+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 / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / proteasome accessory complex / integrator 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 / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / proteasome accessory complex / integrator complex / purine ribonucleoside triphosphate binding / deubiquitinase activity / regulation of chemotaxis / meiosis I / positive regulation of proteasomal protein catabolic process / proteasome regulatory particle / cytosolic proteasome complex / proteasome regulatory particle, lid subcomplex / proteasome-activating activity / proteasome regulatory particle, base subcomplex / protein K63-linked deubiquitination / metal-dependent deubiquitinase activity / regulation of endopeptidase activity / negative regulation of programmed cell death / hypothalamus gonadotrophin-releasing hormone neuron development / 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 / Homologous DNA Pairing and Strand Exchange / Regulation of ornithine decarboxylase (ODC) / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / female meiosis I / proteasome core complex / positive regulation of protein monoubiquitination / Resolution of D-loop Structures through Holliday Junction Intermediates / Cross-presentation of soluble exogenous antigens (endosomes) / mitochondrion transport along microtubule / fat pad development / Somitogenesis / K63-linked deubiquitinase activity / Impaired BRCA2 binding to RAD51 / endopeptidase inhibitor activity / immune system process / myofibril / proteasome binding / female gonad development / seminiferous tubule development / regulation of protein catabolic process / male meiosis I / proteasome storage granule / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Presynaptic phase of homologous DNA pairing and strand exchange / transcription factor binding / blastocyst development / general transcription initiation factor binding / NF-kappaB binding / endopeptidase activator activity / polyubiquitin modification-dependent protein binding / proteasome assembly / proteasome endopeptidase complex / positive regulation of RNA polymerase II transcription preinitiation complex assembly / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / negative regulation of ubiquitin-dependent protein catabolic process / mRNA export from nucleus / enzyme regulator activity / neuron projection morphogenesis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / ERAD pathway / energy homeostasis / inclusion body / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / negative regulation of inflammatory response to antigenic stimulus / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / 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 / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes 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 |
-Validation report
Summary document | emd_9511_validation.pdf.gz | 524.7 KB | Display | EMDB validaton report |
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Full document | emd_9511_full_validation.pdf.gz | 524.3 KB | Display | |
Data in XML | emd_9511_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | emd_9511_validation.cif.gz | 9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9511 ftp://ftp.pdbj.org/pub/emdb/validation_reports/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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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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 |