9MZU | pdb_00009mzu

Structure of PorKN from Porphyromonas gingivalis

PDB DOI: https://doi.org/10.2210/pdb9MZU/pdb
EM Map EMD-48769: EMDB EMDataResource

Classification: PROTEIN TRANSPORT
Organism(s): Porphyromonas gingivalis
Mutation(s): No

Deposited: 2025-01-23 Released: 2025-04-16
Deposition Author(s): Lea, S.M., Deme, J.C., Berks, B.C.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9MZU

This is version 1.0 of the entry. See complete history.

Literature

A central role for disulfide bonds in Bacteroidota protein transportation and gliding motility

Liu, X., Avaramova, M., Deme, J.C., Lundgren, C., Jones, R.M., Lea, S.M., Berks, B.C.

To be published.

Macromolecule Content

Total Structure Weight: 299.16 kDa
Atom Count: 17,511
Modeled Residue Count: 2,094
Deposited Residue Count: 2,556
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PorK	A, C, E	491	Porphyromonas gingivalis	Mutation(s): 0
UniProt
Find proteins for Q7MXB7 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83)) Explore Q7MXB7 Go to UniProtKB: Q7MXB7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7MXB7
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain C Focus chain E
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Gliding motility protein GldN	B, D, F	361	Porphyromonas gingivalis	Mutation(s): 0
UniProt
Find proteins for Q7MXB4 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83)) Explore Q7MXB4 Go to UniProtKB: Q7MXB4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7MXB4
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B Focus chain D Focus chain F
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-fucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-2)-[alpha-L-rhamnopyranose-(1-4)]alpha-D-mannopyranose	G, H, I, J, K G, H, I, J, K, L	5		O-Glycosylation	Interactions Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Interactions & Density Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MAN Query on MAN Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain Q [auth D] SDF format, chain U [auth F] SDF format, chain T [auth F] SDF format, chain R [auth D] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth D] MOL2 format, chain U [auth F] MOL2 format, chain T [auth F] MOL2 format, chain R [auth D] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth D] mmCIF format, chain U [auth F] mmCIF format, chain T [auth F] mmCIF format, chain R [auth D]	N [auth B] O [auth B] Q [auth D] R [auth D] T [auth F] N [auth B], O [auth B], Q [auth D], R [auth D], T [auth F], U [auth F]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth D] Focus chain R [auth D] Focus chain T [auth F] Focus chain U [auth F] Interactions & Density Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth D] Focus chain R [auth D] Focus chain T [auth F] Focus chain U [auth F]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain S [auth E] SDF format, chain P [auth C] SDF format, chain M [auth A] MOL2 format, chain S [auth E] MOL2 format, chain P [auth C] MOL2 format, chain M [auth A] mmCIF format, chain S [auth E] mmCIF format, chain P [auth C] mmCIF format, chain M [auth A]	M [auth A], P [auth C], S [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain P [auth C] Focus chain S [auth E] Interactions & Density Focus chain M [auth A] Focus chain P [auth C] Focus chain S [auth E]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	dev_5430

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-04-16

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--

Revision History (Full details and data files)

Version 1.0: 2025-04-16
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.