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Open data
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Basic information
| Entry | Database: EMDB / ID: EMD-9511 | ||||||||||||
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| Title | Cryo-EM map of the human 26S proteasome bound to USP14_UbAl | ||||||||||||
Map data | Human 26S proteasome bound to USP14-UbAl | ||||||||||||
Sample |
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Keywords | protein complex / human proteasome / HYDROLASE | ||||||||||||
| Function / homology | Function and homology informationnegative regulation of ERAD pathway / regulation of chemotaxis / protein K48-linked deubiquitination / deubiquitinase activity / positive regulation of inclusion body assembly / thyrotropin-releasing hormone receptor binding / nuclear proteasome complex / host-mediated perturbation of viral transcription / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) ...negative regulation of ERAD pathway / regulation of chemotaxis / protein K48-linked deubiquitination / deubiquitinase activity / positive regulation of inclusion body assembly / thyrotropin-releasing hormone receptor binding / nuclear proteasome complex / host-mediated perturbation of viral transcription / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / proteasome accessory complex / purine ribonucleoside triphosphate binding / integrator complex / proteasome regulatory particle / CD8-positive, alpha-beta T cell differentiation / thymic T cell selection / cytosolic proteasome complex / CD8-positive, alpha-beta T cell homeostasis / positive regulation of proteasomal protein catabolic process / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / proteasome-activating activity / Antigen processing: Ub, ATP-independent proteasomal degradation / seminiferous tubule development / proteasome regulatory particle, lid subcomplex / proteasome regulatory particle, base subcomplex / positive regulation of protein monoubiquitination / fat pad development / negative regulation of programmed cell death / mitochondrion transport along microtubule / negative regulation of regulatory T cell differentiation / T-helper 1 cell differentiation / protein K63-linked deubiquitination / cellular response to type I interferon / metal-dependent deubiquitinase activity / Regulation of ornithine decarboxylase (ODC) / proteasome core complex / Proteasome assembly / T-helper 17 cell differentiation / endopeptidase inhibitor activity / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / Cross-presentation of soluble exogenous antigens (endosomes) / transcription factor binding / Somitogenesis / female gonad development / flagellated sperm motility / K63-linked deubiquitinase activity / Homologous DNA Pairing and Strand Exchange / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / proteasome binding / male meiosis I / Impaired BRCA2 binding to RAD51 / myofibril / positive regulation of RNA polymerase II transcription preinitiation complex assembly / proteasomal ubiquitin-independent protein catabolic process / general transcription initiation factor binding / proteasome storage granule / Presynaptic phase of homologous DNA pairing and strand exchange / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / AMPK-induced ERAD and lysosome mediated degradation of PD-L1(CD274) / negative regulation of ubiquitin-dependent protein catabolic process / protein deubiquitination / polyubiquitin modification-dependent protein binding / proteasome endopeptidase complex / NF-kappaB binding / proteasome core complex, beta-subunit complex / energy homeostasis / endopeptidase activator activity / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / proteasome assembly / mRNA export from nucleus / GSK3B-mediated proteasomal degradation of PD-L1(CD274) / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / SPOP-mediated proteasomal degradation of PD-L1(CD274) / presynaptic cytosol / immune system process / regulation of G1/S transition of mitotic cell cycle / enzyme regulator activity / regulation of macroautophagy / positive regulation of interleukin-2 production / neuron projection morphogenesis / ERAD pathway / ciliary tip / Ribosome Quality Control (RQC) complex extracts and degrades nascent peptide / response to type II interferon / Maturation of protein E / inclusion body / Maturation of protein E / ER Quality Control Compartment (ERQC) / regulation of neuron apoptotic process / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis Similarity search - Function | ||||||||||||
| Biological species | Homo sapiens (human) | ||||||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 4.35 Å | ||||||||||||
Authors | Huang XL / Luan B / Wu JP / Shi YG | ||||||||||||
| Funding support | China, 3 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2016Title: 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 |
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| Structure viewer | EM map: SurfView Molmil Jmol/JSmol |
| Supplemental images |
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Downloads & links
-EMDB archive
| Map data | emd_9511.map.gz | 480 MB | EMDB map data format | |
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| Header (meta data) | emd-9511-v30.xml emd-9511.xml | 60.1 KB 60.1 KB | Display Display | EMDB header |
| Images | emd_9511.png | 45.1 KB | ||
| Filedesc metadata | emd-9511.cif.gz | 16 KB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9511 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9511 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 5gjqMC ![]() 9507C ![]() 9508C ![]() 9509C ![]() 9510C ![]() 9512C ![]() 5gjrC C: citing same article ( M: atomic model generated by this map |
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| Similar structure data |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_9511.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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| Annotation | Human 26S proteasome bound to USP14-UbAl | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 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
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Sample components
+Entire : human 26S proteasome bound to USP14-UbAl
+Supramolecule #1: human 26S proteasome bound to USP14-UbAl
+Macromolecule #1: Proteasome subunit beta type-6
+Macromolecule #2: Proteasome subunit alpha type-6
+Macromolecule #3: Proteasome subunit beta type-7
+Macromolecule #4: Proteasome subunit alpha type-2
+Macromolecule #5: Proteasome subunit beta type-3
+Macromolecule #6: Proteasome subunit alpha type-4
+Macromolecule #7: Proteasome subunit beta type-2
+Macromolecule #8: Proteasome subunit alpha type-7
+Macromolecule #9: Proteasome subunit beta type-5
+Macromolecule #10: Proteasome subunit alpha type-5
+Macromolecule #11: Proteasome subunit beta type-1
+Macromolecule #12: Proteasome subunit alpha type-1
+Macromolecule #13: Proteasome subunit beta type-4
+Macromolecule #14: 26S protease regulatory subunit 7
+Macromolecule #15: 26S protease regulatory subunit 4
+Macromolecule #16: 26S protease regulatory subunit 8
+Macromolecule #17: 26S protease regulatory subunit 6B
+Macromolecule #18: 26S protease regulatory subunit 10B
+Macromolecule #19: 26S protease regulatory subunit 6A
+Macromolecule #20: 26S proteasome non-ATPase regulatory subunit 1
+Macromolecule #21: Proteasome subunit alpha type-3
+Macromolecule #22: 26S proteasome non-ATPase regulatory subunit 13
+Macromolecule #23: 26S proteasome non-ATPase regulatory subunit 12
+Macromolecule #24: 26S proteasome non-ATPase regulatory subunit 11
+Macromolecule #25: 26S proteasome non-ATPase regulatory subunit 6
+Macromolecule #26: 26S proteasome non-ATPase regulatory subunit 3
+Macromolecule #27: 26S proteasome non-ATPase regulatory subunit 8
+Macromolecule #28: 26S proteasome non-ATPase regulatory subunit 7
+Macromolecule #29: 26S proteasome non-ATPase regulatory subunit 14
+Macromolecule #30: 26S proteasome non-ATPase regulatory subunit 4
+Macromolecule #31: 26S proteasome complex subunit DSS1
+Macromolecule #32: 26S proteasome non-ATPase regulatory subunit 2
+Macromolecule #33: Ubiquitin carboxyl-terminal hydrolase 14
+Macromolecule #34: Polyubiquitin-B
+Macromolecule #35: ADENOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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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 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR | ||||||||||||
| Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 2 seconds before plunging. | ||||||||||||
| Details | This sample was monodisperse. |
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Electron microscopy
| Microscope | FEI TITAN KRIOS |
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| Temperature | Min: 70.0 K |
| Details | Preliminary grid screening was performed manually |
| Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 1-26 / 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 / Cs: 2.7 mm |
| Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi



Keywords
Homo sapiens (human)
Authors
China, 3 items
Citation
UCSF Chimera








































Z (Sec.)
Y (Row.)
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