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- PDB-5tfy: The archaeal flagellum of Methanospirillum hungatei strain JF1. -

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Basic information

Entry
Database: PDB / ID: 5tfy
TitleThe archaeal flagellum of Methanospirillum hungatei strain JF1.
ComponentsFlagellin
KeywordsCELL ADHESION / cell motility and adhesion
Function / homologyarchaeal-type flagellum / Flagellin, archaea / Archaebacterial flagellin / Flagellin/pilin, N-terminal / archaeal or bacterial-type flagellum-dependent cell motility / membrane => GO:0016020 / structural molecule activity / Flagellin
Function and homology information
Biological speciesMethanospirillum hungatei JF-1 (archaea)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsPoweleit, N. / Peng, G. / Gunsalus, R.P. / Zhou, Z.H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/Office of the Director1S10OD018111 United States
National Science Foundation (NSF, United States)DBI-1338135 United States
CitationJournal: Nat Microbiol / Year: 2016
Title: CryoEM structure of the Methanospirillum hungatei archaellum reveals structural features distinct from the bacterial flagellum and type IV pilus.
Authors: Nicole Poweleit / Peng Ge / Hong H Nguyen / Rachel R Ogorzalek Loo / Robert P Gunsalus / Z Hong Zhou /
Abstract: Archaea use flagella known as archaella-distinct both in protein composition and structure from bacterial flagella-to drive cell motility, but the structural basis of this function is unknown. Here, ...Archaea use flagella known as archaella-distinct both in protein composition and structure from bacterial flagella-to drive cell motility, but the structural basis of this function is unknown. Here, we report an atomic model of the archaella, based on the cryo electron microscopy (cryoEM) structure of the Methanospirillum hungatei archaellum at 3.4 Å resolution. Each archaellum contains ∼61,500 archaellin subunits organized into a curved helix with a diameter of 10 nm and average length of 10,000 nm. The tadpole-shaped archaellin monomer has two domains, a β-barrel domain and a long, mildly kinked α-helix tail. Our structure reveals multiple post-translational modifications to the archaella, including six O-linked glycans and an unusual N-linked modification. The extensive interactions among neighbouring archaellins explain how the long but thin archaellum maintains the structural integrity required for motility-driving rotation. These extensive inter-subunit interactions and the absence of a central pore in the archaellum distinguish it from both the bacterial flagellum and type IV pili.
History
DepositionSep 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Data collection / Category: em_software / pdbx_audit_support
Item: _em_software.name / _pdbx_audit_support.funding_organization
Revision 1.3Nov 8, 2017Group: Derived calculations / Category: pdbx_struct_assembly
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure viewerMolecule:
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Assembly

Deposited unit
I: Flagellin
A: Flagellin
B: Flagellin
C: Flagellin
D: Flagellin
E: Flagellin
F: Flagellin
G: Flagellin
H: Flagellin
J: Flagellin
K: Flagellin
L: Flagellin
M: Flagellin
N: Flagellin
O: Flagellin
P: Flagellin
Q: Flagellin
R: Flagellin
S: Flagellin
T: Flagellin
U: Flagellin
V: Flagellin
W: Flagellin
X: Flagellin
Y: Flagellin
Z: Flagellin


Theoretical massNumber of molelcules
Total (without water)455,62726
Polymers455,62726
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area145920 Å2
ΔGint-1116 kcal/mol
Surface area113360 Å2

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Components

#1: Protein ...
Flagellin /


Mass: 17524.129 Da / Num. of mol.: 26 / Source method: isolated from a natural source
Source: (natural) Methanospirillum hungatei JF-1 (strain ATCC 27890 / DSM 864 / NBRC 100397 / JF-1) (archaea)
Strain: ATCC 27890 / DSM 864 / NBRC 100397 / JF-1 / References: UniProt: Q2FUM4

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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: The flagellum of the archaea Methanospirillum hungatei
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: NATURAL
Molecular weightValue: 20.048 kDa/nm / Experimental value: YES
Source (natural)Organism: Methanospirillum hungatei JF-1 (archaea) / Strain: JF1
Buffer solutionpH: 7.2
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMsodium chlorideNaClSodium chloride1
250 mMTrisC4H11NO31
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingAverage exposure time: 0.25 sec. / Electron dose: 2.667 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 2
Image scansMovie frames/image: 30 / Used frames/image: 3-13

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Processing

EM software
IDNameVersionCategoryDetails
2RELION1.3image acquisitionCustom modified to use IHRSR-like helical reconstruction
3EMAN1.8image acquisitionHelixboxer and pro2d, proc3d
4Leginonimage acquisitionAutomated image collection
6CTFFIND3CTF correction
CTF correctionType: PHASE FLIPPING ONLY
Helical symmertyAngular rotation/subunit: 108 ° / Axial rise/subunit: 5.2 Å / Axial symmetry: C1
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.33 CUT-OFF / Num. of particles: 90118 / Symmetry type: HELICAL
Atomic model buildingB value: 200 / Protocol: AB INITIO MODEL / Space: REAL

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