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- EMDB-24956: Structure of PorLM, the proton-powered motor that drives Type IX ... -

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Basic information

Entry
Database: EMDB / ID: EMD-24956
TitleStructure of PorLM, the proton-powered motor that drives Type IX protein secretion
Map dataPostprocessed map.
Sample
  • Complex: Type IX Secretion System PorLM motor complex
    • Protein or peptide: Por secretion system protein porM/gldM
    • Protein or peptide: Por secretion system protein porL/gldL
Keywordstype IX secretion system / MOTOR PROTEIN
Function / homology
Function and homology information


membrane / metal ion binding
Similarity search - Function
: / : / 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 / Gliding motility-associated protein, GldL / GldL N-terminal domain
Similarity search - Domain/homology
Por secretion system protein porM/gldM / Por secretion system protein porL/gldL
Similarity search - Component
Biological speciesPorphyromonas gingivalis ATCC 33277 (bacteria) / Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 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_24956.png

Downloads & links

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Map

FileDownload / File: emd_24956.map.gz / Format: CCP4 / Size: 28.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocessed map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 196 pix.
= 209.328 Å		1.07 Å/pix.
x 196 pix.
= 209.328 Å		1.07 Å/pix.
x 196 pix.
= 209.328 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.068 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.080766216 - 0.12710094
Average (Standard dev.)0.00019377493 (±0.0046378016)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions196196196
Spacing196196196
CellA=B=C: 209.32799 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_24956_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: Output map from 3D refinement.

Fileemd_24956_additional_1.map
AnnotationOutput map from 3D refinement.
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_24956_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_24956_half_map_2.map
Projections & Slices
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Sample components

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Entire : Type IX Secretion System PorLM motor complex

EntireName: Type IX Secretion System PorLM motor complex
Components
  • Complex: Type IX Secretion System PorLM motor complex
    • Protein or peptide: Por secretion system protein porM/gldM
    • Protein or peptide: Por secretion system protein porL/gldL

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Supramolecule #1: Type IX Secretion System PorLM motor complex

SupramoleculeName: Type IX Secretion System PorLM motor complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Porphyromonas gingivalis ATCC 33277 (bacteria)
Molecular weightTheoretical: 233.1 KDa

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Macromolecule #1: Por secretion system protein porM/gldM

MacromoleculeName: Por secretion system protein porM/gldM / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561) (bacteria)
Strain: ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561
Molecular weightTheoretical: 29.323125 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MAVGSNGNAN RQKMINLMYL VFIAMMALNV SSEVLDGFDK VDKSLTSSID GSDKRNNLVL SELNTAYRTN PEKVKVWYER SLVLQKEAD SLCTFIDDLK LAIARESDGK DAKVNDIRRK DNLDASSVVM LNPINGKGST LRKEVDKFRE LVATLMTDKA K LKLIEQAL ...String:
MAVGSNGNAN RQKMINLMYL VFIAMMALNV SSEVLDGFDK VDKSLTSSID GSDKRNNLVL SELNTAYRTN PEKVKVWYER SLVLQKEAD SLCTFIDDLK LAIARESDGK DAKVNDIRRK DNLDASSVVM LNPINGKGST LRKEVDKFRE LVATLMTDKA K LKLIEQAL NTESGTKGKS WESSLFENMP TVAAITLLTK LQSDVRYAQG EVLADLVKSV DVGDYRVNSE NLYFQGQFGS WS HPQFEKG GGSGGGSGGG SWSHPQFEK

UniProtKB: Por secretion system protein porM/gldM

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Macromolecule #2: Por secretion system protein porL/gldL

MacromoleculeName: Por secretion system protein porL/gldL / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561) (bacteria)
Strain: ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561
Molecular weightTheoretical: 34.940586 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MGHYRRYKNI LEMYLASHKG RRLLNIVYSW GAAVVILGAL FKLLHLPMGN EMLFVGMITE FLVFFISGFE KPAMEYHWEE VFPELDSKN PMDRREMEQR REYLREKAKE AAAYAERPSS VRLASASLGT QPQEQPKPAT PFQSQLTGIL PEEQIQRLSE G IDKLAEAG ...String:
MGHYRRYKNI LEMYLASHKG RRLLNIVYSW GAAVVILGAL FKLLHLPMGN EMLFVGMITE FLVFFISGFE KPAMEYHWEE VFPELDSKN PMDRREMEQR REYLREKAKE AAAYAERPSS VRLASASLGT QPQEQPKPAT PFQSQLTGIL PEEQIQRLSE G IDKLAEAG EQLARIGRTA AAMTESYEQM QADQEGLRLN SQSYIQQMES LSRNISGLNT IYEIQLKGIS SQIDTIDRIN RG LAHIRDM YDNSVIDSSS FRNENERMAR QLTQLNEVYA RLLQALTTNV GLPGMPGNFG ASNPSSSGSS PL

UniProtKB: Por secretion system protein porL/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
0.02 %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: 55.0 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: 8205503
Startup modelType of model: EMDB MAP
EMDB ID:

10893

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Details: RELION 3.1 was used for reconstruction / Number images used: 649359
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: 72.16
Output model

PDB-7sat:
Structure of PorLM, the proton-powered motor that drives Type IX protein secretion

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