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- PDB-5z1l: Cryo-EM structure of Methanoccus maripaludis archaellum -

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Entry
Database: PDB / ID: 5z1l
TitleCryo-EM structure of Methanoccus maripaludis archaellum
ComponentsFlagellin
KeywordsPROTEIN FIBRIL / Archaellum / archea / flagellum / metal binding / motility / helical
Function / homologyFlagellin, archaea / Flagellin/pilin, N-terminal / Archaebacterial flagellin / archaeal-type flagellum / structural molecule activity / integral component of membrane / Flagellin
Function and homology information
Specimen sourceMethanococcus maripaludis (archaea)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / 4 Å resolution
AuthorsMeshcheryakov, V.A. / Shibata, S. / Schreiber, M.T. / Villar-Briones, A. / Jarrell, K.F. / Aizawa, S. / Wolf, M.
CitationJournal: To Be Published
Title: Cryo-EM structure of Methanoccus maripaludis archaellum
Authors: Meshcheryakov, V.A. / Shibata, S. / Schreiber, M.T. / Villar-Briones, A. / Jarrell, K.F. / Aizawa, S. / Wolf, M.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 26, 2017 / Release: Feb 13, 2019

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Structure visualization

Movie
  • Deposited structure unit
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  • Superimposition on EM map
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)389,50818
Polyers389,50818
Non-polymers00
Water0
1


  • idetical with deposited unit
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  • Evidence: scanning transmission electron microscopy, helical diffraction
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TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)66190
ΔGint (kcal/M)-503
Surface area (Å2)151850

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Components

#1: Protein/peptide
Flagellin /


Mass: 21639.359 Da / Num. of mol.: 18
Source: (natural) Methanococcus maripaludis (strain S2 / LL) (archaea)
Strain: S2 / LL / References: UniProt: Q6LWP3

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: helical reconstruction

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Sample preparation

ComponentName: M.maripaludis archaellin FlaB1 filament / Type: COMPLEX / Entity ID: 1 / Source: NATURAL
Molecular weightUnits: KILODALTONS/NANOMETER / Experimental value: NO
Source (natural)Organism: Methanococcus maripaludis S2 (archaea)
Source (recombinant)Organism: Escherichia coli (E. coli)
Plasmid: pET15b-H3.1, pET15b-H4, pET15b-H2A, pET15b-H2B, pGEM-T-Easy-(186 base-pair mouse ALB1 enhancer DNA)
Buffer solutionpH: 7
Buffer componentName: Water / Formula: H2O
SpecimenConc.: .8 mg/ml / Details: sample was monodisperse / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Gatan Solarus / Grid material: COPPER / Grid mesh size: 200 / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 289 kelvins / Details: 3 second blot, 3.5uL

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS / Details: nanoprobe, parallel beam illumination
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 105000 / Calibrated magnification: 47619 / Nominal defocus max: -2500 nm / Nominal defocus min: -1500 nm / Calibrated defocus min: -1500 nm / Calibrated defocus max: -2500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 microns / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 100 kelvins / Temperature (min): 77 kelvins / Residual tilt: 0.1 mradians
Image recordingAverage exposure time: 12 sec. / Electron dose: 96 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 1 / Number of real images: 2000
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter upper: 20 eV / Energyfilter lower: 0 eV
Image scansSampling size: 5 microns / Width: 7676 / Height: 7420 / Movie frames/image: 4 / Used frames/image: 1-48

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM software
IDNameVersionCategoryDetails
1EMAN22.1particle selectione2helixboxer.py
2Leginon3.2image acquisition
4CTFFIND4.1CTF correction
7Cootmodel fitting
9SPRING0.84initial Euler assignment
10SPRING0.84final Euler assignment
11SPRING0.84classificationsparx k-means
12SPRING0.843D reconstruction
13PHENIXmodel refinement
Image processingDetails: frame alignment and integration with motioncor2 incl. dose weighting and 2x Fourier cropping
CTF correctionDetails: deconvolution in SPRING / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 108.2 deg. / Axial rise/subunit: 5.7 Å / Axial symmetry: C1
Particle selectionNumber of particles selected: 110747
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 110747 / Algorithm: FOURIER SPACE / Number of class averages: 100 / Symmetry type: POINT
Atomic model buildingRef protocol: FLEXIBLE FIT / Ref space: REAL
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00425848
ELECTRON MICROSCOPYf_angle_d0.96935244
ELECTRON MICROSCOPYf_dihedral_angle_d4.35815318
ELECTRON MICROSCOPYf_chiral_restr0.0694464
ELECTRON MICROSCOPYf_plane_restr0.0064554

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