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Yorodumi- EMDB-65839: Structure of human 26S proteasome complexed with midnolin, 19S pr... -
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Basic information
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| Title | Structure of human 26S proteasome complexed with midnolin, 19S proteasome with Ubl and Catch domain resolved | |||||||||
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Keywords | proteasome / midnolin / HYDROLASE | |||||||||
| Function / homology | Function and homology informationnegative regulation of glucokinase activity / thyrotropin-releasing hormone receptor binding / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / nuclear proteasome complex / host-mediated perturbation of viral transcription / positive regulation of inclusion body assembly / integrator complex / proteasome accessory complex / meiosis I ...negative regulation of glucokinase activity / thyrotropin-releasing hormone receptor binding / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / nuclear proteasome complex / host-mediated perturbation of viral transcription / positive regulation of inclusion body assembly / integrator complex / proteasome accessory complex / meiosis I / proteasome regulatory particle / cytosolic proteasome complex / positive regulation of proteasomal protein catabolic process / proteasome-activating activity / proteasome regulatory particle, lid subcomplex / proteasome regulatory particle, base subcomplex / protein K63-linked deubiquitination / negative regulation of programmed cell death / Regulation of ornithine decarboxylase (ODC) / metal-dependent deubiquitinase activity / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / 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) / transcription factor binding / Resolution of D-loop Structures through Holliday Junction Intermediates / detection of maltose stimulus / proteasome binding / maltose transport complex / Impaired BRCA2 binding to RAD51 / regulation of protein catabolic process / carbohydrate transport / proteasome storage granule / proteasomal ubiquitin-independent protein catabolic process / Presynaptic phase of homologous DNA pairing and strand exchange / general transcription initiation factor binding / carbohydrate transmembrane transporter activity / positive regulation of RNA polymerase II transcription preinitiation complex assembly / maltose binding / protein deubiquitination / blastocyst development / polyubiquitin modification-dependent protein binding / maltose transport / maltodextrin transmembrane transport / endopeptidase activator activity / proteasome assembly / mRNA export from nucleus / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / enzyme regulator activity / ERAD pathway / regulation of proteasomal protein catabolic process / inclusion body / ATP-binding cassette (ABC) transporter complex / proteasome complex / TBP-class protein binding / stem cell differentiation / Regulation of activated PAK-2p34 by proteasome mediated degradation / cell chemotaxis / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / ubiquitin binding / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / P-body / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Degradation of DVL / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of CRY and PER proteins / Degradation of AXIN / Hh mutants are degraded by ERAD / Activation of NF-kappaB in B cells / G2/M Checkpoints / Hedgehog ligand biogenesis / Degradation of GLI1 by the proteasome / Defective CFTR causes cystic fibrosis / Autodegradation of the E3 ubiquitin ligase COP1 / Regulation of RUNX3 expression and activity / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Negative regulation of NOTCH4 signaling / Hedgehog 'on' state / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Vif-mediated degradation of APOBEC3G / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / negative regulation of insulin secretion Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) / Pseudotamlana agarivorans (bacteria) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 4.23 Å | |||||||||
Authors | Zhu C / Qin L / Liang L | |||||||||
| Funding support | China, 1 items
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Citation | Journal: Nat Commun / Year: 2026Title: Structural dynamics of the midnolin-proteasome during ubiquitin-independent substrate turnover Authors: Zhu C / Qin L | |||||||||
| History |
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_65839.map.gz | 121.5 MB | EMDB map data format | |
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| Header (meta data) | emd-65839-v30.xml emd-65839.xml | 40.9 KB 40.9 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_65839_fsc.xml | 13.2 KB | Display | FSC data file |
| Images | emd_65839.png | 53.3 KB | ||
| Filedesc metadata | emd-65839.cif.gz | 12 KB | ||
| Others | emd_65839_half_map_1.map.gz emd_65839_half_map_2.map.gz | 226.9 MB 226.9 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-65839 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-65839 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9wbgMC ![]() 9mboC ![]() 9mbpC ![]() 9mbqC ![]() 9u3lC ![]() 9u4mC ![]() 9u7rC ![]() 9w39C M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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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_65839.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Half map: #1
| File | emd_65839_half_map_1.map | ||||||||||||
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-Half map: #2
| File | emd_65839_half_map_2.map | ||||||||||||
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| Density Histograms |
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Sample components
+Entire : 26S proteasome complex with midnolin
+Supramolecule #1: 26S proteasome complex with midnolin
+Macromolecule #1: Maltose/maltodextrin-binding periplasmic protein,Midnolin
+Macromolecule #2: 26S proteasome regulatory subunit 8
+Macromolecule #3: 26S proteasome regulatory subunit 6B
+Macromolecule #4: 26S proteasome non-ATPase regulatory subunit 3
+Macromolecule #5: 26S proteasome non-ATPase regulatory subunit 12
+Macromolecule #6: 26S proteasome non-ATPase regulatory subunit 11
+Macromolecule #7: 26S proteasome non-ATPase regulatory subunit 6
+Macromolecule #8: 26S proteasome non-ATPase regulatory subunit 7
+Macromolecule #9: 26S proteasome non-ATPase regulatory subunit 13
+Macromolecule #10: 26S proteasome non-ATPase regulatory subunit 4
+Macromolecule #11: 26S proteasome non-ATPase regulatory subunit 8
+Macromolecule #12: 26S proteasome complex subunit SEM1
+Macromolecule #13: Substrate
+Macromolecule #14: 26S proteasome non-ATPase regulatory subunit 1
+Macromolecule #15: Ubiquitin C-terminal hydrolase PSMD14,Uncharacterized protein
+Macromolecule #16: 26S proteasome regulatory subunit 7
+Macromolecule #17: 26S proteasome regulatory subunit 4
+Macromolecule #18: 26S proteasome regulatory subunit 10B
+Macromolecule #19: 26S proteasome regulatory subunit 6A
+Macromolecule #20: Early growth response protein 1
+Macromolecule #21: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #22: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #23: ZINC ION
+Macromolecule #24: MAGNESIUM ION
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Buffer | pH: 7.4 |
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| Vitrification | Cryogen name: ETHANE |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi



Keywords
Homo sapiens (human)
Pseudotamlana agarivorans (bacteria)
Authors
China, 1 items
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Processing
FIELD EMISSION GUN

