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- EMDB-68645: Client peptide-bound structure of a MucD trimer within a 24mer cage -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-68645
TitleClient peptide-bound structure of a MucD trimer within a 24mer cage
Map data
Sample
  • Complex: Client peptide-bound structure of a MucD trimer within a 24mer cage
    • Protein or peptide: Probable periplasmic serine endoprotease DegP-like
    • Protein or peptide: Alginate biosynthesis protein AlgK
KeywordsComplex / Protease / Cryo-EM / HYDROLASE
Function / homology
Function and homology information


alginic acid biosynthetic process / peptidase Do / cell outer membrane / periplasmic space / serine-type endopeptidase activity / signal transduction / proteolysis
Similarity search - Function
AlgK tetratricopeptide repeat domain / : / : / Peptidase S1C, Do / Sel1 repeat / Sel1-like repeat / Sel1-like repeats. / PDZ domain / Peptidase S1C / Trypsin-like peptidase domain ...AlgK tetratricopeptide repeat domain / : / : / Peptidase S1C, Do / Sel1 repeat / Sel1-like repeat / Sel1-like repeats. / PDZ domain / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Tetratricopeptide-like helical domain superfamily / Peptidase S1, PA clan
Similarity search - Domain/homology
Probable periplasmic serine endoprotease DegP-like / Alginate biosynthesis protein AlgK
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsJiang YJ / Gao YG
Funding support Singapore, 1 items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore) Singapore
CitationJournal: To Be Published
Title: Cryo-EM Structure of a 24mer MucD cage bound to the client peptide AlgK_369-388
Authors: Jiang YJ / Gao YG
History
DepositionJan 22, 2026-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_68645.png

Downloads & links

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Map

FileDownload / File: emd_68645.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 400 pix.
= 388. Å		0.97 Å/pix.
x 400 pix.
= 388. Å		0.97 Å/pix.
x 400 pix.
= 388. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.97 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.027
Minimum - Maximum-0.12444641 - 0.27808347
Average (Standard dev.)0.0003761929 (±0.004527412)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 388.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_68645_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_68645_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Client peptide-bound structure of a MucD trimer within a 24mer cage

EntireName: Client peptide-bound structure of a MucD trimer within a 24mer cage
Components
  • Complex: Client peptide-bound structure of a MucD trimer within a 24mer cage
    • Protein or peptide: Probable periplasmic serine endoprotease DegP-like
    • Protein or peptide: Alginate biosynthesis protein AlgK

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Supramolecule #1: Client peptide-bound structure of a MucD trimer within a 24mer cage

SupramoleculeName: Client peptide-bound structure of a MucD trimer within a 24mer cage
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)

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Macromolecule #1: Probable periplasmic serine endoprotease DegP-like

MacromoleculeName: Probable periplasmic serine endoprotease DegP-like / type: protein_or_peptide / ID: 1
Details: All chains contain S217A mutation and 6*His tag at C-terminus.
Number of copies: 6 / Enantiomer: LEVO / EC number: peptidase Do
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 51.192441 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString: MHTLKRCMAA MVALLALSLA MTARAELPDF TPLVEQASPA VVNISTRQKL PDRAMARGQL SIPDLEGLPP MFRDFLERSI PQVPRNPRG QQREAQSLGS GFIISNDGYI LTNNHVVADA DEILVRLSDR SEHKAKLIGA DPRSDVAVLK IEAKNLPTLK L GDSNKLKV ...String:
MHTLKRCMAA MVALLALSLA MTARAELPDF TPLVEQASPA VVNISTRQKL PDRAMARGQL SIPDLEGLPP MFRDFLERSI PQVPRNPRG QQREAQSLGS GFIISNDGYI LTNNHVVADA DEILVRLSDR SEHKAKLIGA DPRSDVAVLK IEAKNLPTLK L GDSNKLKV GEWVLAIGSP FGFDHSVTAG IVSAKGRSLP NESYVPFIQT DVAINPGNAG GPLLNLQGEV VGINSQIFTR SG GFMGLSF AIPIDVALNV ADQLKKAGKV SRGWLGVVIQ EVNKDLAESF GLDKPSGALV AQLVEDGPAA KGGLQVGDVI LSL NGQSIN ESADLPHLVG NMKPGDKINL DVIRNGQRKS LSMAVGSLPD DDEEIASMGA PGAERSSNRL GVTVADLTAE QRKS LDIQG GVVIKEVQDG PAAVIGLRPG DVITHLDNKA VTSTKVFADV AKALPKNRSV SMRVLRQGRA SFITFKLAEH HHHHH

UniProtKB: Probable periplasmic serine endoprotease DegP-like

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Macromolecule #2: Alginate biosynthesis protein AlgK

MacromoleculeName: Alginate biosynthesis protein AlgK / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 1.996292 KDa
SequenceString:
VDHLILAARA GQASADMALA

UniProtKB: Alginate biosynthesis protein AlgK

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 216709
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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