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- EMDB-18588: CryoEM structure of the type IV pilin PilA4 from Thermus thermophilus -

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Basic information

Entry
Database: EMDB / ID: EMD-18588
TitleCryoEM structure of the type IV pilin PilA4 from Thermus thermophilus
Map data
Sample
  • Complex: Thermus thermophilus wide pilus
    • Protein or peptide: Type IV wide pilus major component PilA4
  • Ligand: alpha-D-mannopyranose
  • Ligand: 2-acetamido-2-deoxy-alpha-D-galactopyranose
KeywordsType IV pilin glycosylation / twitching motility / PROTEIN FIBRIL
Function / homology
Function and homology information


protein secretion by the type II secretion system / type II protein secretion system complex / cell outer membrane / periplasmic space / plasma membrane
Similarity search - Function
Bacterial general secretion pathway protein G-type pilin / : / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like
Similarity search - Domain/homology
Type IV wide pilus major component PilA4
Similarity search - Component
Biological speciesThermus thermophilus HB27 (bacteria) / Thermus thermophilus (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 2.4 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
History
DepositionOct 4, 2023-
Header (metadata) releaseOct 16, 2024-
Map releaseOct 16, 2024-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18588.png

Downloads & links

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Map

FileDownload / File: emd_18588.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: 0.035
Minimum - Maximum-0.078599975 - 0.34300625
Average (Standard dev.)0.00023322304 (±0.0077365907)
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_18588_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_18588_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 wide pilus major component PilA4
  • Ligand: alpha-D-mannopyranose
  • Ligand: 2-acetamido-2-deoxy-alpha-D-galactopyranose

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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 wide pilus major component PilA4

MacromoleculeName: Type IV wide pilus major component PilA4 / type: protein_or_peptide / ID: 1 / Number of copies: 45 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (bacteria)
Molecular weightTheoretical: 13.251123 KDa
SequenceString:
FTLIELLIVI AIIAILAAVL IPNLLAARKR ANDTVVTAYL NDAVKFQEMY QIDNNSYTSN QAALISLGLK STPANVTFSI VSASANSYC MIAGHSGGTV WFAATPDKGV YKTNTAVTSS QPESCP

UniProtKB: Type IV wide pilus major component PilA4

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Macromolecule #4: alpha-D-mannopyranose

MacromoleculeName: alpha-D-mannopyranose / type: ligand / ID: 4 / Number of copies: 45 / Formula: MAN
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-MAN:
alpha-D-mannopyranose

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Macromolecule #5: 2-acetamido-2-deoxy-alpha-D-galactopyranose

MacromoleculeName: 2-acetamido-2-deoxy-alpha-D-galactopyranose / type: ligand / ID: 5 / Number of copies: 45 / Formula: A2G
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-A2G:
2-acetamido-2-deoxy-alpha-D-galactopyranose

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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 / 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: 9.242 Å
Applied symmetry - Helical parameters - Δ&Phi: 92.36 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4) / Number images used: 654248
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8qqd:
CryoEM structure of the type IV pilin PilA4 from Thermus thermophilus

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