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- EMDB-30131: Cryo-EM structure of the encapsulated DyP-type peroxidase from My... -

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Basic information

Entry
Database: EMDB / ID: EMD-30131
TitleCryo-EM structure of the encapsulated DyP-type peroxidase from Mycobacterium smegmatis
Map dataPost-processed Cryo-EM map generated by RELION
Sample
  • Complex: Encapsulin from Mycobacterium smegmatis
    • Protein or peptide: Dyp-type peroxidaseDye decolorizing peroxidase
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
KeywordsCargo protein / Dodecamer / Heme-containing enzyme / Oxidoreductase
Function / homologyDyp-type peroxidase, N-terminal / DyP-type peroxidase family. / Dyp-type peroxidase / peroxidase / Dimeric alpha-beta barrel / peroxidase activity / heme binding / Dyp-type peroxidase
Function and homology information
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsTang YT / Mu A / Gong HR / Wang Q / Rao ZH
Funding support China, 4 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81520108019 China
National Natural Science Foundation of China (NSFC)813300237 China
Ministry of Science and Technology (MoST, China)2017YFC0840300 China
Chinese Academy of SciencesXDB08020200 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: Cryo-EM structure of DyP-loaded encapsulin.
Authors: Yanting Tang / An Mu / Yuying Zhang / Shan Zhou / Weiwei Wang / Yuezheng Lai / Xiaoting Zhou / Fengjiang Liu / Xiuna Yang / Hongri Gong / Quan Wang / Zihe Rao /
Abstract: Encapsulins containing dye-decolorizing peroxidase (DyP)-type peroxidases are ubiquitous among prokaryotes, protecting cells against oxidative stress. However, little is known about how they interact ...Encapsulins containing dye-decolorizing peroxidase (DyP)-type peroxidases are ubiquitous among prokaryotes, protecting cells against oxidative stress. However, little is known about how they interact and function. Here, we have isolated a native cargo-packaging encapsulin from and determined its complete high-resolution structure by cryogenic electron microscopy (cryo-EM). This encapsulin comprises an icosahedral shell and a dodecameric DyP cargo. The dodecameric DyP consists of two hexamers with a twofold axis of symmetry and stretches across the interior of the encapsulin. Our results reveal that the encapsulin shell plays a role in stabilizing the dodecameric DyP. Furthermore, we have proposed a potential mechanism for removing the hydrogen peroxide based on the structural features. Our study also suggests that the DyP is the primary cargo protein of mycobacterial encapsulins and is a potential target for antituberculosis drug discovery.
History
DepositionMar 19, 2020-
Header (metadata) releaseMar 24, 2021-
Map releaseMar 24, 2021-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.025
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  • Surface view with fitted model
  • Atomic models: PDB-7bok
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30131.png

Downloads & links

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Map

FileDownload / File: emd_30131.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost-processed Cryo-EM map generated by RELION
Voxel sizeX=Y=Z: 1.04 Å
Density
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.025
Minimum - Maximum-0.035847817 - 0.07887428
Average (Standard dev.)0.00015577735 (±0.0036115523)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 374.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z374.400374.400374.400
α/β/γ90.00090.00090.000
start NX/NY/NZ1219875
NX/NY/NZ141223232
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0360.0790.000

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Supplemental data

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Mask #1

Fileemd_30131_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Second one of the half map after 3D-refinement generated by RELION

Fileemd_30131_half_map_1.map
AnnotationSecond one of the half map after 3D-refinement generated by RELION
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: First one of the half map after 3D-refinement generated by RELION

Fileemd_30131_half_map_2.map
AnnotationFirst one of the half map after 3D-refinement generated by RELION
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Encapsulin from Mycobacterium smegmatis

EntireName: Encapsulin from Mycobacterium smegmatis
Components
  • Complex: Encapsulin from Mycobacterium smegmatis
    • Protein or peptide: Dyp-type peroxidaseDye decolorizing peroxidase
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE

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Supramolecule #1: Encapsulin from Mycobacterium smegmatis

SupramoleculeName: Encapsulin from Mycobacterium smegmatis / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)

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Macromolecule #1: Dyp-type peroxidase

MacromoleculeName: Dyp-type peroxidase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: peroxidase
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 37.25234 KDa
SequenceString: MPAPQPQPVL APLTPAAVFL VATIDEGQEA TVYDALPDIS GLVRAIGFRD PAKRLSAITS IGSDAWDRLF SGPRPAELHP FREIDGGRH HAPATPGDLL FHLRAESMDV CFELATKLVE AMSGAITIVD ETHGFRFFDN RDLMGFVDGT ENPDGNLAVV A TQIGDEDP ...String:
MPAPQPQPVL APLTPAAVFL VATIDEGQEA TVYDALPDIS GLVRAIGFRD PAKRLSAITS IGSDAWDRLF SGPRPAELHP FREIDGGRH HAPATPGDLL FHLRAESMDV CFELATKLVE AMSGAITIVD ETHGFRFFDN RDLMGFVDGT ENPDGNLAVV A TQIGDEDP DFAGGCYVHV QKYLHDMASW NSLSVEEQER VIGRTKLDDI ELDDDVKPAN SHVALNVIED EDGNELKIIR HN MPFGEIG KGEFGTYYIG YSRTPSVTER MLDNMFIGDP PGNTDRILDF STAITGGLFF TPTVDFLDDP PPLPSEDDRA EPA SAPSAD PVHTDGSLGI GSLKGTR

UniProtKB: Dyp-type peroxidase

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Macromolecule #2: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 2 / Number of copies: 6 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE / Heme B

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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

Concentration10 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-40 / Average exposure time: 6.4 sec. / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 13937
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4gu7


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient
Output model

PDB-7bok:
Cryo-EM structure of the encapsulated DyP-type peroxidase from Mycobacterium smegmatis

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