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- EMDB-48722: cryo electron microscopy map of porK/N ring with alternative C32 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-48722
Titlecryo electron microscopy map of porK/N ring with alternative C32 symmetry
Map datarefined map
Sample
  • Complex: PorK/N protein complex
    • Protein or peptide: PorN
    • Protein or peptide: PorK
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsHanssen E / Gorasia D / Veith P / Reynolds E
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 20, 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_48722.png

Downloads & links

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Map

FileDownload / File: emd_48722.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationrefined map
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: 0.1
Minimum - Maximum-0.14707585 - 0.49171305
Average (Standard dev.)-0.000055423105 (±0.01534195)
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_48722_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_48722_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_48722_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 : PorK/N protein complex

EntireName: PorK/N protein complex
Components
  • Complex: PorK/N protein complex
    • Protein or peptide: PorN
    • Protein or peptide: PorK

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Supramolecule #1: PorK/N protein complex

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

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Macromolecule #1: PorN

MacromoleculeName: PorN / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis (bacteria) / Strain: W83
SequenceString: MFMKVFKAVI GAILAATVSI SSVAQENTNN RSPQVGRAPR NTEVEQTTTL SNRAQEFNRR LTQKTDNAP WRRVVYRRVD LMEESNAVLY YPPRPIGDRK NLFSTIFGLI NSNSLDVYEY L DGFEAFTD QYKIKFQEFL DRFGIYYQPS TNKNAELFKV ADSDIPSAEV ...String:
MFMKVFKAVI GAILAATVSI SSVAQENTNN RSPQVGRAPR NTEVEQTTTL SNRAQEFNRR LTQKTDNAP WRRVVYRRVD LMEESNAVLY YPPRPIGDRK NLFSTIFGLI NSNSLDVYEY L DGFEAFTD QYKIKFQEFL DRFGIYYQPS TNKNAELFKV ADSDIPSAEV KAYYVKEEWY FT PTNSDVD IKIQAICPIM TGQDEFGEVR NQPLFWIPYE NIRPYIARER VMLSSLNNTR NST IDDFFR LNLYKGDIVK TENLHNRALA EYCPTPDSMK MESKRIDKEL QGFRDGLFVT QDTT WMKQA ETKKSKGKKL EKARGKNITS RTRGQGEGAA ETEAVEPKKQ KASKNKAATR SVRRR K

UniProtKB: Gliding motility protein GldN

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Macromolecule #2: PorK

MacromoleculeName: PorK / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis (bacteria) / Strain: W83
SequenceString: MCRKNRFFAL AGFFLFGVFT ISSCGSSKRA VGGELTGAKL SSWNEPSPFG MIQVPRGSIV LGNKEADSL WGIPAESRPI SVDAFWMDRT EITNAQYRQF VYYVRDSIIR ERLADPAYGG N EEYKITEN KFGEPVTPHL DWSKPIPSEK RATEEEIAAI NSVYYTNPVT ...String:
MCRKNRFFAL AGFFLFGVFT ISSCGSSKRA VGGELTGAKL SSWNEPSPFG MIQVPRGSIV LGNKEADSL WGIPAESRPI SVDAFWMDRT EITNAQYRQF VYYVRDSIIR ERLADPAYGG N EEYKITEN KFGEPVTPHL DWSKPIPSEK RATEEEIAAI NSVYYTNPVT HDRKLNPDQM VY RYEVYDY RSAALREHQL KAAKRNLNTD IKVDPNAVVM ISKDTAFVDE SGNIISETIT RPL SSEYDF LNTYIVPIYP DETCWVNDFP NARTEIYTRM YFNHPGYDDY PVVGISWEQA QAFC AWRSE FFRKGIRLPE GQIMDDFRLP TEAEWEYAAR MGDSNNKYPW STEDLRTGRG CFLGN FKPG EGDYTADGHL IPSRVSSFSP NDFGLYDMAG NVAEWTSTAF SESGLKQMSD INPELE YKA ALTDPYILKQ KVVRGGSWKD VARFIRSATR SHEYQNVGRS YIGFRCVRTS IAFSSGK AP KSSRRSTKK

UniProtKB: Lipoprotein, putative

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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 mMC4H11NO3HClTris-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
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: C32 (32 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.1) / Number images used: 60779
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

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