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- EMDB-24958: Structure of GldLM, the proton-powered motor that drives Type IX ... -

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Basic information

Entry
Database: EMDB / ID: EMD-24958
TitleStructure of GldLM, the proton-powered motor that drives Type IX protein secretion and gliding motility in Sphingobacterium wenxiniae
Map dataPostprocessed EM density map.
Sample
  • Complex: Type IX Secretion System/gliding motility GldLM motor complex
    • Protein or peptide: GldM
    • Protein or peptide: GldL
Keywordstype IX secretion system / MOTOR PROTEIN
Function / homology
Function and homology information


Gliding motility-associated protein, GldL / : / GldL N-terminal domain / : / : / GldM second domain / GldM third domain / Gliding motility-associated protein GldM / Gliding motility-associated protein GldM, C-terminal / Gliding motility-associated protein GldM, N-terminal ...Gliding motility-associated protein, GldL / : / GldL N-terminal domain / : / : / GldM second domain / GldM third domain / Gliding motility-associated protein GldM / Gliding motility-associated protein GldM, C-terminal / Gliding motility-associated protein GldM, N-terminal / GldM C-terminal domain / GldM N-terminal domain
Similarity search - Domain/homology
Gliding motility-associated protein GldM / Gliding motility-associated protein GldL
Similarity search - Component
Biological speciesSphingobacterium wenxiniae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsHennell James R / Deme JC
Funding supportEuropean Union, 4 items
OrganizationGrant numberCountry
Wellcome Trust102164/Z/13/ZEuropean Union
Wellcome Trust107929/Z/15/ZEuropean Union
Wellcome Trust219477/Z/19/ZEuropean Union
European Research Council (ERC)833713European Union
CitationJournal: mBio / Year: 2022
Title: Structures of the Type IX Secretion/Gliding Motility Motor from across the Phylum .
Authors: Rory Hennell James / Justin C Deme / Alicia Hunter / Ben C Berks / Susan M Lea /
Abstract: Gliding motility using cell surface adhesins, and export of proteins by the type IX secretion system (T9SS) are two phylum-specific features of the Bacteroidetes. Both of these processes are ...Gliding motility using cell surface adhesins, and export of proteins by the type IX secretion system (T9SS) are two phylum-specific features of the Bacteroidetes. Both of these processes are energized by the GldLM motor complex, which transduces the proton motive force at the inner membrane into mechanical work at the outer membrane. We previously used cryo-electron microscopy to solve the structure of the GldLM motor core from Flavobacterium johnsoniae at 3.9-Å resolution (R. Hennell James, J. C. Deme, A. Kjaer, F. Alcock, et al., Nat Microbiol 6:221-233, 2021, https://dx.doi.org/10.1038/s41564-020-00823-6). Here, we present structures of homologous complexes from a range of pathogenic and environmental species at up to 3.0-Å resolution. These structures show that the architecture of the GldLM motor core is conserved across the phylum, although there are species-specific differences at the N terminus of GldL. The resolution improvements reveal a cage-like structure that ties together the membrane-proximal cytoplasmic region of GldL and influences gliding function. These findings add detail to our structural understanding of bacterial ion-driven motors that drive the T9SS and gliding motility. Many bacteria in the phylum use the type IX secretion system to secrete proteins across their outer membrane. Most of these bacteria can also glide across surfaces using adhesin proteins that are propelled across the cell surface. Both secretion and gliding motility are driven by the GldLM protein complex, which forms a nanoscale electrochemical motor. We used cryo-electron microscopy to study the structure of the GldLM protein complex from different species, including the human pathogens Porphyromonas gingivalis and Capnocytophaga canimorsus. The organization of the motor is conserved across species, but we find species-specific structural differences and resolve motor features at higher resolution. This work improves our understanding of the type IX secretion system, which is a virulence determinant in human and animal diseases.
History
DepositionSep 23, 2021-
Header (metadata) releaseMar 23, 2022-
Map releaseMar 23, 2022-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_24958.png

Downloads & links

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Map

FileDownload / File: emd_24958.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocessed EM density map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 212.992 Å		0.83 Å/pix.
x 256 pix.
= 212.992 Å		0.83 Å/pix.
x 256 pix.
= 212.992 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.07944406 - 0.13873568
Average (Standard dev.)0.000037367907 (±0.0049622217)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.992 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_24958_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Refined EM density map.

Fileemd_24958_additional_1.map
AnnotationRefined EM density map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_24958_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_24958_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Type IX Secretion System/gliding motility GldLM motor complex

EntireName: Type IX Secretion System/gliding motility GldLM motor complex
Components
  • Complex: Type IX Secretion System/gliding motility GldLM motor complex
    • Protein or peptide: GldM
    • Protein or peptide: GldL

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Supramolecule #1: Type IX Secretion System/gliding motility GldLM motor complex

SupramoleculeName: Type IX Secretion System/gliding motility GldLM motor complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Sphingobacterium wenxiniae (bacteria)
Molecular weightTheoretical: 172.5 KDa

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Macromolecule #1: GldM

MacromoleculeName: GldM / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Sphingobacterium wenxiniae (bacteria)
Molecular weightTheoretical: 28.533041 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MAGKKETPRQ RMIGILYLVL LGLVALNVSD SILDAFKNLG NSLNTSTQNT QAGIDNMFLA FRETKLKENP ERAQPILQKA EQAQALVQQ LTSKVGELTT LLEGEGGGLD EETGDVKYRS STDISARLMI NEGRAKELRE VITKTKAELL TLTNNEINLT L EAEDPAPR ...String:
MAGKKETPRQ RMIGILYLVL LGLVALNVSD SILDAFKNLG NSLNTSTQNT QAGIDNMFLA FRETKLKENP ERAQPILQKA EQAQALVQQ LTSKVGELTT LLEGEGGGLD EETGDVKYRS STDISARLMI NEGRAKELRE VITKTKAELL TLTNNEINLT L EAEDPAPR GGIKKTWEQA NFGDGIPLTA AITALEKINA DAKNAESAVV KHIFGKMDQA VVNLDQENLY FQGQFGSWSH PQ FEKGGGS GGGSGGGSWS HPQFEK

UniProtKB: Gliding motility-associated protein GldM

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Macromolecule #2: GldL

MacromoleculeName: GldL / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Sphingobacterium wenxiniae (bacteria)
Molecular weightTheoretical: 23.072148 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MAKKTKFKFG INTLINWGAT VVIIGLMFKI LHLKGGEWMI GVGLAVEALL FFIMGFMQAE QEPDWTRVYP ELDEDYNGEL PTRSVRAVA QPVATGNTAA LDKLLQDAKI DENLIGNLGD GLRTFSDKVA SISKVADTAV ATNQFADKLN AASTGAAQLS N AFERAASD ...String:
MAKKTKFKFG INTLINWGAT VVIIGLMFKI LHLKGGEWMI GVGLAVEALL FFIMGFMQAE QEPDWTRVYP ELDEDYNGEL PTRSVRAVA QPVATGNTAA LDKLLQDAKI DENLIGNLGD GLRTFSDKVA SISKVADTAV ATNQFADKLN AASTGAAQLS N AFERAASD LQTFNESAAD MQQFKEQVST FNKNLSSLNA IYGNMLSAMN TNRS

UniProtKB: Gliding motility-associated protein GldL

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.0 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
100.0 mMNH2C(CH2OH)3.HClTris-HCl
150.0 mMNaClsodium chloride
0.01 %C47H88O22Lauryl Maltose Neopentyl Glycol
1.0 mMC10H16N2O8Ethylenediaminetetraacetic acid
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Details: 15 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: Wait time 10 s Blot time 2 s.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 56.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 7167266
Startup modelType of model: EMDB MAP
EMDB ID:

10893

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 111727
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsA homology model based on the structure of FjoGldLM (PDB 6YS8) was used as a starting model and modified to fit the EM density using Coot. Refinement was carried out using Phenix.
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 63.2
Output model

PDB-7sax:
Structure of GldLM, the proton-powered motor that drives Type IX protein secretion and gliding motility in Sphingobacterium wenxiniae

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