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- EMDB-22992: Cryo-EM structure of a thermostable encapsulin from T. maritima -

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Basic information

Entry
Database: EMDB / ID: EMD-22992
TitleCryo-EM structure of a thermostable encapsulin from T. maritima
Map dataDensity-modified map made with PHENIX ResolveCryoEM in a 342-pixel box.
Sample
  • Complex: Encapsulin
    • Protein or peptide: Maritimacin
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: water
KeywordsEncapsulin / HK97 fold / flavin-binding / icosahedral / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


encapsulin nanocompartment / Hydrolases; Acting on peptide bonds (peptidases) / iron ion transport / peptidase activity / intracellular iron ion homeostasis / proteolysis
Similarity search - Function
Type 1 encapsulin shell protein / Encapsulating protein for peroxidase / :
Similarity search - Domain/homology
Type 1 encapsulin shell protein
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria) / Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.0 Å
AuthorsWiryaman TI / Toor N
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM123275 United States
National Institutes of Health/Office of the Director2T32GM007240 United States
National Institutes of Health/Office of the DirectorU24GM129547 United States
CitationJournal: IUCrJ / Year: 2021
Title: Cryo-EM structure of a thermostable bacterial nanocompartment.
Authors: Timothy Wiryaman / Navtej Toor /
Abstract: Protein nanocompartments are widespread in bacteria and archaea, but their functions are not yet well understood. Here, the cryo-EM structure of a nanocompartment from the thermophilic bacterium is ...Protein nanocompartments are widespread in bacteria and archaea, but their functions are not yet well understood. Here, the cryo-EM structure of a nanocompartment from the thermophilic bacterium is reported at 2.0 Å resolution. The high resolution of this structure shows that interactions in the E-loop domain may be important for the thermostability of the nanocompartment assembly. Also, the channels at the fivefold axis, threefold axis and dimer interface are assessed for their ability to transport iron. Finally, an unexpected flavin ligand was identified on the exterior of the shell, indicating that this nanocompartment may also play a direct role in iron metabolism.
History
DepositionNov 13, 2020-
Header (metadata) releaseApr 28, 2021-
Map releaseApr 28, 2021-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7kq5
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7kq5
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22992.png

Downloads & links

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Map

FileDownload / File: emd_22992.map.gz / Format: CCP4 / Size: 152.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDensity-modified map made with PHENIX ResolveCryoEM in a 342-pixel box.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.72 Å/pix.
x 342 pix.
= 246.001 Å		0.72 Å/pix.
x 342 pix.
= 246.001 Å		0.72 Å/pix.
x 342 pix.
= 246.001 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7193 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-13.838706 - 14.340474
Average (Standard dev.)-0.000000000001971 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions342342342
Spacing342342342
CellA=B=C: 246.0006 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.719301169590640.719301169590640.71930116959064
M x/y/z342342342
origin x/y/z0.0000.0000.000
length x/y/z246.001246.001246.001
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ342342342
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS342342342
D min/max/mean-13.83914.340-0.000

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Supplemental data

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Additional map: EM map from RELION Refine3D (note that model...

Fileemd_22992_additional_1.map
AnnotationEM map from RELION Refine3D (note that model is placed in a 342-pixel box whereas this map is in a 426-pixel box).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 from RELION Refine3D

Fileemd_22992_half_map_1.map
AnnotationHalf map 1 from RELION Refine3D
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 from RELION Refine3D

Fileemd_22992_half_map_2.map
AnnotationHalf map 2 from RELION Refine3D
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

EntireName: Encapsulin
Components
  • Complex: Encapsulin
    • Protein or peptide: Maritimacin
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: water

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Supramolecule #1: Encapsulin

SupramoleculeName: Encapsulin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Thermotoga maritima MSB8 (bacteria)
Molecular weightTheoretical: 1.82868 MDa

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Macromolecule #1: Maritimacin

MacromoleculeName: Maritimacin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on peptide bonds (peptidases)
Source (natural)Organism: Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099
Molecular weightTheoretical: 30.516787 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MEFLKRSFAP LTEKQWQEID NRAREIFKTQ LYGRKFVDVE GPYGWEYAAH PLGEVEVLSD ENEVVKWGLR KSLPLIELRA TFTLDLWEL DNLERGKPNV DLSSLEETVR KVAEFEDEVI FRGCEKSGVK GLLSFEERKI ECGSTPKDLL EAIVRALSIF S KDGIEGPY ...String:
MEFLKRSFAP LTEKQWQEID NRAREIFKTQ LYGRKFVDVE GPYGWEYAAH PLGEVEVLSD ENEVVKWGLR KSLPLIELRA TFTLDLWEL DNLERGKPNV DLSSLEETVR KVAEFEDEVI FRGCEKSGVK GLLSFEERKI ECGSTPKDLL EAIVRALSIF S KDGIEGPY TLVINTDRWI NFLKEEAGHY PLEKRVEECL RGGKIITTPR IEDALVVSER GGDFKLILGQ DLSIGYEDRE KD AVRLFIT ETFTFQVVNP EALILLKF

UniProtKB: Type 1 encapsulin shell protein

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Macromolecule #2: FLAVIN MONONUCLEOTIDE

MacromoleculeName: FLAVIN MONONUCLEOTIDE / type: ligand / ID: 2 / Number of copies: 1 / Formula: FMN
Molecular weightTheoretical: 456.344 Da
Chemical component information

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 148 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration2 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMC4H11NO3tris
150.0 mMNaClsodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: OTHER / Details: Plasma cleaned in Gatan Solarus system
VitrificationCryogen name: PROPANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: LEICA EM GP
Details: 3 ul sample applied to the carbon side of the grid and blotted for 4s before plunging..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 11520 pixel / Digitization - Dimensions - Height: 8184 pixel / Number real images: 2772 / Average exposure time: 2.5 sec. / Average electron dose: 33.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 204251 / Details: Picked with trained cryolo model
Startup modelType of model: OTHER
Details: RELION InitialModel was used to generate an initial model
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 185459
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Software - details: RELION 3.1 Class3D was used to assign the initial angles
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Software - details: Relion 3.1 Refine3D was used to for final refinement
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

3dkt


Chain - Chain ID: A / Chain - Residue range: 4-269 / Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsMap was cropped to a 342 box size and density modified with PHENIX ResolveCryoEM
RefinementProtocol: OTHER
Output model

PDB-7kq5:
Cryo-EM structure of a thermostable encapsulin from T. maritima

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