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Yorodumi- PDB-5a0q: Cryo-EM reveals the conformation of a substrate analogue in the h... -
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Basic information
| Entry | Database: PDB / ID: 5a0q | ||||||
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| Title | Cryo-EM reveals the conformation of a substrate analogue in the human 20S proteasome core | ||||||
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Keywords | HYDROLASE / PROTEASOME / 20S / ADAAHX3L3VS / LIGAND / INHIBITOR / DRUG DESIGN | ||||||
| Function / homology | Function and homology informationpurine ribonucleoside triphosphate binding / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / proteasome core complex / Somitogenesis / myofibril / immune system process / NF-kappaB binding / proteasome endopeptidase complex ...purine ribonucleoside triphosphate binding / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / proteasome core complex / Somitogenesis / myofibril / immune system process / NF-kappaB binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome assembly / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / proteolysis involved in protein catabolic process / proteasome complex / sarcomere / Regulation of activated PAK-2p34 by proteasome mediated degradation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / 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 / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / negative regulation of inflammatory response to antigenic stimulus / Degradation of AXIN / P-body / Hh mutants are degraded by ERAD / lipopolysaccharide binding / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / G2/M Checkpoints / Hedgehog ligand biogenesis / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Defective CFTR causes cystic fibrosis / Autodegradation of the E3 ubiquitin ligase COP1 / Negative regulation of NOTCH4 signaling / Regulation of RUNX3 expression and activity / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / MAPK6/MAPK4 signaling / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / ABC-family proteins mediated transport / CDK-mediated phosphorylation and removal of Cdc6 / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / response to virus / FCERI mediated NF-kB activation / Regulation of expression of SLITs and ROBOs / Regulation of PTEN stability and activity / nuclear matrix / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RAS by GAPs / Regulation of RUNX2 expression and activity / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / KEAP1-NFE2L2 pathway / UCH proteinases / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / peptidase activity / Neddylation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / ER-Phagosome pathway / regulation of inflammatory response / response to oxidative stress / secretory granule lumen / endopeptidase activity / ficolin-1-rich granule lumen / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / Ub-specific processing proteases / nuclear body / cilium / ciliary basal body / ribosome / cadherin binding / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / centrosome / Neutrophil degranulation / mitochondrion / proteolysis / RNA binding / extracellular exosome / extracellular region Similarity search - Function | ||||||
| Biological species | HOMO SAPIENS (human) | ||||||
| Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
Authors | daFonseca, P.C.A. / Morris, E.P. | ||||||
Citation | Journal: Nat Commun / Year: 2015Title: Cryo-EM reveals the conformation of a substrate analogue in the human 20S proteasome core. Authors: Paula C A da Fonseca / Edward P Morris / ![]() Abstract: The proteasome is a highly regulated protease complex fundamental for cell homeostasis and controlled cell cycle progression. It functions by removing a wide range of specifically tagged proteins, ...The proteasome is a highly regulated protease complex fundamental for cell homeostasis and controlled cell cycle progression. It functions by removing a wide range of specifically tagged proteins, including key cellular regulators. Here we present the structure of the human 20S proteasome core bound to a substrate analogue inhibitor molecule, determined by electron cryo-microscopy (cryo-EM) and single-particle analysis at a resolution of around 3.5 Å. Our map allows the building of protein coordinates as well as defining the location and conformation of the inhibitor at the different active sites. These results open new prospects to tackle the proteasome functional mechanisms. Moreover, they also further demonstrate that cryo-EM is emerging as a realistic approach for general structural studies of protein-ligand interactions. | ||||||
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Structure visualization
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| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 5a0q.cif.gz | 943.4 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb5a0q.ent.gz | 739.7 KB | Display | PDB format |
| PDBx/mmJSON format | 5a0q.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 5a0q_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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| Full document | 5a0q_full_validation.pdf.gz | 1.5 MB | Display | |
| Data in XML | 5a0q_validation.xml.gz | 135.7 KB | Display | |
| Data in CIF | 5a0q_validation.cif.gz | 210.9 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/5a0q ftp://data.pdbj.org/pub/pdb/validation_reports/a0/5a0q | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 2981MC M: map data used to model this data C: citing same article ( |
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| Similar structure data | |
| EM raw data | EMPIAR-10038 (Title: Cryo-EM reveals the conformation of a substrate analogue in the human 20S proteasome coreData size: 579.1 Data #1: raw micrographs of the human 20S proteasome core complex bound to the ligand AdaAhx3L3VS [micrographs - multiframe]) |
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Links
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Assembly
| Deposited unit | ![]()
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Components
-PROTEASOME SUBUNIT ALPHA TYPE- ... , 7 types, 14 molecules AOBPCQDRESFTGU
| #1: Protein | Mass: 27432.459 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell: ERYTHROCYTESReferences: UniProt: P60900, proteasome endopeptidase complex #2: Protein | Mass: 25927.535 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell: ERYTHROCYTESReferences: UniProt: P25787, proteasome endopeptidase complex #3: Protein | Mass: 29525.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell: ERYTHROCYTESReferences: UniProt: P25789, proteasome endopeptidase complex #4: Protein | Mass: 27929.891 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell: ERYTHROCYTESReferences: UniProt: O14818, proteasome endopeptidase complex #5: Protein | Mass: 26435.977 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell: ERYTHROCYTESReferences: UniProt: P28066, proteasome endopeptidase complex #6: Protein | Mass: 29595.627 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell: ERYTHROCYTESReferences: UniProt: P25786, proteasome endopeptidase complex #7: Protein | Mass: 28469.252 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell: ERYTHROCYTESReferences: UniProt: P25788, proteasome endopeptidase complex |
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-PROTEASOME SUBUNIT BETA TYPE- ... , 7 types, 14 molecules HVIWJXKYLZMaNb
| #8: Protein | Mass: 21921.836 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: SUBUNIT PARTIALLY BOUND TO THE INHIBITOR ADAMANTANE-ACETYL-(6-AMINOHEXANOYL)3-(LEUCINYL)3-VINYL-(METHYL)-SULFONE (ADAAHX3L3VS) Source: (natural) HOMO SAPIENS (human) / Cell: ERYTHROCYTESReferences: UniProt: P28072, proteasome endopeptidase complex #9: Protein | Mass: 25321.980 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: SUBUNIT PARTIALLY BOUND TO THE INHIBITOR ADAMANTANE-ACETYL-(6-AMINOHEXANOYL)3-(LEUCINYL)3-VINYL-(METHYL)-SULFONE (ADAAHX3L3VS) Source: (natural) HOMO SAPIENS (human) / Cell: ERYTHROCYTESReferences: UniProt: Q99436, proteasome endopeptidase complex #10: Protein | Mass: 22841.701 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell: ERYTHROCYTESReferences: UniProt: P49720, proteasome endopeptidase complex #11: Protein | Mass: 22864.277 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell: ERYTHROCYTESReferences: UniProt: P49721, proteasome endopeptidase complex #12: Protein | Mass: 22484.369 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: SUBUNIT BOUND TO THE INHIBITOR ADAMANTANE-ACETYL-(6-AMINOHEXANOYL)3-(LEUCINYL)3-VINYL-(METHYL)-SULFONE (ADAAHX3L3VS) Source: (natural) HOMO SAPIENS (human) / Cell: ERYTHROCYTESReferences: UniProt: P28074, proteasome endopeptidase complex #13: Protein | Mass: 23578.986 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell: ERYTHROCYTESReferences: UniProt: P20618, proteasome endopeptidase complex #14: Protein | Mass: 24414.740 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell: ERYTHROCYTESReferences: UniProt: P28070, proteasome endopeptidase complex |
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-Non-polymers , 1 types, 6 molecules 
| #15: Chemical | ChemComp-KNM / |
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-Details
| Has protein modification | Y |
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-Experimental details
-Experiment
| Experiment | Method: ELECTRON MICROSCOPY |
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| EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
| Component | Name: HUMAN 20S PROTEASOME CORE / Type: COMPLEX Details: THE POWER SPECTRA OF THE IMAGES SELECTED FOR ANALYSIS HAD ISOTROPIC THON RINGS DIRECTLY OBSERVED TO 4 ANGSTROMS OR BETTER |
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| Buffer solution | Name: 50 MM TRIS-HCL, 5 MM MGCL2 AND 1MM DITHIOTREITOL / pH: 7.5 / Details: 50 MM TRIS-HCL, 5 MM MGCL2 AND 1MM DITHIOTREITOL |
| Specimen | Conc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
| Specimen support | Details: CARBON |
| Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 95, TEMPERATURE- 120, INSTRUMENT- FEI VITROBOT MARK III, METHOD- BLOT 2. 5 SECONDS BEFORE PLUNGING, |
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Electron microscopy imaging
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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| Microscopy | Model: FEI TITAN KRIOS / Date: Feb 4, 2014 Details: EACH EXPOSURE WAS RECORDED AS 17 INDIVIDUAL FRAMES CAPTURED AT A RATE OF 0.056 SECONDS PER FRAME, WITH AN ELECTRON DOSE OF 2.8 ELECTRONS PER SQUARE ANGSTROM. DATA-SET RECORDED USING EPU SOFTWARE. |
| Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
| Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 75000 X / Calibrated magnification: 134461 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1700 nm / Cs: 2.7 mm |
| Specimen holder | Temperature: 85 K |
| Image recording | Electron dose: 4.8 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
| Image scans | Num. digital images: 960 |
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Processing
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| CTF correction | Details: FULL RECORDED IMAGE | ||||||||||||||||||
| Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||
| 3D reconstruction | Method: PROJECTION MATCHING / Resolution: 3.5 Å / Num. of particles: 76500 / Actual pixel size: 1.04 Å Details: DISORDERED REGIONS, NOT RECOVERED IN THE EM MAP, WHERE NOT MODELED. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2981. (DEPOSITION ID: 13310). Symmetry type: POINT | ||||||||||||||||||
| Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Details: METHOD--FLEXIBLE | ||||||||||||||||||
| Atomic model building | PDB-ID: 3UNE Accession code: 3UNE / Source name: PDB / Type: experimental model | ||||||||||||||||||
| Refinement | Highest resolution: 3.5 Å | ||||||||||||||||||
| Refinement step | Cycle: LAST / Highest resolution: 3.5 Å
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