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Yorodumi- EMDB-22095: CryoEM structure of the apo-SrpI encapasulin complex from Synecho... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22095 | |||||||||
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Title | CryoEM structure of the apo-SrpI encapasulin complex from Synechococcus elongatus PCC 7942 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | encapsulin / 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 species | Synechococcus elongatus (strain PCC 7942 / FACHB-805) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | LaFrance BJ / Nichols RJ / Phillips NR / Oltrogge LM / Valentin-Alvarado LE / Bischoff AJ / Savage DF / Nogales E | |||||||||
Funding support | United States, 2 items
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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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_22095.map.gz | 21.6 MB | EMDB map data format | |
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Header (meta data) | emd-22095-v30.xml emd-22095.xml | 21.8 KB 21.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_22095_fsc.xml | 12.7 KB | Display | FSC data file |
Images | emd_22095.png | 200.8 KB | ||
Masks | emd_22095_msk_1.map | 178 MB | Mask map | |
Filedesc metadata | emd-22095.cif.gz | 6.5 KB | ||
Others | emd_22095_additional.map.gz emd_22095_additional_1.map.gz emd_22095_half_map_1.map.gz emd_22095_half_map_2.map.gz | 4.4 MB 4.4 MB 140.1 MB 140.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22095 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22095 | HTTPS FTP |
-Related structure data
Related structure data | 6x8tMC 6x8mC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | |
EM raw data | EMPIAR-10510 (Title: CryoEM SPA of Apo-SrpI Encapsulin Complex (Raw Frames) Data size: 1.6 TB Data #1: Raw Movies for Apo-SrpI Encapsulin collected on 200kV Arctica [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_22095.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.14 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_22095_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Segmented difference map resulting from subtracting classes of...
File | emd_22095_additional.map | ||||||||||||
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Annotation | Segmented difference map resulting from subtracting classes of EMD-22095 from the related map EMD-22094 after each map was symmetry-expanded and classified | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Segmented difference map resulting from subtracting classes of...
File | emd_22095_additional_1.map | ||||||||||||
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Annotation | Segmented difference map resulting from subtracting classes of EMD-22095 from the related map EMD-22094 after each map was symmetry-expanded and classified | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_22095_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_22095_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SrpI encapsulin apo complex
Entire | Name: SrpI encapsulin apo complex |
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Components |
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-Supramolecule #1: SrpI encapsulin apo complex
Supramolecule | Name: SrpI encapsulin apo complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Synechococcus elongatus (strain PCC 7942 / FACHB-805) (bacteria) |
Molecular weight | Theoretical: 2.1 MDa |
-Macromolecule #1: Protein SrpI
Macromolecule | Name: Protein SrpI / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Synechococcus elongatus (strain PCC 7942 / FACHB-805) (bacteria) Strain: PCC 7942 / FACHB-805 |
Molecular weight | Theoretical: 35.371121 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.6 mg/mL |
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Buffer | pH: 10 |
Grid | Model: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY |
Vitrification | Cryogen 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. |
-Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.6 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 36000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Software | Name: SerialEM |
Details | Residual beam tilt corrected in RELION/3.1. CTF refinement performed in RELION/3.1. |
Image recording | Film 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 |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Software | Name: PHENIX (ver. 1.18_3845) |
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Details | One subunit was built completely de novo based on sequence/density, and iteratively real space refined with neighboring subunits using PHENIX. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 20 / Target criteria: Correlation coefficient |
Output model | PDB-6x8t: |