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- PDB-4apw: Alp12 filament structure -

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Basic information

Entry
Database: PDB / ID: 4apw
TitleAlp12 filament structure
ComponentsALP12
KeywordsSTRUCTURAL PROTEIN / ALP12 / ACTIN-LIKE PROTEIN
Function / homologyActin-like protein, N-terminal / Actin like proteins N terminal domain / ParM-like / ATPase, nucleotide binding domain / ALP_N domain-containing protein
Function and homology information
Biological speciesCLOSTRIDIUM TETANI (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / negative staining / Resolution: 19.7 Å
AuthorsPopp, D. / Narita, A. / Lee, L.J. / Ghoshdastider, U. / Xue, B. / Srinivasan, R. / Balasubramanian, M.K. / Tanaka, T. / Robinson, R.C.
CitationJournal: J Biol Chem / Year: 2012
Title: Novel actin-like filament structure from Clostridium tetani.
Authors: David Popp / Akihiro Narita / Lin Jie Lee / Umesh Ghoshdastider / Bo Xue / Ramanujam Srinivasan / Mohan K Balasubramanian / Toshitsugu Tanaka / Robert C Robinson /
Abstract: Eukaryotic F-actin is constructed from two protofilaments that gently wind around each other to form a helical polymer. Several bacterial actin-like proteins (Alps) are also known to form F-actin- ...Eukaryotic F-actin is constructed from two protofilaments that gently wind around each other to form a helical polymer. Several bacterial actin-like proteins (Alps) are also known to form F-actin-like helical arrangements from two protofilaments, yet with varied helical geometries. Here, we report a unique filament architecture of Alp12 from Clostridium tetani that is constructed from four protofilaments. Through fitting of an Alp12 monomer homology model into the electron microscopy data, the filament was determined to be constructed from two antiparallel strands, each composed of two parallel protofilaments. These four protofilaments form an open helical cylinder separated by a wide cleft. The molecular interactions within single protofilaments are similar to F-actin, yet interactions between protofilaments differ from those in F-actin. The filament structure and assembly and disassembly kinetics suggest Alp12 to be a dynamically unstable force-generating motor involved in segregating the pE88 plasmid, which encodes the lethal tetanus toxin, and thus a potential target for drug design. Alp12 can be repeatedly cycled between states of polymerization and dissociation, making it a novel candidate for incorporation into fuel-propelled nanobiopolymer machines.
History
DepositionApr 6, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2012Group: Other
Revision 1.2Sep 25, 2013Group: Other
Revision 1.3Oct 3, 2018Group: Author supporting evidence / Data collection
Category: diffrn_radiation / diffrn_radiation_wavelength ...diffrn_radiation / diffrn_radiation_wavelength / em_single_particle_entity / em_software
Item: _em_software.image_processing_id

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Structure visualization

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Assembly

Deposited unit
A: ALP12
B: ALP12
C: ALP12
D: ALP12
E: ALP12
F: ALP12
G: ALP12
H: ALP12
I: ALP12
J: ALP12
K: ALP12
L: ALP12
M: ALP12
N: ALP12
O: ALP12
P: ALP12


Theoretical massNumber of molelcules
Total (without water)591,87116
Polymers591,87116
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
ALP12


Mass: 36991.953 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM TETANI (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q89A01

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: FILAMENT STRUCTURE OF AN ACTIN -LIKE PROTEIN, ALP12, IN CLOSTRIDIUM TETANI
Type: COMPLEX
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: NO
EM stainingType: NEGATIVE / Material: uranyl acetate
Specimen supportDetails: CARBON
VitrificationDetails: NEGATIVELY STAINED

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Electron microscopy imaging

MicroscopyModel: HITACHI H7600 / Date: Sep 6, 2011
Electron gunElectron source: LAB6 / Accelerating voltage: 100 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 40000 X / Nominal defocus max: 5000 nm / Nominal defocus min: 800 nm
Image recordingFilm or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 31

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Processing

EM softwareName: EOS / Category: 3D reconstruction
CTF correctionDetails: EACH SCANNED IMAGE
3D reconstructionMethod: SINGLE PARTICLE ANALYSIS / Resolution: 19.7 Å / Num. of particles: 5582 / Nominal pixel size: 2.68 Å / Actual pixel size: 2.68 Å
Details: SINGLE PARTICLE ANALYSIS USING EOS SOFTWARE PACKAGE SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2068. (DEPOSITION ID: 10712).
Symmetry type: HELICAL
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--X-RAY
Atomic model buildingPDB-ID: 3JS6
RefinementHighest resolution: 19.7 Å
Refinement stepCycle: LAST / Highest resolution: 19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms40752 0 0 0 40752

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