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- EMDB-37331: Cryo-EM structure of the DegQ dodecamer with a lysozyme -

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Basic information

Entry
Database: EMDB / ID: EMD-37331
TitleCryo-EM structure of the DegQ dodecamer with a lysozyme
Map data
Sample
  • Complex: DegQ in complex with lysozyme
    • Other: DegQ-lysozyme complex
KeywordsSeine protease / HYDROLASE
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.05 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 29, 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_37331.png

Downloads & links

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Map

FileDownload / File: emd_37331.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.848 Å
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Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.10390915 - 0.20929107
Average (Standard dev.)0.0002768475 (±0.011708032)
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_37331_half_map_1.map
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Half map: #1

Fileemd_37331_half_map_2.map
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Sample components

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Entire : DegQ in complex with lysozyme

EntireName: DegQ in complex with lysozyme
Components
  • Complex: DegQ in complex with lysozyme
    • Other: DegQ-lysozyme complex

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Supramolecule #1: DegQ in complex with lysozyme

SupramoleculeName: DegQ in complex with lysozyme / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: DegQ-lysozyme complex

MacromoleculeName: DegQ-lysozyme complex / type: other / ID: 1 / Classification: other
Source (natural)Organism: Escherichia coli (E. coli)
SequenceString: MKKQTQLLSA LALSVGLTLS ASFQAVASIP GQVADQAPLP SLAPMLEKVL PAVVSVRVEG TASQGQKIPE EFKKFFGDDL PDQPAQPFEG LGSGVIINAS KGYVLTNNHV INQAQKISIQ LNDGREFDAK LIGSDDQSDI ALLQIQNPSK LTQIAIADSD KLRVGDFAVA ...String:
MKKQTQLLSA LALSVGLTLS ASFQAVASIP GQVADQAPLP SLAPMLEKVL PAVVSVRVEG TASQGQKIPE EFKKFFGDDL PDQPAQPFEG LGSGVIINAS KGYVLTNNHV INQAQKISIQ LNDGREFDAK LIGSDDQSDI ALLQIQNPSK LTQIAIADSD KLRVGDFAVA VGNPFGLGQT ATSGIVSALG RSGLNLEGLE NFIQTDASIN RGNSGGALLN LNGELIGINT AILAPGGGSV GIGFAIPSNM ARTLAQQLID FGEIKRGLLG IKGTEMSADI AKAFNLDVQR GAFVSEVLPG SGSAKAGVKA GDIITSLNGK PLNSFAELRS RIATTEPGTK VKLGLLRNGK PLEVEVTLDT STSSSASAEM ITPALEGATL SDGQLKDGGK GIKIDEVVKG SPAAQAGLQK DDVIIGVNRD RVNSIAEMRK VLAAKPAIIA LQIVRGNESI YLLMR
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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 GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.9 µm

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.05 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 326131
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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