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Yorodumi- EMDB-9512: Cryo-EM map of the human 26S proteasome at 3.5A resolution with C... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9512 | ||||||||||||
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Title | Cryo-EM map of the human 26S proteasome at 3.5A resolution with C2 symmetry | ||||||||||||
Map data | with C2 symmetry | ||||||||||||
Sample |
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Function / homology | Function and homology information 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 / meiosis I / positive regulation of proteasomal protein catabolic process / metal-dependent deubiquitinase activity ...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 / meiosis I / positive regulation of proteasomal protein catabolic process / metal-dependent deubiquitinase activity / proteasome regulatory particle / purine ribonucleoside triphosphate binding / cytosolic proteasome complex / proteasome regulatory particle, lid subcomplex / proteasome-activating activity / proteasome regulatory particle, base subcomplex / protein K63-linked deubiquitination / negative regulation of programmed cell death / 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 / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Regulation of ornithine decarboxylase (ODC) / proteasome core complex / Resolution of D-loop Structures through Holliday Junction Intermediates / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / Impaired BRCA2 binding to RAD51 / K63-linked deubiquitinase activity / immune system process / myofibril / proteasome binding / regulation of protein catabolic process / proteasome storage granule / Presynaptic phase of homologous DNA pairing and strand exchange / blastocyst development / transcription factor binding / polyubiquitin modification-dependent protein binding / general transcription initiation factor binding / endopeptidase activator activity / NF-kappaB 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 / regulation of proteasomal protein catabolic process / enzyme regulator activity / mRNA export from nucleus / inclusion body / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / : / negative regulation of inflammatory response to antigenic stimulus / : / response to organonitrogen compound / sarcomere / proteolysis involved in protein catabolic process / proteasome complex / Regulation of activated PAK-2p34 by proteasome mediated degradation / ciliary basal body / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Degradation of DVL / TNFR2 non-canonical NF-kB pathway / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / proteasomal protein catabolic process / stem cell differentiation / P-body / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants are degraded by ERAD / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Degradation of GLI1 by the proteasome / lipopolysaccharide binding / Degradation of AXIN / Defective CFTR causes cystic fibrosis / Activation of NF-kappaB in B cells / Negative regulation of NOTCH4 signaling / Hedgehog ligand biogenesis / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / double-strand break repair via homologous recombination / Vif-mediated degradation of APOBEC3G / G2/M Checkpoints / Hedgehog 'on' state / Autodegradation of the E3 ubiquitin ligase COP1 / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Regulation of RUNX3 expression and activity / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / response to virus Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) / Human (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 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_9512.map.gz | 478.8 MB | EMDB map data format | |
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Header (meta data) | emd-9512-v30.xml emd-9512.xml | 50.5 KB 50.5 KB | Display Display | EMDB header |
Images | emd_9512.png | 32.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9512 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9512 | HTTPS FTP |
-Related structure data
Related structure data | 5gjrMC 9507C 9508C 9509C 9510C 9511C 5gjqC 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_9512.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | with C2 symmetry | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
+Supramolecule #1: human 26S proteasome
+Macromolecule #1: 26S protease regulatory subunit 4
+Macromolecule #2: 26S protease regulatory subunit 7
+Macromolecule #3: 26S protease regulatory subunit 10B
+Macromolecule #4: 26S protease regulatory subunit 6A
+Macromolecule #5: 26S protease regulatory subunit 8
+Macromolecule #6: 26S protease regulatory subunit 6B
+Macromolecule #7: 26S proteasome non-ATPase regulatory subunit 1
+Macromolecule #8: 26S proteasome non-ATPase regulatory subunit 13
+Macromolecule #9: 26S proteasome non-ATPase regulatory subunit 12
+Macromolecule #10: 26S proteasome non-ATPase regulatory subunit 11
+Macromolecule #11: 26S proteasome non-ATPase regulatory subunit 6
+Macromolecule #12: 26S proteasome non-ATPase regulatory subunit 3
+Macromolecule #13: 26S proteasome non-ATPase regulatory subunit 8
+Macromolecule #14: 26S proteasome non-ATPase regulatory subunit 7
+Macromolecule #15: 26S proteasome non-ATPase regulatory subunit 14
+Macromolecule #16: 26S proteasome non-ATPase regulatory subunit 4
+Macromolecule #17: 26S proteasome complex subunit DSS1
+Macromolecule #18: 26S proteasome non-ATPase regulatory subunit 2
+Macromolecule #19: Proteasome subunit alpha type-6
+Macromolecule #20: Proteasome subunit alpha type-2
+Macromolecule #21: Proteasome subunit alpha type-4
+Macromolecule #22: Proteasome subunit alpha type-7
+Macromolecule #23: Proteasome subunit alpha type-5
+Macromolecule #24: Proteasome subunit alpha type-1
+Macromolecule #25: Proteasome subunit alpha type-3
+Macromolecule #26: Proteasome subunit beta type-6
+Macromolecule #27: Proteasome subunit beta type-7
+Macromolecule #28: Proteasome subunit beta type-3
+Macromolecule #29: Proteasome subunit beta type-2
+Macromolecule #30: Proteasome subunit beta type-5
+Macromolecule #31: Proteasome subunit beta type-1
+Macromolecule #32: Proteasome subunit beta type-4
+Macromolecule #33: 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 | Calibrated defocus max: 0.0026 µm / Calibrated defocus min: 0.0016 µm / 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: 443359 |
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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 / Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Details: apply C2 symmetry / Number images used: 165699 |