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- PDB-8w69: DegQ-b-casein complex -

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Basic information

Entry
Database: PDB / ID: 8w69
TitleDegQ-b-casein complex
Components
  • (Casein fragment) x 2
  • peptidase Do
KeywordsHYDROLASE / Complex
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)
Bos taurus (domestic cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsLee, I.-G. / Jeon, H.
Funding support1items
OrganizationGrant numberCountry
Other privateLF-RSP2022-02
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 28, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: peptidase Do
C: peptidase Do
B: peptidase Do
D: peptidase Do
F: peptidase Do
E: peptidase Do
G: Casein fragment
H: Casein fragment
I: Casein fragment


Theoretical massNumber of molelcules
Total (without water)292,1789
Polymers292,1789
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
peptidase Do


Mass: 48361.047 Da / Num. of mol.: 6 / Mutation: S214A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: degQ / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: C3SRW2
#2: Protein/peptide Casein fragment


Mass: 783.958 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: We would like to assign these residues as unknown (UNK).
Source: (natural) Bos taurus (domestic cattle) / Plasmid details: Purified from bovine milk
#3: Protein/peptide Casein fragment


Mass: 613.749 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: We would like to assign these residues as unknown (UNK)
Source: (natural) Bos taurus (domestic cattle) / Plasmid details: Purified from bovine milk
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: DegQ-beta casein complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: BL21(DE3)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1000000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0048619
ELECTRON MICROSCOPYf_angle_d0.67711637
ELECTRON MICROSCOPYf_dihedral_angle_d4.071221
ELECTRON MICROSCOPYf_chiral_restr0.0461401
ELECTRON MICROSCOPYf_plane_restr0.0071533

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