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- EMDB-29215: Structure of the Haloferax volcanii archaeal type IV pilus -

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Basic information

Entry
Database: EMDB / ID: EMD-29215
TitleStructure of the Haloferax volcanii archaeal type IV pilus
Map data
Sample
  • Complex: Archaeal type IV pilus
    • Protein or peptide: Pilin_N domain-containing protein
KeywordsArchaea / type IV pili / STRUCTURAL PROTEIN
Function / homologyArchaeal Type IV pilin, N-terminal / Archaeal Type IV pilin, N-terminal / Flagellin/pilin, N-terminal / membrane / Archaeal Type IV pilin N-terminal domain-containing protein
Function and homology information
Biological speciesHaloferax volcanii (archaea) / Haloferax volcanii (strain ATCC 29605 / DSM 3757 / JCM 8879 / NBRC 14742 / NCIMB 2012 / VKM B-1768 / DS2) (archaea)
Methodhelical reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsWang F / Kreutzberger MA / Baquero DP / Krupovic M / Egelman EH
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122510 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: The evolution of archaeal flagellar filaments.
Authors: Mark A B Kreutzberger / Virginija Cvirkaite-Krupovic / Ying Liu / Diana P Baquero / Junfeng Liu / Ravi R Sonani / Chris R Calladine / Fengbin Wang / Mart Krupovic / Edward H Egelman /
Abstract: Flagellar motility has independently arisen three times during evolution: in bacteria, archaea, and eukaryotes. In prokaryotes, the supercoiled flagellar filaments are composed largely of a single ...Flagellar motility has independently arisen three times during evolution: in bacteria, archaea, and eukaryotes. In prokaryotes, the supercoiled flagellar filaments are composed largely of a single protein, bacterial or archaeal flagellin, although these two proteins are not homologous, while in eukaryotes, the flagellum contains hundreds of proteins. Archaeal flagellin and archaeal type IV pilin are homologous, but how archaeal flagellar filaments (AFFs) and archaeal type IV pili (AT4Ps) diverged is not understood, in part, due to the paucity of structures for AFFs and AT4Ps. Despite having similar structures, AFFs supercoil, while AT4Ps do not, and supercoiling is essential for the function of AFFs. We used cryo-electron microscopy to determine the atomic structure of two additional AT4Ps and reanalyzed previous structures. We find that all AFFs have a prominent 10-strand packing, while AT4Ps show a striking structural diversity in their subunit packing. A clear distinction between all AFF and all AT4P structures involves the extension of the N-terminal α-helix with polar residues in the AFFs. Additionally, we characterize a flagellar-like AT4P from with filament and subunit structure similar to that of AFFs which can be viewed as an evolutionary link, showing how the structural diversity of AT4Ps likely allowed for an AT4P to evolve into a supercoiling AFF.
History
DepositionDec 19, 2022-
Header (metadata) releaseJun 28, 2023-
Map releaseJun 28, 2023-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29215.png

Downloads & links

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Map

FileDownload / File: emd_29215.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 320 pix.
= 358.4 Å		1.12 Å/pix.
x 320 pix.
= 358.4 Å		1.12 Å/pix.
x 320 pix.
= 358.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.12 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.348
Minimum - Maximum-1.8740386 - 2.894986
Average (Standard dev.)0.0047428305 (±0.07672055)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 358.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_29215_msk_1.map
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Half map: #1

Fileemd_29215_half_map_1.map
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Half map: #2

Fileemd_29215_half_map_2.map
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Sample components

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Entire : Archaeal type IV pilus

EntireName: Archaeal type IV pilus
Components
  • Complex: Archaeal type IV pilus
    • Protein or peptide: Pilin_N domain-containing protein

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Supramolecule #1: Archaeal type IV pilus

SupramoleculeName: Archaeal type IV pilus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Haloferax volcanii (archaea)
Strain: ATCC 29605 / DSM 3757 / JCM 8879 / NBRC 14742 / NCIMB 2012 / VKM B-1768 / DS2

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Macromolecule #1: Pilin_N domain-containing protein

MacromoleculeName: Pilin_N domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 20 / Enantiomer: LEVO
Source (natural)Organism: Haloferax volcanii (strain ATCC 29605 / DSM 3757 / JCM 8879 / NBRC 14742 / NCIMB 2012 / VKM B-1768 / DS2) (archaea)
Strain: ATCC 29605 / DSM 3757 / JCM 8879 / NBRC 14742 / NCIMB 2012 / VKM B-1768 / DS2
Molecular weightTheoretical: 14.841991 KDa
Recombinant expressionOrganism: Haloferax volcanii (archaea)
SequenceString:
MQLTTLFNDD SAVSPVIGVI LMVAITVILA AVIGTFVLGL GDQVSETSPQ ASFDFDYTNT SGNLTITHES GTSIDADSVS ISGPVGDDG KTWADIDGSA TEITAGSSIT VTANGSSFDS GETVRVIWTS DSGSSSSTLQ SWTYNG

UniProtKB: Archaeal Type IV pilin N-terminal domain-containing protein

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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: 6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 5.155 Å
Applied symmetry - Helical parameters - Δ&Phi: 106.297 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1660828
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE

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