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- EMDB-10894: PorLM complex from Porphyromonas gingivalis solubilised in LMNG m... -

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Basic information

Entry
Database: EMDB / ID: EMD-10894
TitlePorLM complex from Porphyromonas gingivalis solubilised in LMNG micelle
Map dataVolume of full length PorLM in LMNG micelle
Sample
  • Complex: PorLM
    • Protein or peptide: PorL
    • Protein or peptide: PorM
Biological speciesFlavobacterium johnsoniae (bacteria) / Porphyromonas gingivalis (bacteria) / Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.6 Å
AuthorsHennell James R / Deme JC / Lea SM
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Wellcome Trust107929/Z/15/Z United Kingdom
Wellcome Trust100298/Z/12/Z United Kingdom
Wellcome Trust201536/Z/16/Z United Kingdom
CitationJournal: Nat Microbiol / Year: 2021
Title: Structure and mechanism of the proton-driven motor that powers type 9 secretion and gliding motility.
Authors: Rory Hennell James / Justin C Deme / Andreas Kjӕr / Felicity Alcock / Augustinas Silale / Frédéric Lauber / Steven Johnson / Ben C Berks / Susan M Lea /
Abstract: Three classes of ion-driven protein motors have been identified to date: ATP synthase, the bacterial flagellar motor and a proton-driven motor that powers gliding motility and the type 9 protein ...Three classes of ion-driven protein motors have been identified to date: ATP synthase, the bacterial flagellar motor and a proton-driven motor that powers gliding motility and the type 9 protein secretion system in Bacteroidetes bacteria. Here, we present cryo-electron microscopy structures of the gliding motility/type 9 protein secretion system motors GldLM from Flavobacterium johnsoniae and PorLM from Porphyromonas gingivalis. The motor is an asymmetric inner membrane protein complex in which the single transmembrane helices of two periplasm-spanning GldM/PorM proteins are positioned inside a ring of five GldL/PorL proteins. Mutagenesis and single-molecule tracking identify protonatable amino acid residues in the transmembrane domain of the complex that are important for motor function. Our data provide evidence for a mechanism in which proton flow results in rotation of the periplasm-spanning GldM/PorM dimer inside the intra-membrane GldL/PorL ring to drive processes at the bacterial outer membrane.
History
DepositionApr 21, 2020-
Header (metadata) releaseOct 14, 2020-
Map releaseOct 14, 2020-
UpdateMay 26, 2021-
Current statusMay 26, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00295
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.00295
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10894.png

Downloads & links

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Map

FileDownload / File: emd_10894.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationVolume of full length PorLM in LMNG micelle
Voxel sizeX=Y=Z: 0.822 Å
Density
Contour LevelBy AUTHOR: 0.0029 / Movie #1: 0.00295
Minimum - Maximum-0.004757663 - 0.016916998
Average (Standard dev.)-3.5655674e-05 (±0.0005748212)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 394.56 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8220.8220.822
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z394.560394.560394.560
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.0050.017-0.000

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Supplemental data

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Mask #1

Fileemd_10894_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_10894_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_10894_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PorLM

EntireName: PorLM
Components
  • Complex: PorLM
    • Protein or peptide: PorL
    • Protein or peptide: PorM

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Supramolecule #1: PorLM

SupramoleculeName: PorLM / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Flavobacterium johnsoniae (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: PorL

MacromoleculeName: PorL / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGHYRRYKNI LEMYLASHKG RRLLNIVYSW GAAVVILGAL FKLLHLPMGN EMLFVGMITE FLVFFISGF EKPAMEYHWE EVFPELDSKN PMDRREMEQR REYLREKAKE AAAYAERSSS V RLASASLG TQPQEQSKPA TPFQSQLTGI LPEEQIQRLS EGIDKLAEAG ...String:
MGHYRRYKNI LEMYLASHKG RRLLNIVYSW GAAVVILGAL FKLLHLPMGN EMLFVGMITE FLVFFISGF EKPAMEYHWE EVFPELDSKN PMDRREMEQR REYLREKAKE AAAYAERSSS V RLASASLG TQPQEQSKPA TPFQSQLTGI LPEEQIQRLS EGIDKLAEAG EQLARIGRTA AA MTESYEQ MQADQEGLRL NSQSYIQQME SLSRNISGLN TIYEIQLKGI SSQIDTIDRI NRG LAHIRD MYDNSVIDSS SFRNENERMA RQLTQLNEVY ARLLQALTTN VGLPGMPGNF GASN PSSSG SSPL

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Macromolecule #2: PorM

MacromoleculeName: PorM / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561) (bacteria)
SequenceString: MAVGSNGNAN RQKMINLMYL VFIAMMALNV SSEVLDGFDK VDKSLTSSID GSDKRNNLVL SELNTAYRT NPEKVKVWYE RSLVLQKEAD SLCTFIDDLK LAIARESDGK DAKVNDIRRK D NLDASSVV MLNPINGKGS TLRKEVDKFR ELVATLMTDK AKLKLIEQAL ...String:
MAVGSNGNAN RQKMINLMYL VFIAMMALNV SSEVLDGFDK VDKSLTSSID GSDKRNNLVL SELNTAYRT NPEKVKVWYE RSLVLQKEAD SLCTFIDDLK LAIARESDGK DAKVNDIRRK D NLDASSVV MLNPINGKGS TLRKEVDKFR ELVATLMTDK AKLKLIEQAL NTESGTKGKS WE SSLFENM PTVAAITLLT KLQSDVRYAQ GEVLADLVKS VDVGDYRVNS ITAQVIPQSQ IVM SGDTYK ANIVLSSVDT TQRPDVFVNG KLLSPENMGL FTATAGAPGT YPVKGYIEMM GNDG VKIRR DFESEYFVTE PMASVAPTMM NVLYAGIDNP INIAVPGVAQ QNVSATINNG TLTRR GNLW IARPTKVGSE AIISVTAQSG GRTIQMAKTT LRVRALPDPL PYIEYKDVQG NTKRFK GGR LGKREILAAG GIKAALDDDL LEVNYTVVKF QLVFYDSMGN SIPEVSDGAS FSERQKR QI QNLGKGKRFY VTEVIARGPD GIERKIPAIE VIVN

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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

BufferpH: 7.5
Component:
ConcentrationName
20.0 mMHEPES
150.0 mMNaClSodium chloride
0.02 %LMNG
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 0.0003 µm / Nominal defocus min: 0.0001 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 48.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1133336
CTF correctionSoftware - Name: SIMPLE (ver. 3.0)
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: SIMPLE (ver. 3.0)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 199929

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