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- EMDB-37257: Bacterial serine protease -

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Basic information

Entry
Database: EMDB / ID: EMD-37257
TitleBacterial serine protease
Map data
Sample
  • Complex: Bacterial serine protease-lysozyme complex
    • Protein or peptide: peptidase Do
    • Protein or peptide: Lysozyme fragment (unknown sequence)
    • Protein or peptide: Lysozyme fragment (unknown sequence)
    • Protein or peptide: Lysozyme fragment (unknown sequence)
KeywordsSeine protease / HYDROLASE
Function / homology
Function and homology information


peptidase Do / cell envelope / : / periplasmic space / serine-type endopeptidase activity / identical protein binding
Similarity search - Function
Peptidase S1C, Do / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Peptidase S1, PA clan
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli) / Gallus gallus (chicken)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsLee I-G / Jeon H
Funding support Korea, Republic Of, 1 items
OrganizationGrant numberCountry
Other privateLF-RSP2022-02 Korea, Republic Of
CitationJournal: Adv Mater / Year: 2024
Title: Polymorphic Self-Assembly with Procedural Flexibility for Monodisperse Quaternary Protein Structures of DegQ Enzymes.
Authors: Hanul Jeon / Ah-Reum Han / Sangmin Oh / Jin-Gyeong Park / Myeong Namkoong / Kyeong-Mi Bang / Ho Min Kim / Nak-Kyoon Kim / Kwang Yeon Hwang / Kahyun Hur / Bong-Jin Lee / Jeongyun Heo / Sehoon ...Authors: Hanul Jeon / Ah-Reum Han / Sangmin Oh / Jin-Gyeong Park / Myeong Namkoong / Kyeong-Mi Bang / Ho Min Kim / Nak-Kyoon Kim / Kwang Yeon Hwang / Kahyun Hur / Bong-Jin Lee / Jeongyun Heo / Sehoon Kim / Hyun Kyu Song / Hyesung Cho / In-Gyun Lee /
Abstract: As large molecular tertiary structures, some proteins can act as small robots that find, bind, and chaperone target protein clients, showing the potential to serve as smart building blocks in self- ...As large molecular tertiary structures, some proteins can act as small robots that find, bind, and chaperone target protein clients, showing the potential to serve as smart building blocks in self-assembly fields. Instead of using such intrinsic functions, most self-assembly methodologies for proteins aim for de novo-designed structures with accurate geometric assemblies, which can limit procedural flexibility. Here, a strategy enabling polymorphic clustering of quaternary proteins, exhibiting simplicity and flexibility of self-assembling paths for proteins in forming monodisperse quaternary cage particles is presented. It is proposed that the enzyme protomer DegQ, previously solved at low resolution, may potentially be usable as a threefold symmetric building block, which can form polyhedral cages incorporated by the chaperone action of DegQ in the presence of protein clients. To obtain highly monodisperse cage particles, soft, and hence, less resistive client proteins, which can program the inherent chaperone activity of DegQ to efficient formations of polymorphic cages, depending on the size of clients are utilized. By reconstructing the atomic resolution cryogenic electron microscopy DegQ structures using obtained 12- and 24-meric clusters, the polymorphic clustering of DegQ enzymes is validated in terms of soft and rigid domains, which will provide effective routes for protein self-assemblies with procedural flexibility.
History
DepositionAug 23, 2023-
Header (metadata) releaseSep 4, 2024-
Map releaseSep 4, 2024-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37257.png

Downloads & links

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Map

FileDownload / File: emd_37257.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 360 pix.
= 305.28 Å		0.85 Å/pix.
x 360 pix.
= 305.28 Å		0.85 Å/pix.
x 360 pix.
= 305.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.848 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.29871672 - 0.6491614
Average (Standard dev.)-0.00085075083 (±0.010204346)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 305.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_37257_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_37257_half_map_2.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Bacterial serine protease-lysozyme complex

EntireName: Bacterial serine protease-lysozyme complex
Components
  • Complex: Bacterial serine protease-lysozyme complex
    • Protein or peptide: peptidase Do
    • Protein or peptide: Lysozyme fragment (unknown sequence)
    • Protein or peptide: Lysozyme fragment (unknown sequence)
    • Protein or peptide: Lysozyme fragment (unknown sequence)

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Supramolecule #1: Bacterial serine protease-lysozyme complex

SupramoleculeName: Bacterial serine protease-lysozyme complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: peptidase Do

MacromoleculeName: peptidase Do / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 48.361047 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKKQTQLLSA LALSVGLTLS ASFQAVASIP GQVADQAPLP SLAPMLEKVL PAVVSVRVEG TASQGQKIPE EFKKFFGDDL PDQPAQPFE GLGSGVIINA SKGYVLTNNH VINQAQKISI QLNDGREFDA KLIGSDDQSD IALLQIQNPS KLTQIAIADS D KLRVGDFA ...String:
MKKQTQLLSA LALSVGLTLS ASFQAVASIP GQVADQAPLP SLAPMLEKVL PAVVSVRVEG TASQGQKIPE EFKKFFGDDL PDQPAQPFE GLGSGVIINA SKGYVLTNNH VINQAQKISI QLNDGREFDA KLIGSDDQSD IALLQIQNPS KLTQIAIADS D KLRVGDFA VAVGNPFGLG QTATSGIVSA LGRSGLNLEG LENFIQTDAS INRGNAGGAL LNLNGELIGI NTAILAPGGG SV GIGFAIP SNMARTLAQQ LIDFGEIKRG LLGIKGTEMS ADIAKAFNLD VQRGAFVSEV LPGSGSAKAG VKAGDIITSL NGK PLNSFA ELRSRIATTE PGTKVKLGLL RNGKPLEVEV TLDTSTSSSA SAEMITPALE GATLSDGQLK DGGKGIKIDE VVKG SPAAQ AGLQKDDVII GVNRDRVNSI AEMRKVLAAK PAIIALQIVR GNESIYLLMR LWHHHHHH

UniProtKB: peptidase Do

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Macromolecule #2: Lysozyme fragment (unknown sequence)

MacromoleculeName: Lysozyme fragment (unknown sequence) / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Gallus gallus (chicken) / Organ: egg white
Molecular weightTheoretical: 698.854 Da
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #3: Lysozyme fragment (unknown sequence)

MacromoleculeName: Lysozyme fragment (unknown sequence) / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Gallus gallus (chicken) / Organ: egg white
Molecular weightTheoretical: 443.539 Da
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #4: Lysozyme fragment (unknown sequence)

MacromoleculeName: Lysozyme fragment (unknown sequence) / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Gallus gallus (chicken) / Organ: Chichken egg white
Molecular weightTheoretical: 613.749 Da
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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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: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 67.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 382427
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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