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- PDB-8won: Cryo-EM structure of the 10-subunits Mmp1 complex from Mycobacter... -

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Entry
Database: PDB / ID: 8won
TitleCryo-EM structure of the 10-subunits Mmp1 complex from Mycobacterium smegmatis
ComponentsMajor membrane protein I
KeywordsSTRUCTURAL PROTEIN / 10-subunits Mmp1 complex
Function / homology: / Type 2A encapsulin shell protein SrpI-like / Type 2A encapsulin shell protein SrpI-like / Major membrane protein I
Function and homology information
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.69 Å
AuthorsZhang, M. / Tang, Y. / Gao, Y. / Liu, X. / Lan, W. / Liu, Y. / Ma, M.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32201033 China
National Natural Science Foundation of China (NSFC)32171259 China
Other government2022YFA1305900 China
Other government23QA1406400 China
CitationJournal: Commun Biol / Year: 2024
Title: The structural and functional analysis of mycobacteria cysteine desulfurase-loaded encapsulin.
Authors: Yanting Tang / Yanyan Liu / Mingjing Zhang / Weiqi Lan / Mengyuan Ma / Cheng Chen / Saibin Wu / Rong Chen / Yiran Yan / Lu Feng / Ying Li / Luke W Guddat / Yan Gao / Xiang Liu / Zihe Rao /
Abstract: Encapsulin nanocompartments loaded with dedicated cargo proteins via unique targeting peptides, play a key role in stress resistance, iron storage and natural product biosynthesis. Mmp1 and cysteine ...Encapsulin nanocompartments loaded with dedicated cargo proteins via unique targeting peptides, play a key role in stress resistance, iron storage and natural product biosynthesis. Mmp1 and cysteine desulfurase (Enc-CD) have been identified as the most abundant representatives of family 2 encapsulin systems. However, the molecular assembly, catalytic mechanism, and physiological functions of the Mmp1 encapsulin system have not been studied in detail. Here we isolate and characterize an Enc-CD-loaded Mmp1 encapsulin system from Mycobacterium smegmatis mc155. The cryo-EM structure of the Mmp1 encapsulin and the crystal structure of the naked cargo Enc-CD have been determined. The structure shows that the Mmp1 protomer assembles two conformation models, the icosahedron (T = 1) and homodecamer, with the resolution of 2.60 Å and 2.69 Å. The Enc-CD at 2.10 Å resolution is dimeric and loaded into the Mmp1 (T = 1) encapsulin through the N-terminal long disordered region. Mmp1 encapsulin protects Enc-CD against oxidation as well as to maintain structural stability. These studies provide new insights into the mechanism by which Enc-CD-loaded encapsulin stores sulfur and provides a framework for discovery of new anti-mycobacterial therapeutics.
History
DepositionOct 7, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2025Provider: repository / Type: Initial release
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Revision 1.1Jun 18, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jun 18, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major membrane protein I
B: Major membrane protein I
C: Major membrane protein I
D: Major membrane protein I
E: Major membrane protein I
F: Major membrane protein I
G: Major membrane protein I
H: Major membrane protein I
I: Major membrane protein I
J: Major membrane protein I


Theoretical massNumber of molelcules
Total (without water)317,69810
Polymers317,69810
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Major membrane protein I


Mass: 31769.803 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: mmpI, BIN_B_05759 / Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0A653FP42
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Mmp1 encapasulin / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Source (recombinant)Organism: Mycolicibacterium smegmatis (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 293579 / Symmetry type: POINT

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