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- EMDB-24961: Structure of the periplasmic domain of GldM from Capnocytophaga c... -

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Basic information

Entry
Database: EMDB / ID: EMD-24961
TitleStructure of the periplasmic domain of GldM from Capnocytophaga canimorsus
Map data
Sample
  • Complex: Type IX Secretion System/gliding motility GldM periplasmic domain
    • Protein or peptide: GldM
Keywordstype IX secretion system / MOTOR PROTEIN
Function / homology
Function and homology information


: / : / 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 protein GldM
Similarity search - Component
Biological speciesCapnocytophaga canimorsus Cc5 (bacteria) / Capnocytophaga canimorsus (strain 5) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 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_24961.png

Downloads & links

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Map

FileDownload / File: emd_24961.map.gz / Format: CCP4 / Size: 34.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.648 Å
Density
Contour LevelBy AUTHOR: 0.045
Minimum - Maximum-0.060285985 - 0.17165019
Average (Standard dev.)-0.000023668228 (±0.0038925912)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions208208208
Spacing208208208
CellA=B=C: 342.784 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_24961_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Additional map: #1

Fileemd_24961_additional_1.map
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Half map: #2

Fileemd_24961_half_map_1.map
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Half map: #1

Fileemd_24961_half_map_2.map
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Sample components

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Entire : Type IX Secretion System/gliding motility GldM periplasmic domain

EntireName: Type IX Secretion System/gliding motility GldM periplasmic domain
Components
  • Complex: Type IX Secretion System/gliding motility GldM periplasmic domain
    • Protein or peptide: GldM

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Supramolecule #1: Type IX Secretion System/gliding motility GldM periplasmic domain

SupramoleculeName: Type IX Secretion System/gliding motility GldM periplasmic domain
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: The structure of the periplasmic domain of GldM was solved using a sample that also included GldL and was used to solve a structure of GldLM
Source (natural)Organism: Capnocytophaga canimorsus Cc5 (bacteria)

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Macromolecule #1: GldM

MacromoleculeName: GldM / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Capnocytophaga canimorsus (strain 5) (bacteria)
Molecular weightTheoretical: 41.123895 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MAGGNSPRQK MINLMYLVFI SMLALNMGKE VLSAFGLMNE KLEASNEKAN NANINAIQAL EQNNAENPDQ FAEAFQKSKK VKELSDSFY NYIEGIKGEV MNQVGEDKKD YQVMDKSDYL DQKFFVGDNY KPEGEEFVRQ INDYKTQLVE LLGGKEGTYG E LVGKIDGN ...String:
MAGGNSPRQK MINLMYLVFI SMLALNMGKE VLSAFGLMNE KLEASNEKAN NANINAIQAL EQNNAENPDQ FAEAFQKSKK VKELSDSFY NYIEGIKGEV MNQVGEDKKD YQVMDKSDYL DQKFFVGDNY KPEGEEFVRQ INDYKTQLVE LLGGKEGTYG E LVGKIDGN FNTNDVVDRE GVTRKWLNYN FEGFPYIASV AKLSMMQSDI RATEQEVYAE MLKGQLKSQI SMTNYTTLLE QS KGAYYQG ESFDGAIVLG RKDASTRPNE VELMLDGRKL SASEFQIEDG KVKLKVGAGN AGEHKITGNL YFDQDGKRIA VPV SQVFST IPKPENLYFQ GQFGSWSHPQ FEKGGGSGGG SGGGSWSHPQ FEK

UniProtKB: Gliding motility protein GldM

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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.
DetailsThe structure of the periplasmic domain of GldM was solved using a sample that also included GldL and was used to solve a structure of GldLM

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 59.0 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: 9197926
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 595559
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 FjoGldM (PDB 6EY4) 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: 93.02
Output model

PDB-7sb2:
Structure of the periplasmic domain of GldM from Capnocytophaga canimorsus

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