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- EMDB-4194: Thermus thermophilus PilF ATPase (AMPPNP-bound form) -

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Basic information

Entry
Database: EMDB / ID: 4194
TitleThermus thermophilus PilF ATPase (AMPPNP-bound form)
Map dataThermus thermophilus PilF ATPase (AMPPNP-bound form)
SampleThermus thermophilus PilF ATPase (AMPPNP-bound form):
Type IV pilus assembly protein PilF
Function / homologyType II/IV secretion system protein / General secretory system II, protein E, N-terminal / P-loop containing nucleoside triphosphate hydrolase / General secretory system II, protein E, N-terminal superfamily / Type II/IV secretion system protein / Type II secretion system (T2SS), protein E, N-terminal domain / Bacterial type II secretion system protein E signature. / ATP binding / metal ion binding / Type IV pilus assembly protein PilF
Function and homology information
SourceThermus thermophilus HB8 (bacteria) / Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Methodsingle particle reconstruction / cryo EM / 8 Å resolution
AuthorsDerrick JP / Collins RF
CitationJournal: Sci Rep / Year: 2018
Title: Structural cycle of the Thermus thermophilus PilF ATPase: the powering of type IVa pilus assembly.
Authors: Richard Collins / Vijaykumar Karuppiah / C Alistair Siebert / Rana Dajani / Angela Thistlethwaite / Jeremy P Derrick
Validation ReportPDB-ID: 6f8l

SummaryFull reportAbout validation report
DateDeposition: Dec 13, 2017 / Header (metadata) release: Jan 17, 2018 / Map release: Aug 1, 2018 / Last update: Oct 24, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.45
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1.45
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6f8l
  • Surface level: 1.45
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_4194.map.gz (map file in CCP4 format, 28312 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
192 pix
1.78 Å/pix.
= 341.76 Å
192 pix
1.78 Å/pix.
= 341.76 Å
192 pix
1.78 Å/pix.
= 341.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.78 Å
Density
Contour Level:1.45 (by author), 1.45 (movie #1):
Minimum - Maximum-4.813376 - 5.397968
Average (Standard dev.)0.021497991 (0.28989422)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions192192192
Origin-96.0-96.0-96.0
Limit95.095.095.0
Spacing192192192
CellA=B=C: 341.76 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.781.781.78
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z341.760341.760341.760
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-96-96-96
NC/NR/NS192192192
D min/max/mean-4.8135.3980.021

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Supplemental data

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Sample components

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Entire Thermus thermophilus PilF ATPase (AMPPNP-bound form)

EntireName: Thermus thermophilus PilF ATPase (AMPPNP-bound form) / Number of components: 2

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Component #1: protein, Thermus thermophilus PilF ATPase (AMPPNP-bound form)

ProteinName: Thermus thermophilus PilF ATPase (AMPPNP-bound form) / Recombinant expression: No
SourceSpecies: Thermus thermophilus HB8 (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, Type IV pilus assembly protein PilF

ProteinName: Type IV pilus assembly protein PilF / Number of Copies: 18 / Recombinant expression: No
MassTheoretical: 101.021289 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.2 mg/ml
Buffer solution: 25 mM HEPES pH 7.5, 150 mM NaCl, 5 mM MgCl2 and 5 % glycerol (v/v)
pH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 45 e/Å2 / Illumination mode: OTHER
LensCs: 2.7 mm / Imaging mode: OTHER / Defocus: 1000.0 - 4500.0 nm / Energy filter: k2 / Energy window: 20-20 eV
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 BASE (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 450000
3D reconstructionSoftware: RELION / Resolution: 8 Å / Resolution method: FSC 0.5 CUT-OFF

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Atomic model buiding

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