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- PDB-5jyg: Cryo-EM structure of the MamK filament at 6.5 A -

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Basic information

Entry
Database: PDB / ID: 5jyg
TitleCryo-EM structure of the MamK filament at 6.5 A
ComponentsActin-like ATPase
KeywordsSTRUCTURAL PROTEIN / Actin-like / Magnetosome / bacteria
Function / homology
Function and homology information


magnetosome assembly / magnetosome membrane / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / cytoskeleton / GTP binding / ATP hydrolysis activity / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
: / MreB/Mbl protein / Actin family / Actin / ATPase, nucleotide binding domain
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Actin-like protein MamK
Similarity search - Component
Biological speciesMagnetospirillum magneticum (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 6.5 Å
AuthorsBergeron, J.R.C. / Hutto, R. / Kollman, J.M.
CitationJournal: Protein Sci / Year: 2017
Title: Structure of the magnetosome-associated actin-like MamK filament at subnanometer resolution.
Authors: Julien R C Bergeron / Rachel Hutto / Ertan Ozyamak / Nancy Hom / Jesse Hansen / Olga Draper / Meghan E Byrne / Sepehr Keyhani / Arash Komeili / Justin M Kollman /
Abstract: Magnetotactic bacteria possess cellular compartments called magnetosomes that sense magnetic fields. Alignment of magnetosomes in the bacterial cell is necessary for their function, and this is ...Magnetotactic bacteria possess cellular compartments called magnetosomes that sense magnetic fields. Alignment of magnetosomes in the bacterial cell is necessary for their function, and this is achieved through anchoring of magnetosomes to filaments composed of the protein MamK. MamK is an actin homolog that polymerizes upon ATP binding. Here, we report the structure of the MamK filament at ∼6.5 Å, obtained by cryo-Electron Microscopy. This structure confirms our previously reported double-stranded, nonstaggered architecture, and reveals the molecular basis for filament formation. While MamK is closest in sequence to the bacterial actin MreB, the longitudinal contacts along each MamK strand most closely resemble those of eukaryotic actin. In contrast, the cross-strand interface, with a surprisingly limited set of contacts, is novel among actin homologs and gives rise to the nonstaggered architecture.
History
DepositionMay 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_image_scans
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
A: Actin-like ATPase
B: Actin-like ATPase
C: Actin-like ATPase
D: Actin-like ATPase
E: Actin-like ATPase
F: Actin-like ATPase
G: Actin-like ATPase
H: Actin-like ATPase
I: Actin-like ATPase
J: Actin-like ATPase
K: Actin-like ATPase
L: Actin-like ATPase
M: Actin-like ATPase
N: Actin-like ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)533,50842
Polymers527,18714
Non-polymers6,32128
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Actin-like ATPase


Mass: 37656.180 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetospirillum magneticum (strain AMB-1 / ATCC 700264) (bacteria)
Strain: AMB-1 / ATCC 700264 / Gene: amb0965 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2W8Q6
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Magnetosome-associated MamK filament / Type: ORGANELLE OR CELLULAR COMPONENT / Details: ADP-bound MamK / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Magnetospirillum magneticum AMB-1 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Plasmid: pET29a
Buffer solutionpH: 7
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: OTHER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: Rosetta / Version: 3.5 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 24 ° / Axial rise/subunit: 53.8 Å / Axial symmetry: C2
3D reconstructionResolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8129 / Symmetry type: HELICAL
Atomic model buildingProtocol: OTHER

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