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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 | ||||||
Components |
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Keywords | HYDROLASE / PROTEASOME / 20S / ADAAHX3L3VS / LIGAND / INHIBITOR / DRUG DESIGN | ||||||
Function / homology | Function and homology information purine ribonucleoside triphosphate binding / regulation of endopeptidase activity / Regulation of ornithine decarboxylase (ODC) / proteasome core complex / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / immune system process / myofibril / NF-kappaB binding / proteasome endopeptidase complex ...purine ribonucleoside triphosphate binding / regulation of endopeptidase activity / Regulation of ornithine decarboxylase (ODC) / proteasome core complex / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / immune system process / myofibril / NF-kappaB binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / negative regulation of inflammatory response to antigenic stimulus / response to organonitrogen compound / proteolysis involved in protein catabolic process / proteasome complex / sarcomere / Regulation of activated PAK-2p34 by proteasome mediated degradation / ciliary basal body / 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 / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Degradation of DVL / proteasomal protein catabolic process / 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 AXIN / Defective CFTR causes cystic fibrosis / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / lipopolysaccharide binding / Hedgehog ligand biogenesis / Negative regulation of NOTCH4 signaling / G2/M Checkpoints / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Autodegradation of the E3 ubiquitin ligase COP1 / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / Regulation of RUNX3 expression and activity / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / response to virus / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / ABC-family proteins mediated transport / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / response to organic cyclic compound / CDK-mediated phosphorylation and removal of Cdc6 / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / nuclear matrix / Regulation of expression of SLITs and ROBOs / FCERI mediated NF-kB activation / Regulation of PTEN stability and activity / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RAS by GAPs / Separation of Sister Chromatids / Regulation of RUNX2 expression and activity / UCH proteinases / The role of GTSE1 in G2/M progression after G2 checkpoint / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / Neddylation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / positive regulation of NF-kappaB transcription factor activity / peptidase activity / ER-Phagosome pathway / regulation of inflammatory response / postsynapse / proteasome-mediated ubiquitin-dependent protein catabolic process / secretory granule lumen / endopeptidase activity / response to oxidative stress / ficolin-1-rich granule lumen / nuclear body / Ub-specific processing proteases / ribosome / cadherin binding / intracellular membrane-bounded organelle / centrosome / synapse / ubiquitin protein ligase binding / Neutrophil degranulation / mitochondrion / proteolysis 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: 2015 Title: 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. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5a0q.cif.gz | 936.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a0q.ent.gz | 759 KB | Display | PDB format |
PDBx/mmJSON format | 5a0q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/5a0q ftp://data.pdbj.org/pub/pdb/validation_reports/a0/5a0q | HTTPS FTP |
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-Related structure data
Related structure data | 2981MC M: map data used to model this data C: citing same article (ref.) |
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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 core Data size: 579.1 Data #1: raw micrographs of the human 20S proteasome core complex bound to the ligand AdaAhx3L3VS [micrographs - multiframe]) |
-Links
-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: ERYTHROCYTES References: 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: ERYTHROCYTES References: 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: ERYTHROCYTES References: 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: ERYTHROCYTES References: 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: ERYTHROCYTES References: 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: ERYTHROCYTES References: 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: ERYTHROCYTES References: 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: ERYTHROCYTES References: 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: ERYTHROCYTES References: 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: ERYTHROCYTES References: 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: ERYTHROCYTES References: 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: ERYTHROCYTES References: 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: ERYTHROCYTES References: 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: ERYTHROCYTES References: UniProt: P28070, proteasome endopeptidase complex |
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-Non-polymers , 1 types, 6 molecules
#15: Chemical | ChemComp-KNM / |
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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 |
-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, |
-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 FIELDBright-field microscopy / 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 |
-Processing
EM software |
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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 | ||||||||||||||||||
Refinement | Highest resolution: 3.5 Å | ||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 3.5 Å
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