+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14204 | |||||||||
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Title | Proteasome-ZFAND5 Complex Z+D state | |||||||||
Map data | ZFAND5-proteasome complex Z D state | |||||||||
Sample |
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Function / homology | Function and homology information Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / thyrotropin-releasing hormone receptor binding / modulation by host of viral transcription / respiratory system process / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / smooth muscle tissue development / proteasome accessory complex / integrator complex / purine ribonucleoside triphosphate binding ...Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / thyrotropin-releasing hormone receptor binding / modulation by host of viral transcription / respiratory system process / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / smooth muscle tissue development / proteasome accessory complex / integrator complex / purine ribonucleoside triphosphate binding / fibroblast migration / meiosis I / positive regulation of proteasomal protein catabolic process / proteasome regulatory particle / cytosolic proteasome complex / proteasome regulatory particle, lid subcomplex / proteasome-activating activity / vasculature development / proteasome regulatory particle, base subcomplex / protein K63-linked deubiquitination / metal-dependent deubiquitinase activity / regulation of endopeptidase activity / negative regulation of programmed cell death / 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) / skeletal system morphogenesis / proteasome core complex / Resolution of D-loop Structures through Holliday Junction Intermediates / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / K63-linked deubiquitinase activity / Impaired BRCA2 binding to RAD51 / immune system process / myofibril / proteasome binding / regulation of protein catabolic process / face development / proteasome storage granule / Presynaptic phase of homologous DNA pairing and strand exchange / transcription factor binding / blastocyst development / platelet-derived growth factor receptor signaling pathway / general transcription initiation factor binding / NF-kappaB binding / endopeptidase activator activity / polyubiquitin modification-dependent protein binding / proteasome assembly / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / mRNA export from nucleus / enzyme regulator activity / regulation of proteasomal protein catabolic process / inclusion body / negative regulation of inflammatory response to antigenic stimulus / : / sarcomere / proteasome complex / Regulation of activated PAK-2p34 by proteasome mediated degradation / ciliary basal body / proteolysis involved in protein catabolic process / 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 / TNFR2 non-canonical NF-kB pathway / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Degradation of DVL / stem cell differentiation / CDK-mediated phosphorylation and removal of Cdc6 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Hh mutants are degraded by ERAD / lipopolysaccharide binding / SCF(Skp2)-mediated degradation of p27/p21 / Degradation of AXIN / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / Negative regulation of NOTCH4 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / G2/M Checkpoints / Vif-mediated degradation of APOBEC3G / Autodegradation of the E3 ubiquitin ligase COP1 / Hedgehog 'on' state / Regulation of RUNX3 expression and activity / P-body / Degradation of GLI2 by the proteasome Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / human (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||
Authors | Zhu Y / Lu Y | |||||||||
Funding support | 1 items
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Citation | Journal: To Be Published Title: Mechanism of 26S proteasome activation by the 19S-interacting protein ZFAND5 Authors: Zhu Y / Lu Y | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14204.map.gz | 114.4 MB | EMDB map data format | |
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Header (meta data) | emd-14204-v30.xml emd-14204.xml | 44.5 KB 44.5 KB | Display Display | EMDB header |
Images | emd_14204.png | 74.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14204 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14204 | HTTPS FTP |
-Validation report
Summary document | emd_14204_validation.pdf.gz | 637.9 KB | Display | EMDB validaton report |
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Full document | emd_14204_full_validation.pdf.gz | 637.5 KB | Display | |
Data in XML | emd_14204_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | emd_14204_validation.cif.gz | 7.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14204 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14204 | HTTPS FTP |
-Related structure data
Related structure data | 7qxwMC 7qxnC 7qxpC 7qxuC 7qxxC 7qy7C 7qyaC 7qybC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_14204.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | ZFAND5-proteasome complex Z D state | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.37 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
+Entire : human proteasome zfand5 complex Z+D state
+Supramolecule #1: human proteasome zfand5 complex Z+D state
+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 non-ATPase regulatory subunit 2
+Macromolecule #12: 26S protease regulatory subunit 7
+Macromolecule #13: 26S proteasome regulatory subunit 4
+Macromolecule #14: Isoform 2 of 26S proteasome regulatory subunit 8
+Macromolecule #15: 26S protease regulatory subunit 6B
+Macromolecule #16: 26S proteasome regulatory subunit 10B
+Macromolecule #17: 26S protease regulatory subunit 6A
+Macromolecule #18: 26S proteasome complex subunit SEM1
+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: AN1-type zinc finger protein 5
+Macromolecule #34: ZINC ION
+Macromolecule #35: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #36: MAGNESIUM ION
+Macromolecule #37: ADENOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 7 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 46.6 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: 2.0 µm / Nominal defocus min: 2.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 28928 |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 28928 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |