+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32549 | |||||||||
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Title | Cryo-EM Structure QD@HCcmL complex | |||||||||
Map data | Cryo-EM Structure QD@HCcmL complex | |||||||||
Sample |
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Function / homology | Function and homology information structural constituent of carboxysome shell / carboxysome / carbon fixation / photosynthesis Similarity search - Function | |||||||||
Biological species | Thermosynechococcus elongatus BP-1 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 9.2 Å | |||||||||
Authors | Zhang K / Li S | |||||||||
Funding support | China, 1 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2022 Title: A prototype protein nanocage minimized from carboxysomes with gated oxygen permeability. Authors: Ruimin Gao / Huan Tan / Shanshan Li / Shaojie Ma / Yufu Tang / Kaiming Zhang / Zhiping Zhang / Quli Fan / Jun Yang / Xian-En Zhang / Feng Li / Abstract: Protein nanocages (PNCs) in cells and viruses have inspired the development of self-assembling protein nanomaterials for various purposes. Despite the successful creation of artificial PNCs, the de ...Protein nanocages (PNCs) in cells and viruses have inspired the development of self-assembling protein nanomaterials for various purposes. Despite the successful creation of artificial PNCs, the de novo design of PNCs with defined permeability remains challenging. Here, we report a prototype oxygen-impermeable PNC (OIPNC) assembled from the vertex protein of the β-carboxysome shell, CcmL, with quantum dots as the template via interfacial engineering. The structure of the cage was solved at the atomic scale by combined solid-state NMR spectroscopy and cryoelectron microscopy, showing icosahedral assembly of CcmL pentamers with highly conserved interpentamer interfaces. Moreover, a gating mechanism was established by reversibly blocking the pores of the cage with molecular patches. Thus, the oxygen permeability, which was probed by an oxygen sensor inside the cage, can be completely controlled. The CcmL OIPNC represents a PNC platform for oxygen-sensitive or oxygen-responsive storage, catalysis, delivery, sensing, etc. | |||||||||
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_32549.map.gz | 3.8 MB | EMDB map data format | |
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Header (meta data) | emd-32549-v30.xml emd-32549.xml | 8.4 KB 8.4 KB | Display Display | EMDB header |
Images | emd_32549.png | 100.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32549 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32549 | HTTPS FTP |
-Validation report
Summary document | emd_32549_validation.pdf.gz | 308.8 KB | Display | EMDB validaton report |
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Full document | emd_32549_full_validation.pdf.gz | 308.3 KB | Display | |
Data in XML | emd_32549_validation.xml.gz | 5.5 KB | Display | |
Data in CIF | emd_32549_validation.cif.gz | 6.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32549 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32549 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_32549.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM Structure QD@HCcmL complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.14 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : QD@HCcmL complex
Entire | Name: QD@HCcmL complex |
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Components |
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-Supramolecule #1: QD@HCcmL complex
Supramolecule | Name: QD@HCcmL complex / type: complex / Chimera: Yes / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Thermosynechococcus elongatus BP-1 (bacteria) |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Molecular weight | Experimental: 400 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 54.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 9.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 55578 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |