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- EMDB-48741: Structure of P. gingivalis PorK and PorN complexes from cryo elec... -

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Basic information

Entry
Database: EMDB / ID: EMD-48741
TitleStructure of P. gingivalis PorK and PorN complexes from cryo electron microscopy
Map data
Sample
  • Complex: PorK/N protein complex
    • Protein or peptide: Gliding motility protein GldN
    • Protein or peptide: Lipoprotein, putative
  • Ligand: alpha-D-mannopyranose
  • Ligand: CALCIUM ION
KeywordsT9SS / porphyromonas gingivalis / TRANSPORT PROTEIN
Function / homology
Function and homology information


formylglycine-generating oxidase activity
Similarity search - Function
Gliding motility associated protein GldN / Gliding motility associated protein GldN / : / Sulfatase-modifying factor enzyme / Sulfatase-modifying factor enzyme 1-like domain / Sulfatase-modifying factor enzyme superfamily / C-type lectin fold / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Gliding motility protein GldN / Lipoprotein, putative
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria) / Porphyromonas gingivalis W83 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.57 Å
AuthorsHanssen E / Morton CJ / Gorasia DG / Veith PD / Reynolds EC
Funding support Australia, 2 items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1123866 Australia
National Health and Medical Research Council (NHMRC, Australia)1193647 Australia
CitationJournal: Biorxiv / Year: 2025
Title: Near-atomic structure of the PorKN rings, disulfide bonded to PorG and bound to Attachment Complexes, provide mechanistic insights into the type IX secretion system
Authors: Gorasia D / Hanssen E / Mudaliyar M / Morton C / Valimehr S / Seers C / Zhang L / Ghosal D / Veith P / Reynolds E
History
DepositionJan 21, 2025-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48741.png

Downloads & links

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Map

FileDownload / File: emd_48741.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 600 pix.
= 792. Å		1.32 Å/pix.
x 600 pix.
= 792. Å		1.32 Å/pix.
x 600 pix.
= 792. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-0.16611439 - 0.5590389
Average (Standard dev.)-0.000061105384 (±0.018384067)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 792.00006 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48741_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_48741_additional_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_48741_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_48741_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : PorK/N protein complex

EntireName: PorK/N protein complex
Components
  • Complex: PorK/N protein complex
    • Protein or peptide: Gliding motility protein GldN
    • Protein or peptide: Lipoprotein, putative
  • Ligand: alpha-D-mannopyranose
  • Ligand: CALCIUM ION

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Supramolecule #1: PorK/N protein complex

SupramoleculeName: PorK/N protein complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Porphyromonas gingivalis (bacteria) / Strain: W83
Molecular weightTheoretical: 3.5 MDa

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Macromolecule #1: Gliding motility protein GldN

MacromoleculeName: Gliding motility protein GldN / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis W83 (bacteria) / Strain: W83
Molecular weightTheoretical: 30.080869 KDa
SequenceString: LSNRAQEFNR RLTQKTDNAP WRRVVYRRVD LMEESNAVLY YPPRPIGDRK NLFSTIFGLI NSNSLDVYEY LDGFEAFTDQ YKIKFQEFL DRFGIYYQPS TNKNAELFKV ADSDIPSAEV KAYYVKEEWY FTPTNSDVDI KIQAICPIMT GQDEFGEVRN Q PLFWIPYE ...String:
LSNRAQEFNR RLTQKTDNAP WRRVVYRRVD LMEESNAVLY YPPRPIGDRK NLFSTIFGLI NSNSLDVYEY LDGFEAFTDQ YKIKFQEFL DRFGIYYQPS TNKNAELFKV ADSDIPSAEV KAYYVKEEWY FTPTNSDVDI KIQAICPIMT GQDEFGEVRN Q PLFWIPYE NIRPYIARER VMLSSLNNTR NSTIDDFFRL NLYKGDIVKT ENLHNRALAE YCPTPDSMKM ESKRIDKELQ GF RDGLFVT QDTTWMK

UniProtKB: Gliding motility protein GldN

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Macromolecule #2: Lipoprotein, putative

MacromoleculeName: Lipoprotein, putative / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis W83 (bacteria) / Strain: W83
Molecular weightTheoretical: 50.067676 KDa
SequenceString: EPSPFGMIQV PRGSIVLGNK EADSLWGIPA ESRPISVDAF WMDRTEITNA QYRQFVYYVR DSIIRERLAD PAYGGNEEYK ITENKFGEP VTPHLDWSKP IPSEKRATEE EIAAINSVYY TNPVTHDRKL NPDQMVYRYE VYDYRSAALR EHQLKAAKRN L NTDIKVDP ...String:
EPSPFGMIQV PRGSIVLGNK EADSLWGIPA ESRPISVDAF WMDRTEITNA QYRQFVYYVR DSIIRERLAD PAYGGNEEYK ITENKFGEP VTPHLDWSKP IPSEKRATEE EIAAINSVYY TNPVTHDRKL NPDQMVYRYE VYDYRSAALR EHQLKAAKRN L NTDIKVDP NAVVMISKDT AFVDESGNII SETITRPLSS EYDFLNTYIV PIYPDETCWV NDFPNARTEI YTRMYFNHPG YD DYPVVGI SWEQAQAFCA WRSEFFRKGI RLPEGQIMDD FRLPTEAEWE YAARMGDSNN KYPWSTEDLR TGRGCFLGNF KPG EGDYTA DGHLIPSRVS SFSPNDFGLY DMAGNVAEWT STAFSESGLK QMSDINPELE YKAALTDPYI LKQKVVRGGS WKDV ARFIR SATRSHEYQN VGRSYIGFRC VRTSIAFSSG KA

UniProtKB: Lipoprotein, putative

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Macromolecule #4: alpha-D-mannopyranose

MacromoleculeName: alpha-D-mannopyranose / type: ligand / ID: 4 / Number of copies: 1 / Formula: MAN
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-MAN:
alpha-D-mannopyranose

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Macromolecule #5: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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

Concentration1.2 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMC4H12ClNO3Tris-HCL
50.0 mMNaClSodium chloride
0.5 %C24H46O11n-Dodecyl-B-D-maltoside
1.0 MCH4N2OUrea
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Details: 15mA
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV / Details: Blot forace -1 blot time 3sec sample size 4ul.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 8909 / Average exposure time: 5.34 sec. / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 64000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 556522
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C33 (33 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.1) / Number images used: 69982
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9myj:
Structure of P. gingivalis PorK and PorN complexes from cryo electron microscopy

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