[English] 日本語
Yorodumi
- PDB-9myj: Structure of P. gingivalis PorK and PorN complexes from cryo elec... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9myj
TitleStructure of P. gingivalis PorK and PorN complexes from cryo electron microscopy
Components
  • Gliding motility protein GldN
  • Lipoprotein, putative
KeywordsTRANSPORT PROTEIN / T9SS / porphyromonas gingivalis
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
alpha-D-mannopyranose / Gliding motility protein GldN / Lipoprotein, putative
Similarity search - Component
Biological speciesPorphyromonas gingivalis W83 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.57 Å
AuthorsHanssen, E. / Morton, C.J. / Gorasia, D.G. / Veith, P.D. / Reynolds, E.C.
Funding support Australia, 2items
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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Gliding motility protein GldN
B: Lipoprotein, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8036
Polymers80,1492
Non-polymers2,6544
Water00
1
A: Gliding motility protein GldN
B: Lipoprotein, putative
hetero molecules
x 33


Theoretical massNumber of molelcules
Total (without water)2,732,498198
Polymers2,644,90266
Non-polymers87,596132
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation32
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: C33 (33 fold cyclic))

-
Components

#1: Protein Gliding motility protein GldN


Mass: 30080.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis W83 (bacteria) / Strain: W83 / References: UniProt: Q7MXB4
#2: Protein Lipoprotein, putative


Mass: 50067.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis W83 (bacteria) / Strain: W83 / References: UniProt: Q7MXB7
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)- ...2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-beta-L-fucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-2)-[alpha-L-rhamnopyranose-(1-4)]alpha-D-mannopyranose


Type: oligosaccharide / Mass: 1217.088 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpNAcb1-3DGalpNAcb1-4LFucpb1-4DGlcpb1-4DGlcpAa1-2[LRhapa1-4]DManpa1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/6,7,6/[a1122h-1a_1-5][a2122A-1a_1-5][a2122h-1b_1-5][a1221m-1b_1-5][a2112h-1b_1-5_2*NCC/3=O][a2211m-1a_1-5]/1-2-3-4-5-5-6/a2-b1_a4-g1_b4-c1_c4-d1_d4-e1_e3-f1WURCSPDB2Glycan 1.1.0
[]{[(3+1)][b-D-Manp]{[(2+1)][a-D-GlcpA]{[(4+1)][b-D-Glcp]{[(4+1)][b-L-Fucp]{[(4+1)][b-D-GalpNAc]{[(3+1)][b-D-GalpNAc]{}}}}}[(4+1)][a-L-Rhap]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: PorK/N protein complex / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Molecular weightValue: 3.5 MDa / Experimental value: NO
Source (natural)Organism: Porphyromonas gingivalis (bacteria) / Strain: W83
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTris-HCLC4H12ClNO31
250 mMSodium chlorideNaCl1
30.5 %n-Dodecyl-B-D-maltosideC24H46O111
41 MUreaCH4N2O1
SpecimenConc.: 1.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 15mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 295 K / Details: Blot forace -1 blot time 3sec sample size 4ul

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 64000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 5.34 sec. / Electron dose: 54 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8909
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 10 eV

-
Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5.1particle selection
2EPUimage acquisition
4cryoSPARC4.5.1CTF correction
7Coot0.9.8.93model fitting
9cryoSPARC4.5.1initial Euler assignment
10cryoSPARC4.5.1final Euler assignment
12cryoSPARC4.5.13D reconstruction
13PHENIX1.19.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 556522
SymmetryPoint symmetry: C33 (33 fold cyclic)
3D reconstructionResolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 69982 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementHighest resolution: 3.57 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0035978
ELECTRON MICROSCOPYf_angle_d0.488115
ELECTRON MICROSCOPYf_dihedral_angle_d6.5351077
ELECTRON MICROSCOPYf_chiral_restr0.068875
ELECTRON MICROSCOPYf_plane_restr0.0031043

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more