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- PDB-6ejf: Thermus thermophilus PilF ATPase (apoprotein form) -

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Basic information

Entry
Database: PDB / ID: 6ejf
TitleThermus thermophilus PilF ATPase (apoprotein form)
Components(Type IV pilus assembly protein PilF) x 3
KeywordsMOTOR PROTEIN / type IV pilus / type II secretion / macromolecular machine
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
Specimen sourceThermus thermophilus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 8 Å resolution
AuthorsDerrick, J.P. / Collins, R.F.
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 Report
SummaryFull reportAbout validation report
DateDeposition: Sep 21, 2017 / Release: Aug 1, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 1, 2018Structure modelrepositoryInitial release
1.1Oct 24, 2018Structure modelData collection / Database referencescitation / citation_author_citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Assembly

Deposited unit
G: Type IV pilus assembly protein PilF
J: Type IV pilus assembly protein PilF
K: Type IV pilus assembly protein PilF
L: Type IV pilus assembly protein PilF
H: Type IV pilus assembly protein PilF
I: Type IV pilus assembly protein PilF
M: Type IV pilus assembly protein PilF
N: Type IV pilus assembly protein PilF
O: Type IV pilus assembly protein PilF
P: Type IV pilus assembly protein PilF
Q: Type IV pilus assembly protein PilF
R: Type IV pilus assembly protein PilF
A: Type IV pilus assembly protein PilF
B: Type IV pilus assembly protein PilF
C: Type IV pilus assembly protein PilF
D: Type IV pilus assembly protein PilF
E: Type IV pilus assembly protein PilF
F: Type IV pilus assembly protein PilF


Theoretical massNumber of molelcules
Total (without water)461,36618
Polyers461,36618
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide
Type IV pilus assembly protein PilF


Mass: 16249.751 Da / Num. of mol.: 6
Details: Domain is part of the larger protein but connectivity to other domains cannot be confirmed.
Fragment: UNP residues 330-475
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / Gene: TTHA0364 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SLC9
#2: Protein/peptide
Type IV pilus assembly protein PilF


Mass: 15440.708 Da / Num. of mol.: 6
Details: Domain is part of the larger protein but connectivity to other domains cannot be confirmed.
Fragment: UNP residues 163-299
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / Gene: TTHA0364 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SLC9
#3: Protein/peptide
Type IV pilus assembly protein PilF


Mass: 45203.906 Da / Num. of mol.: 6
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / Gene: TTHA0364 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SLC9

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Thermus thermophilus PilF ATPase (AMPPNP-bound form) / Type: COMPLEX / Entity ID: 1,2,3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionDetails: 25 mM HEPES pH 7.5, 150 mM NaCl, 5 mM MgCl2 and 5 % glycerol (v/v)
pH: 7.5
SpecimenConc.: 0.2 mg/ml / Details: Monodisperse / 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: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 4500 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 4500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 8 Å / Resolution method: FSC 0.5 CUT-OFF / Number of particles: 45000 / Symmetry type: POINT
Atomic model buildingRef protocol: FLEXIBLE FIT / Ref space: REAL

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