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- EMDB-18593: CryoEM structure of the type IV pilin PilA5 from Thermus thermophilus -

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Basic information

Entry
Database: EMDB / ID: EMD-18593
TitleCryoEM structure of the type IV pilin PilA5 from Thermus thermophilus
Map data
Sample
  • Complex: Thermus thermophilus wide pilus
    • Protein or peptide: Type IV narrow pilus major component PilA5
  • Ligand: MAGNESIUM ION
KeywordsType IV pilin glycosylation / twitching motility / PROTEIN FIBRIL
Function / homology: / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like / cell outer membrane / periplasmic space / plasma membrane / Type IV narrow pilus major component PilA5
Function and homology information
Biological speciesThermus thermophilus HB27 (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 2.63 Å
AuthorsGold VAM / Neuhaus A / Gaines M / Isupov M / McLaren M
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R008639/1 United Kingdom
CitationJournal: To Be Published
Title: CryoEM structure of the type IV pilin PilA4 from Thermus thermophilus
Authors: Gold VAM / Neuhaus A / Gaines M / Isupov M / McLaren M
History
DepositionOct 4, 2023-
Header (metadata) releaseOct 16, 2024-
Map releaseOct 16, 2024-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18593.png

Downloads & links

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Map

FileDownload / File: emd_18593.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 512 pix.
= 536.576 Å		1.05 Å/pix.
x 512 pix.
= 536.576 Å		1.05 Å/pix.
x 512 pix.
= 536.576 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.048 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.082781 - 0.9999999
Average (Standard dev.)0.15038465 (±0.016491134)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 536.576 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_18593_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_18593_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Thermus thermophilus wide pilus

EntireName: Thermus thermophilus wide pilus
Components
  • Complex: Thermus thermophilus wide pilus
    • Protein or peptide: Type IV narrow pilus major component PilA5
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Thermus thermophilus wide pilus

SupramoleculeName: Thermus thermophilus wide pilus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Thermus thermophilus HB27 (bacteria)

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Macromolecule #1: Type IV narrow pilus major component PilA5

MacromoleculeName: Type IV narrow pilus major component PilA5 / type: protein_or_peptide / ID: 1 / Number of copies: 31 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB27 (bacteria)
Molecular weightTheoretical: 11.441797 KDa
SequenceString:
FTLIELAIVI VIIGILVAIA VPRFVDLTDQ ANQANVDATA AAVRSAYAIA TVQAKGIPTC DQVFANLEGG STSGSTWTSS DNSTTVSCN ASADTFTISR GGKTRTLNLT VN

UniProtKB: Type IV narrow pilus major component PilA5

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 31 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Digitization - Frames/image: 1-40 / Number real images: 2455 / Average electron dose: 47.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 11.25 Å
Applied symmetry - Helical parameters - Δ&Phi: 84.0 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.63 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 475441
Segment selectionNumber selected: 2763060 / Software - Name: cryoSPARC
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8qqj:
CryoEM structure of the type IV pilin PilA5 from Thermus thermophilus

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