+Open data
-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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Function / homology | Function and homology information negative regulation of ERAD pathway / positive regulation of inclusion body assembly / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / thyrotropin-releasing hormone receptor binding / modulation by host of viral transcription / deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / proteasome accessory complex / purine ribonucleoside triphosphate binding ...negative regulation of ERAD pathway / positive regulation of inclusion body assembly / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / thyrotropin-releasing hormone receptor binding / modulation by host of viral transcription / deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / proteasome accessory complex / purine ribonucleoside triphosphate binding / regulation of chemotaxis / meiosis I / positive regulation of proteasomal protein catabolic process / metal-dependent deubiquitinase activity / proteasome regulatory particle / cytosolic proteasome complex / proteasome regulatory particle, lid subcomplex / proteasome-activating activity / protein K63-linked deubiquitination / proteasome regulatory particle, base subcomplex / negative regulation of programmed cell death / hypothalamus gonadotrophin-releasing hormone neuron development / regulation of endopeptidase activity / 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 / female meiosis I / proteasome core complex / Homologous DNA Pairing and Strand Exchange / Regulation of ornithine decarboxylase (ODC) / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / Resolution of D-loop Structures through Holliday Junction Intermediates / Cross-presentation of soluble exogenous antigens (endosomes) / fat pad development / Somitogenesis / K63-linked deubiquitinase activity / Impaired BRCA2 binding to RAD51 / endopeptidase inhibitor activity / immune system process / myofibril / female gonad development / proteasome binding / seminiferous tubule development / : / regulation of protein catabolic process / protein deubiquitination / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / proteasome storage granule / Presynaptic phase of homologous DNA pairing and strand exchange / blastocyst development / transcription factor binding / general transcription initiation factor binding / endopeptidase activator activity / NF-kappaB binding / proteasome assembly / polyubiquitin modification-dependent protein binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / positive regulation of RNA polymerase II transcription preinitiation complex assembly / mRNA export from nucleus / enzyme regulator activity / energy homeostasis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Maturation of protein E / Maturation of protein E / inclusion body / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / negative regulation of inflammatory response to antigenic stimulus / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / response to organonitrogen compound / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) / Human (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: 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_9511.map.gz | 480 MB | EMDB map data format | |
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Header (meta data) | emd-9511-v30.xml emd-9511.xml | 52.7 KB 52.7 KB | Display Display | EMDB header |
Images | emd_9511.png | 45.1 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 (ref.) M: atomic model generated by this map |
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Similar 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_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
-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 |
-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 2 seconds before plunging. | ||||||||||||
Details | This sample was monodisperse. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 534096 |
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CTF correction | Software - Name: CTFFIND (ver. 3) |
Startup model | Type of model: EMDB MAP EMDB ID: |
Initial angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 1.4) |
Final 3D classification | Number classes: 5 / Software - Name: RELION (ver. 1.4) |
Final angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 1.4) |
Final reconstruction | Number classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 4.35 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 141293 |