[English] 日本語
Yorodumi- EMDB-9383: Encapsulin iron storage compartment from Quasibacillus thermotolerans -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9383 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Encapsulin iron storage compartment from Quasibacillus thermotolerans | |||||||||
Map data | Final EM map filtered to 3.85A with applied sharpening B-factor of -151 | |||||||||
Sample |
| |||||||||
Keywords | encapsulin / iron storage / IMEF / icosahedral / METAL TRANSPORT | |||||||||
Function / homology | : / Type 1 encapsulin shell protein / Encapsulating protein for peroxidase / encapsulin nanocompartment / iron ion transport / intracellular iron ion homeostasis / Type 1 encapsulin shell protein Function and homology information | |||||||||
Biological species | Bacillus thermotolerans (bacteria) / Quasibacillus thermotolerans (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.85 Å | |||||||||
Authors | Orlando BJ / Giessen TW | |||||||||
Funding support | Germany, 1 items
| |||||||||
Citation | Journal: Elife / Year: 2019 Title: Large protein organelles form a new iron sequestration system with high storage capacity. Authors: Tobias W Giessen / Benjamin J Orlando / Andrew A Verdegaal / Melissa G Chambers / Jules Gardener / David C Bell / Gabriel Birrane / Maofu Liao / Pamela A Silver / Abstract: Iron storage proteins are essential for cellular iron homeostasis and redox balance. Ferritin proteins are the major storage units for bioavailable forms of iron. Some organisms lack ferritins, and ...Iron storage proteins are essential for cellular iron homeostasis and redox balance. Ferritin proteins are the major storage units for bioavailable forms of iron. Some organisms lack ferritins, and it is not known how they store iron. Encapsulins, a class of protein-based organelles, have recently been implicated in microbial iron and redox metabolism. Here, we report the structural and mechanistic characterization of a 42 nm two-component encapsulin-based iron storage compartment from . Using cryo-electron microscopy and x-ray crystallography, we reveal the assembly principles of a thermostable T = 4 shell topology and its catalytic ferroxidase cargo and show interactions underlying cargo-shell co-assembly. This compartment has an exceptionally large iron storage capacity storing over 23,000 iron atoms. Our results reveal a new approach for survival in diverse habitats with limited or fluctuating iron availability via an iron storage system able to store 10 to 20 times more iron than ferritin. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9383.map.gz | 386.8 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-9383-v30.xml emd-9383.xml | 13.2 KB 13.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_9383_fsc.xml | 19.8 KB | Display | FSC data file |
Images | emd_9383.png | 262.1 KB | ||
Filedesc metadata | emd-9383.cif.gz | 5.7 KB | ||
Others | emd_9383_additional.map.gz | 335.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9383 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9383 | HTTPS FTP |
-Validation report
Summary document | emd_9383_validation.pdf.gz | 754.1 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_9383_full_validation.pdf.gz | 753.7 KB | Display | |
Data in XML | emd_9383_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | emd_9383_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9383 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9383 | HTTPS FTP |
-Related structure data
Related structure data | 6nj8MC 6n63C M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_9383.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Final EM map filtered to 3.85A with applied sharpening B-factor of -151 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.365 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Additional map: Final unfiltered EM map
File | emd_9383_additional.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Final unfiltered EM map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Encapsulin iron storage compartment from Quasibacillus thermotolerans
Entire | Name: Encapsulin iron storage compartment from Quasibacillus thermotolerans |
---|---|
Components |
|
-Supramolecule #1: Encapsulin iron storage compartment from Quasibacillus thermotolerans
Supramolecule | Name: Encapsulin iron storage compartment from Quasibacillus thermotolerans type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: Bacillus thermotolerans (bacteria) |
Molecular weight | Theoretical: 9.6 MDa |
-Macromolecule #1: Encapsulating protein for a DyP-type peroxidase
Macromolecule | Name: Encapsulating protein for a DyP-type peroxidase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Quasibacillus thermotolerans (bacteria) |
Molecular weight | Theoretical: 32.239459 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MNKSQLYPDS PLTDQDFNQL DQTVIEAARR QLVGRRFIEL YGPLGRGMQS VFNDIFMESH EAKMDFQGSF DTEVESSRRV NYTIPMLYK DFVLYWRDLE QSKALDIPID FSVAANAARD VAFLEDQMIF HGSKEFDIPG LMNVKGRLTH LIGNWYESGN A FQDIVEAR ...String: MNKSQLYPDS PLTDQDFNQL DQTVIEAARR QLVGRRFIEL YGPLGRGMQS VFNDIFMESH EAKMDFQGSF DTEVESSRRV NYTIPMLYK DFVLYWRDLE QSKALDIPID FSVAANAARD VAFLEDQMIF HGSKEFDIPG LMNVKGRLTH LIGNWYESGN A FQDIVEAR NKLLEMNHNG PYALVLSPEL YSLLHRVHKD TNVLEIEHVR ELITAGVFQS PVLKGKSGVI VNTGRNNLDL AI SEDFETA YLGEEGMNHP FRVYETVVLR IKRPAAICTL IDPEE UniProtKB: Type 1 encapsulin shell protein |
-Macromolecule #2: targeting peptide
Macromolecule | Name: targeting peptide / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Bacillus thermotolerans (bacteria) |
Molecular weight | Theoretical: 716.824 Da |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: TVGSLIQ |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.5 mg/mL |
---|---|
Buffer | pH: 8 |
Grid | Model: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Instrument: GATAN CRYOPLUNGE 3 |
-Electron microscopy
Microscope | FEI TECNAI F20 |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 601 / Average exposure time: 7.2 sec. / Average electron dose: 44.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |