+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9507 | |||||||||
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Title | Cryo-EM map of the RP region of human 26S proteasome at 4.3A | |||||||||
Map data | map of the RP region | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.3 Å | |||||||||
Authors | Huang XL / Luan B / Wu JP / Shi YG | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2016 Title: An atomic structure of the human 26S proteasome. Authors: Xiuliang Huang / Bai Luan / Jianping Wu / Yigong Shi / Abstract: We report the cryo-EM structure of the human 26S proteasome at an average resolution of 3.5 Å, allowing atomic modeling of 28 subunits in the core particle (CP) and 18 subunits in the regulatory ...We report the cryo-EM structure of the human 26S proteasome at an average resolution of 3.5 Å, allowing atomic modeling of 28 subunits in the core particle (CP) and 18 subunits in the regulatory particle (RP). The C-terminal residues of Rpt3 and Rpt5 subunits in the RP can be seen inserted into surface pockets formed between adjacent α subunits in the CP. Each of the six Rpt subunits contains a bound nucleotide, and the central gate of the CP α-ring is closed despite RP association. The six pore 1 loops in the Rpt ring are arranged similarly to a spiral staircase along the axial channel of substrate transport, which is constricted by the pore 2 loops. We also determined the cryo-EM structure of the human proteasome bound to the deubiquitinating enzyme USP14 at 4.35-Å resolution. Together, our structures provide a framework for mechanistic understanding of eukaryotic proteasome function. | |||||||||
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_9507.map.gz | 78.5 MB | EMDB map data format | |
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Header (meta data) | emd-9507-v30.xml emd-9507.xml | 11.7 KB 11.7 KB | Display Display | EMDB header |
Images | emd_9507.png | 37.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9507 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9507 | HTTPS FTP |
-Validation report
Summary document | emd_9507_validation.pdf.gz | 79.3 KB | Display | EMDB validaton report |
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Full document | emd_9507_full_validation.pdf.gz | 78.4 KB | Display | |
Data in XML | emd_9507_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9507 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9507 | HTTPS FTP |
-Related structure data
Related structure data | 9508C 9509C 9510C 9511C 9512C 5gjqC 5gjrC C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_9507.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | map of the RP region | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 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 : human 26S proteasome
Entire | Name: human 26S proteasome |
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Components |
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-Supramolecule #1: human 26S proteasome
Supramolecule | Name: human 26S proteasome / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 2.5 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
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Grid | Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 3.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 2s before plunging. | ||||||||||||
Details | This sample was monodisperse |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 70.0 K |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 4881 / Average exposure time: 1.6 sec. / Average electron dose: 37.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |