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- EMDB-48769: Structure of PorKN from Porphyromonas gingivalis -

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Basic information

Entry
Database: EMDB / ID: EMD-48769
TitleStructure of PorKN from Porphyromonas gingivalis
Map dataunsharpened
Sample
  • Complex: PorKN
    • Protein or peptide: PorK
    • Protein or peptide: Gliding motility protein GldN
  • Ligand: CALCIUM ION
  • Ligand: alpha-D-mannopyranose
  • Ligand: water
KeywordsT9SS Type 9 Secretion System C33 assembly periplasmic assembly membrane protein / PROTEIN TRANSPORT
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: 2.4 Å
AuthorsLea SM / Deme JC / Berks BC
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: To Be Published
Title: A central role for disulfide bonds in Bacteroidota protein transportation and gliding motility
Authors: Liu X / Avaramova M / Deme JC / Lundgren C / Jones RM / Lea SM / Berks BC
History
DepositionJan 23, 2025-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48769.png

Downloads & links

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Map

FileDownload / File: emd_48769.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 512 pix.
= 527.04 Å		1.03 Å/pix.
x 512 pix.
= 527.04 Å		1.03 Å/pix.
x 512 pix.
= 527.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.02938 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.351
Minimum - Maximum-0.8995842 - 2.5108318
Average (Standard dev.)0.0011971553 (±0.044342954)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 527.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48769_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_48769_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: sharpened volume

Fileemd_48769_additional_1.map
Annotationsharpened volume
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_48769_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_48769_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PorKN

EntireName: PorKN
Components
  • Complex: PorKN
    • Protein or peptide: PorK
    • Protein or peptide: Gliding motility protein GldN
  • Ligand: CALCIUM ION
  • Ligand: alpha-D-mannopyranose
  • Ligand: water

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Supramolecule #1: PorKN

SupramoleculeName: PorKN / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Porphyromonas gingivalis (bacteria)

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Macromolecule #1: PorK

MacromoleculeName: PorK / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis (bacteria) / Strain: (strain ATCC BAA-308 / W83)
Molecular weightTheoretical: 55.967539 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 SRRSTKK

UniProtKB: Lipoprotein, putative

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Macromolecule #2: Gliding motility protein GldN

MacromoleculeName: Gliding motility protein GldN / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis (bacteria) / Strain: (strain ATCC BAA-308 / W83)
Molecular weightTheoretical: 41.729207 KDa
SequenceString: MFMKVFKAVI GAILAATVSI SSVAQENTNN RSPQVGRAPR NTEVEQTTTL SNRAQEFNRR LTQKTDNAPW RRVVYRRVDL MEESNAVLY YPPRPIGDRK NLFSTIFGLI NSNSLDVYEY LDGFEAFTDQ YKIKFQEFLD RFGIYYQPST NKNAELFKVA D SDIPSAEV ...String:
MFMKVFKAVI GAILAATVSI SSVAQENTNN RSPQVGRAPR NTEVEQTTTL SNRAQEFNRR LTQKTDNAPW RRVVYRRVDL MEESNAVLY YPPRPIGDRK NLFSTIFGLI NSNSLDVYEY LDGFEAFTDQ YKIKFQEFLD RFGIYYQPST NKNAELFKVA D SDIPSAEV KAYYVKEEWY FTPTNSDVDI KIQAICPIMT GQDEFGEVRN QPLFWIPYEN IRPYIARERV MLSSLNNTRN ST IDDFFRL NLYKGDIVKT ENLHNRALAE YCPTPDSMKM ESKRIDKELQ GFRDGLFVTQ DTTWMKQAET KKSKGKKLEK ARG KNITSR TRGQGEGAAE TEAVEPKKQK ASKNKAATRS VRRRK

UniProtKB: Gliding motility protein GldN

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Macromolecule #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 3 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #5: alpha-D-mannopyranose

MacromoleculeName: alpha-D-mannopyranose / type: ligand / ID: 5 / Number of copies: 6 / Formula: MAN
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-MAN:
alpha-D-mannopyranose

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 3 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: TFS FALCON 4i (4k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 676608
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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