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- EMDB-70857: Cryo-EM structure of the T9SS PORkN ring complex of P. Gingivalis -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-70857
TitleCryo-EM structure of the T9SS PORkN ring complex of P. Gingivalis
Map data
Sample
  • Organelle or cellular component: T9SS PorKN ring complex
  • Protein or peptide: Por secretion system protein porK/gldK
  • Protein or peptide: Por secretion system protein porN/gldN
KeywordsT9SS / Type IX SECRETION SYSTEM / PORKN RING COMPLEX / PORPHYROMONAS GINGIVALIS / PROTEIN TRANSPORT / MEMBRANE 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
Por secretion system protein porN/gldN / Por secretion system protein porK/gldK
Similarity search - Component
Biological speciesPorphyromonas gingivalis ATCC 33277 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLiu X / Song L / Zheng L / Hu B
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: The structure of the T9SS ring complex reveals conformational plasticity based on the repurposed FGE fold
Authors: Liu X / Perpich J / Song L / Cambillau C / Doan T / Zheng L / Lamont RJ / Cascales E / Hu B
History
DepositionMay 27, 2025-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70857.png

Downloads & links

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Map

FileDownload / File: emd_70857.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 200 pix.
= 220. Å		1.1 Å/pix.
x 200 pix.
= 220. Å		1.1 Å/pix.
x 200 pix.
= 220. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.39
Minimum - Maximum-1.3330309 - 2.866349
Average (Standard dev.)0.010063049 (±0.10892707)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 220.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70857_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_70857_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_70857_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 : T9SS PorKN ring complex

EntireName: T9SS PorKN ring complex
Components
  • Organelle or cellular component: T9SS PorKN ring complex
  • Protein or peptide: Por secretion system protein porK/gldK
  • Protein or peptide: Por secretion system protein porN/gldN

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Supramolecule #1: T9SS PorKN ring complex

SupramoleculeName: T9SS PorKN ring complex / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Porphyromonas gingivalis ATCC 33277 (bacteria)

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Macromolecule #1: Por secretion system protein porK/gldK

MacromoleculeName: Por secretion system protein porK/gldK / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis ATCC 33277 (bacteria) / Strain: ATCC 33277
Molecular weightTheoretical: 55.979594 KDa
SequenceString: MCRKNRFFAL AGFFLFGVFT ISSCGSSKRA VGGELTGAKL SSWNEPSPFG MIQVPRGSIV LGNKEADSLW GIPAESRPIS VDAFWMDRT EITNAQYRQF VYYVRDSIIR ERLADPAYGG NEEYKITENK FGEPVTPHLD WSKPIPSEKR ATEEEIAAIN S VYYTNPVT ...String:
MCRKNRFFAL AGFFLFGVFT ISSCGSSKRA VGGELTGAKL SSWNEPSPFG MIQVPRGSIV LGNKEADSLW GIPAESRPIS VDAFWMDRT EITNAQYRQF VYYVRDSIIR ERLADPAYGG NEEYKITENK FGEPVTPHLD WSKPIPSEKR ATEEEIAAIN S VYYTNPVT HDRKLNPDQM VYRYEVYDYR SAALREHQLK AAKRNLNTDI KVDPNAVVMI SKDTAFVDES GNIISETITR PL SSEYDFL NTYIVPIYPD ETCWVNDFPN ARTEIYTRMY FNHPGYDDYP VVGISWEQAQ AFCAWRSEFF RKGIRLPEGQ IMD DFRLPT EAEWEYAARM GDSNNKYPWS TEDLRTGRGC FLGNFKPGEG DYTADGHLIP SRVSSFSPND FGLYDMAGNV AEWT STAFS ESGLKQMSDI NPELEYKAAL TDPYILKQKV VRGGSWKDVA RFIRSATRSH EYQNVGRSYI GFRCVRTSIA FSSGK APKS SRRSIKK

UniProtKB: Por secretion system protein porK/gldK

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Macromolecule #2: Por secretion system protein porN/gldN

MacromoleculeName: Por secretion system protein porN/gldN / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis ATCC 33277 (bacteria) / Strain: ATCC 33277
Molecular weightTheoretical: 41.519016 KDa
SequenceString: MKVFKAVIGA ILAATVSIPS VAQENTNNRS PQVGRAPRNT EVEQMTTLSN RAQEFNRRLT QKTDNAPWRR VVYRRVDLME ESNAVLYYP PRPIGDRKNL FSTIFGLINS NSLDVYEYLD GFEAFTDQYK IKFQEFLDRF GIYYQPSTNK NAELFKVADS D IPSAEVKA ...String:
MKVFKAVIGA ILAATVSIPS VAQENTNNRS PQVGRAPRNT EVEQMTTLSN RAQEFNRRLT QKTDNAPWRR VVYRRVDLME ESNAVLYYP PRPIGDRKNL FSTIFGLINS NSLDVYEYLD GFEAFTDQYK IKFQEFLDRF GIYYQPSTNK NAELFKVADS D IPSAEVKA YYVKEEWYFT PTNSDVDIKI QAICPIMTGQ DEFGEVRNQP LFWIPYENIR PYIARERVML SSLNNTRNST ID DFFRLNL YKGDIVKTEN LHNRALAEYC PTPDSMKMES KRIDKELQGF RDGLFVTQDT TWMKQVETKK SKGKKLEKAR GKN ITSRTR GQGEGAAETE AVEPKKQKAS KNKAATRSVR RRK

UniProtKB: Por secretion system protein porN/gldN

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 2500000
Initial angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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