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- EMDB-60569: cryo-EM map of encapsulin Mmp1 with SufS -

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Basic information

Entry
Database: EMDB / ID: EMD-60569
Titlecryo-EM map of encapsulin Mmp1 with SufS
Map dataholo-Mmp1
Sample
  • Complex: cryo-EM map of encapsulin Mmp1 with SufS
KeywordsComplex / Mmp1 encapasulin / SufS / STRUCTURAL PROTEIN
Biological speciesMycolicibacterium smegmatis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.08 Å
AuthorsZhang M / Tang Y / Gao Y / Liu X / Lan W / Liu Y / Ma M
Funding support China, 4 items
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
DepositionJun 17, 2024-
Header (metadata) releaseNov 27, 2024-
Map releaseNov 27, 2024-
UpdateJan 1, 2025-
Current statusJan 1, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60569.png

Downloads & links

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Map

FileDownload / File: emd_60569.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationholo-Mmp1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 320 pix.
= 339.2 Å		1.06 Å/pix.
x 320 pix.
= 339.2 Å		1.06 Å/pix.
x 320 pix.
= 339.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-2.3313534 - 4.234533
Average (Standard dev.)0.011199251 (±0.24142025)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 339.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: holo-Mmp1

Fileemd_60569_half_map_1.map
Annotationholo-Mmp1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: holo-Mmp1

Fileemd_60569_half_map_2.map
Annotationholo-Mmp1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : cryo-EM map of encapsulin Mmp1 with SufS

EntireName: cryo-EM map of encapsulin Mmp1 with SufS
Components
  • Complex: cryo-EM map of encapsulin Mmp1 with SufS

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Supramolecule #1: cryo-EM map of encapsulin Mmp1 with SufS

SupramoleculeName: cryo-EM map of encapsulin Mmp1 with SufS / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 139110
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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