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- EMDB-22095: CryoEM structure of the apo-SrpI encapasulin complex from Synecho... -

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Basic information

Entry
Database: EMDB / ID: EMD-22095
TitleCryoEM structure of the apo-SrpI encapasulin complex from Synechococcus elongatus PCC 7942
Map data
Sample
  • Complex: SrpI encapsulin apo complex
    • Protein or peptide: Protein SrpI
Keywordsencapsulin / nanocompartment / cysteine desulfurase / HK97-fold / VIRUS LIKE PARTICLE
Function / homology: / Type 2A encapsulin shell protein SrpI-like / Type 2A encapsulin shell protein SrpI-like / encapsulin nanocompartment / Type 2A encapsulin shell protein SrpI
Function and homology information
Biological speciesSynechococcus elongatus (strain PCC 7942 / FACHB-805) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsLaFrance BJ / Nichols RJ / Phillips NR / Oltrogge LM / Valentin-Alvarado LE / Bischoff AJ / Savage DF / Nogales E
Funding support United States, 2 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE- 638 SC00016240 United States
National Science Foundation (NSF, United States)1106400 United States
Citation
Journal: Elife / Year: 2021
Title: Discovery and characterization of a novel family of prokaryotic nanocompartments involved in sulfur metabolism.
Authors: Robert J Nichols / Benjamin LaFrance / Naiya R Phillips / Devon R Radford / Luke M Oltrogge / Luis E Valentin-Alvarado / Amanda J Bischoff / Eva Nogales / David F Savage /
Abstract: Prokaryotic nanocompartments, also known as encapsulins, are a recently discovered proteinaceous organelle-like compartment in prokaryotes that compartmentalize cargo enzymes. While initial studies ...Prokaryotic nanocompartments, also known as encapsulins, are a recently discovered proteinaceous organelle-like compartment in prokaryotes that compartmentalize cargo enzymes. While initial studies have begun to elucidate the structure and physiological roles of encapsulins, bioinformatic evidence suggests that a great diversity of encapsulin nanocompartments remains unexplored. Here, we describe a novel encapsulin in the freshwater cyanobacterium PCC 7942. This nanocompartment is upregulated upon sulfate starvation and encapsulates a cysteine desulfurase enzyme via an N-terminal targeting sequence. Using cryo-electron microscopy, we have determined the structure of the nanocompartment complex to 2.2 Å resolution. Lastly, biochemical characterization of the complex demonstrated that the activity of the cysteine desulfurase is enhanced upon encapsulation. Taken together, our discovery, structural analysis, and enzymatic characterization of this prokaryotic nanocompartment provide a foundation for future studies seeking to understand the physiological role of this encapsulin in various bacteria.
#1: Journal: Biorxiv / Year: 2020
Title: Discovery and characterization of a novel family of prokaryotic nanocompartments involved in sulfur metabolism
Authors: Nichols RJ / LaFrance BJ / Phillips NR / Oltrogge LM / Valentin-Alvarado LE / Bischoff AJ / Nogales E / Savage DF
History
DepositionJun 1, 2020-
Header (metadata) releaseJun 10, 2020-
Map releaseJun 10, 2020-
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: 0.017
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.017
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6x8t
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6x8t
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22095.png

Downloads & links

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Map

FileDownload / File: emd_22095.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.14 Å/pix.
x 360 pix.
= 410.4 Å		1.14 Å/pix.
x 360 pix.
= 410.4 Å		1.14 Å/pix.
x 360 pix.
= 410.4 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.14 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.017 / Movie #1: 0.017
Minimum - Maximum-0.074978404 - 0.12788264
Average (Standard dev.)0.00063060294 (±0.006008465)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 410.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.141.141.14
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z410.400410.400410.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0750.1280.001

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Supplemental data

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Mask #1

Fileemd_22095_msk_1.map
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Additional map: Segmented difference map resulting from subtracting classes of...

Fileemd_22095_additional.map
AnnotationSegmented difference map resulting from subtracting classes of EMD-22095 from the related map EMD-22094 after each map was symmetry-expanded and classified
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Additional map: Segmented difference map resulting from subtracting classes of...

Fileemd_22095_additional_1.map
AnnotationSegmented difference map resulting from subtracting classes of EMD-22095 from the related map EMD-22094 after each map was symmetry-expanded and classified
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Half map: #1

Fileemd_22095_half_map_1.map
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Half map: #2

Fileemd_22095_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : SrpI encapsulin apo complex

EntireName: SrpI encapsulin apo complex
Components
  • Complex: SrpI encapsulin apo complex
    • Protein or peptide: Protein SrpI

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Supramolecule #1: SrpI encapsulin apo complex

SupramoleculeName: SrpI encapsulin apo complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Synechococcus elongatus (strain PCC 7942 / FACHB-805) (bacteria)
Molecular weightTheoretical: 2.1 MDa

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Macromolecule #1: Protein SrpI

MacromoleculeName: Protein SrpI / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus elongatus (strain PCC 7942 / FACHB-805) (bacteria)
Strain: PCC 7942 / FACHB-805
Molecular weightTheoretical: 35.371121 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MTDNAPQLAL RDVAARQLAN ATKTVPQLRT ITPRWLVRLL HWTPVEAGIY RVNQVKDASQ ITVACSERDE SELPETFVDY IDNPREYLL SAVNTVVDVH TRISDLYSNP HDQIREQLRL TIEIMKERQE SELINSREYG LLNNVAPGQL VHTRNGAPTP D DLDELLIR ...String:
MTDNAPQLAL RDVAARQLAN ATKTVPQLRT ITPRWLVRLL HWTPVEAGIY RVNQVKDASQ ITVACSERDE SELPETFVDY IDNPREYLL SAVNTVVDVH TRISDLYSNP HDQIREQLRL TIEIMKERQE SELINSREYG LLNNVAPGQL VHTRNGAPTP D DLDELLIR VWKEPAFFLA HPQAIAAFGR ECTRRGVPPA TVSLFGSSFI TWRGVPLIPS DKVPLENGKT KILLLRVGES RQ GVVGLYQ PNLPGEQGMG LSVRFMGINR KALASYLVSL YCSLAVLTDD ALAVLDNVDV TQYHTYRYNS GHHHHHH

UniProtKB: Type 2A encapsulin shell protein SrpI

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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

Concentration2.6 mg/mL
BufferpH: 10
GridModel: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV
Details: blot force 5, 3 sec blot, 100 humidity, 4C, 1 sec drain time.

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
SoftwareName: SerialEM
DetailsResidual beam tilt corrected in RELION/3.1. CTF refinement performed in RELION/3.1.
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 2966 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.6 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 36000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

DetailsImages collected in super-resolution mode
Particle selectionNumber selected: 57431 / Details: Relion LoG autopicker to select particles
Startup modelType of model: OTHER
Details: Initial reference model was the negative stain structure low pass filtered to 30A. Once the refinement was better than 3.5A, then a 5A map was used as the reference model to enforce proper handedness.
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 34425
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

SoftwareName: PHENIX (ver. 1.18_3845)
DetailsOne subunit was built completely de novo based on sequence/density, and iteratively real space refined with neighboring subunits using PHENIX.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 20 / Target criteria: Correlation coefficient
Output model

PDB-6x8t:
CryoEM structure of the apo-SrpI encapasulin complex from Synechococcus elongatus PCC 7942

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