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- PDB-8wol: Cryo-EM structure of the Mmp1 encapasulin from Mycobacterium smegmatis -

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Basic information

Entry
Database: PDB / ID: 8wol
TitleCryo-EM structure of the Mmp1 encapasulin from Mycobacterium smegmatis
ComponentsMajor membrane protein 1
KeywordsSTRUCTURAL PROTEIN / Mmp1 encapasulin
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: 2.6 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
National Key Research and Development Program of China2022YFA1305900 China
Shanghai Rising-Star Program23QA1406400 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 1.0Nov 27, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: Major membrane protein 1
2: Major membrane protein 1
3: Major membrane protein 1
4: Major membrane protein 1
5: Major membrane protein 1
6: Major membrane protein 1
7: Major membrane protein 1
8: Major membrane protein 1
A: Major membrane protein 1
B: Major membrane protein 1
C: Major membrane protein 1
D: Major membrane protein 1
E: Major membrane protein 1
F: Major membrane protein 1
G: Major membrane protein 1
H: Major membrane protein 1
I: Major membrane protein 1
J: Major membrane protein 1
K: Major membrane protein 1
L: Major membrane protein 1
M: Major membrane protein 1
N: Major membrane protein 1
O: Major membrane protein 1
P: Major membrane protein 1
Q: Major membrane protein 1
R: Major membrane protein 1
S: Major membrane protein 1
T: Major membrane protein 1
U: Major membrane protein 1
V: Major membrane protein 1
W: Major membrane protein 1
X: Major membrane protein 1
Y: Major membrane protein 1
Z: Major membrane protein 1
a: Major membrane protein 1
b: Major membrane protein 1
c: Major membrane protein 1
d: Major membrane protein 1
e: Major membrane protein 1
f: Major membrane protein 1
g: Major membrane protein 1
h: Major membrane protein 1
i: Major membrane protein 1
j: Major membrane protein 1
k: Major membrane protein 1
l: Major membrane protein 1
m: Major membrane protein 1
n: Major membrane protein 1
o: Major membrane protein 1
p: Major membrane protein 1
q: Major membrane protein 1
r: Major membrane protein 1
s: Major membrane protein 1
t: Major membrane protein 1
u: Major membrane protein 1
v: Major membrane protein 1
w: Major membrane protein 1
x: Major membrane protein 1
y: Major membrane protein 1
z: Major membrane protein 1


Theoretical massNumber of molelcules
Total (without water)2,093,10860
Polymers2,093,10860
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 1


Mass: 34885.129 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: mmpI / 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: FEI TITAN 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 83655 / Symmetry type: POINT

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