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Yorodumi- EMDB-63776: Substrate-engaged human 26S proteasome bound to midnolin with RPT... -
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Basic information
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| Title | Substrate-engaged human 26S proteasome bound to midnolin with RPT1 at top of spiral staircase | |||||||||
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Keywords | Midnolin / 26S proteasome / Complex / HYDROLASE | |||||||||
| Function / homology | Function and homology informationnegative regulation of glucokinase activity / thyrotropin-releasing hormone receptor binding / nuclear proteasome complex / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / host-mediated perturbation of viral transcription / positive regulation of inclusion body assembly / proteasome accessory complex / integrator complex / meiosis I ...negative regulation of glucokinase activity / thyrotropin-releasing hormone receptor binding / nuclear proteasome complex / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / host-mediated perturbation of viral transcription / positive regulation of inclusion body assembly / proteasome accessory complex / integrator complex / meiosis I / purine ribonucleoside triphosphate binding / proteasome regulatory particle / cytosolic proteasome complex / positive regulation of proteasomal protein catabolic process / proteasome-activating activity / Antigen processing: Ub, ATP-independent proteasomal degradation / proteasome regulatory particle, lid subcomplex / proteasome regulatory particle, base subcomplex / sperm glycocalyx / protein K63-linked deubiquitination / perinuclear theca / negative regulation of programmed cell death / Regulation of ornithine decarboxylase (ODC) / metal-dependent deubiquitinase activity / Proteasome assembly / proteasome core complex / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / 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) / K63-linked deubiquitinase activity / transcription factor binding / Resolution of D-loop Structures through Holliday Junction Intermediates / proteasome binding / Impaired BRCA2 binding to RAD51 / myofibril / regulation of protein catabolic process / proteasome storage granule / sperm head-tail coupling apparatus / proteasomal ubiquitin-independent protein catabolic process / Presynaptic phase of homologous DNA pairing and strand exchange / general transcription initiation factor binding / protein deubiquitination / polyubiquitin modification-dependent protein binding / blastocyst development / immune system process / NF-kappaB binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / endopeptidase activator activity / threonine-type endopeptidase activity / proteasome assembly / mRNA export from nucleus / proteasome core complex, alpha-subunit complex / enzyme regulator activity / regulation of proteasomal protein catabolic process / inclusion body / ciliary tip / proteasome complex / TBP-class protein binding / : / stem cell differentiation / sarcomere / Regulation of activated PAK-2p34 by proteasome mediated degradation / 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 / sperm end piece / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / centriole / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / negative regulation of inflammatory response to antigenic stimulus / 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 / lipopolysaccharide binding / 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 Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.75 Å | |||||||||
Authors | Zhu C / Qin L / Liang L | |||||||||
| Funding support | China, 1 items
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Citation | Journal: To Be PublishedTitle: Molecular basis for ubiquitin-independent substrate degradation by midnolin-proteasome Authors: Zhu C / Qin L | |||||||||
| History |
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_63776.map.gz | 743 MB | EMDB map data format | |
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| Header (meta data) | emd-63776-v30.xml emd-63776.xml | 63.3 KB 63.3 KB | Display Display | EMDB header |
| Images | emd_63776.png | 53.2 KB | ||
| Filedesc metadata | emd-63776.cif.gz | 14.8 KB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-63776 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-63776 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9mbpMC ![]() 9mboC ![]() 9mbqC ![]() 9u3lC ![]() 9u4mC C: citing same article ( M: atomic model generated by this map |
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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_63776.map.gz / Format: CCP4 / Size: 824 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
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Sample components
+Entire : 26S proteasome complexed with midnolin
+Supramolecule #1: 26S proteasome complexed with midnolin
+Supramolecule #2: midnolin
+Supramolecule #3: 26S proteasome
+Macromolecule #1: 26S proteasome non-ATPase regulatory subunit 1
+Macromolecule #2: 26S proteasome non-ATPase regulatory subunit 3
+Macromolecule #3: 26S proteasome non-ATPase regulatory subunit 12
+Macromolecule #4: 26S proteasome non-ATPase regulatory subunit 11
+Macromolecule #5: 26S proteasome non-ATPase regulatory subunit 6
+Macromolecule #6: 26S proteasome non-ATPase regulatory subunit 7
+Macromolecule #7: 26S proteasome non-ATPase regulatory subunit 13
+Macromolecule #8: 26S proteasome non-ATPase regulatory subunit 4
+Macromolecule #9: 26S proteasome non-ATPase regulatory subunit 14
+Macromolecule #10: 26S proteasome non-ATPase regulatory subunit 8
+Macromolecule #11: 26S proteasome complex subunit SEM1
+Macromolecule #12: 26S proteasome regulatory subunit 7
+Macromolecule #13: 26S proteasome regulatory subunit 4
+Macromolecule #14: 26S proteasome regulatory subunit 8
+Macromolecule #15: 26S proteasome regulatory subunit 6B
+Macromolecule #16: Proteasome 26S subunit, ATPase 6
+Macromolecule #17: 26S proteasome regulatory subunit 6A
+Macromolecule #18: substrate peptide
+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: Isoform Long of 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: Midnolin
+Macromolecule #34: 26S proteasome non-ATPase regulatory subunit 2
+Macromolecule #35: ZINC ION
+Macromolecule #36: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #37: MAGNESIUM ION
+Macromolecule #38: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #39: N-[(benzyloxy)carbonyl]-L-leucyl-N-[(2S)-4-methyl-1-oxopentan-2-y...
-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: 1.2 µm |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi



Keywords
Homo sapiens (human)
Authors
China, 1 items
Citation


























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Processing
FIELD EMISSION GUN
