA [auth A], JB [auth c], JC [auth w], LA [auth B], LB [auth e], LC [auth x], NA [auth D], NB [auth f], PA [auth E], PB [auth h], RA [auth G], RB [auth i], TA [auth H], TB [auth k], VA [auth J], VB [auth l], XA [auth K], XB [auth n], ZA [auth M], ZB [auth o]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.70 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	2.1

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-06-19 
Deposition Author(s): Koh, F., Narita, A., Lee, L.J., Tan, Y.Z., Dandey, V.P., Tanaka, K., Popp, D., Robinson, R.C.

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Funding Organization	Location	Grant Number
Other private	United States	SF349247
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM103310
Other private	United States	F00316

Revision History  

• Version 1.0: 2019-06-19
  Type: Initial release
  
• Version 1.1: 2019-07-10
  Changes: Data collection, Database references
• Version 1.2: 2022-03-23
  Changes: Author supporting evidence, Database references, Derived calculations