+
Open data
-
Basic information
| Entry | Database: PDB / ID: 6e5b | ||||||
|---|---|---|---|---|---|---|---|
| Title | Human Immunoproteasome 20S particle in complex with compound 1 | ||||||
Components |
| ||||||
Keywords | HYDROLASE / MULTICATALYTIC PROTEINASE / 20S PROTEASOME / PROTEASE / PROTEROS / PROTEROS BIOSTRUCTURES GMBH | ||||||
| Function / homology | Function and homology informationspermatoproteasome complex / purine ribonucleoside triphosphate binding / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / proteasome core complex / Somitogenesis / antigen processing and presentation / fat cell differentiation / myofibril ...spermatoproteasome complex / purine ribonucleoside triphosphate binding / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / proteasome core complex / Somitogenesis / antigen processing and presentation / fat cell differentiation / myofibril / humoral immune response / immune system process / NF-kappaB binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / T cell proliferation / 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 / cell morphogenesis / Regulation of RAS by GAPs / Regulation of RUNX2 expression and activity / Interferon alpha/beta signaling / 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 / Neddylation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / ER-Phagosome pathway / regulation of inflammatory response / 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 / cilium / ciliary basal body / ribosome / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / centrosome / Neutrophil degranulation / mitochondrion / RNA binding / extracellular exosome Similarity search - Function | ||||||
| Biological species | Homo sapiens (human) | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.77 Å | ||||||
Authors | Steinbacher, S. / Augustin, M. / Blaesse, M. / Harris, S.F. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2019Title: Design and Evaluation of Highly Selective Human Immunoproteasome Inhibitors Reveal a Compensatory Process That Preserves Immune Cell Viability. Authors: Ladi, E. / Everett, C. / Stivala, C.E. / Daniels, B.E. / Durk, M.R. / Harris, S.F. / Huestis, M.P. / Purkey, H.E. / Staben, S.T. / Augustin, M. / Blaesse, M. / Steinbacher, S. / Eidenschenk, ...Authors: Ladi, E. / Everett, C. / Stivala, C.E. / Daniels, B.E. / Durk, M.R. / Harris, S.F. / Huestis, M.P. / Purkey, H.E. / Staben, S.T. / Augustin, M. / Blaesse, M. / Steinbacher, S. / Eidenschenk, C. / Pappu, R. / Siu, M. | ||||||
| History |
|
-
Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
|---|
-
Downloads & links
-
Download
| PDBx/mmCIF format | 6e5b.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
|---|---|---|---|---|
| PDB format | pdb6e5b.ent.gz | 980.8 KB | Display | PDB format |
| PDBx/mmJSON format | 6e5b.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 6e5b_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
|---|---|---|---|---|
| Full document | 6e5b_full_validation.pdf.gz | 1.5 MB | Display | |
| Data in XML | 6e5b_validation.xml.gz | 218.9 KB | Display | |
| Data in CIF | 6e5b_validation.cif.gz | 284.9 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e5/6e5b ftp://data.pdbj.org/pub/pdb/validation_reports/e5/6e5b | HTTPS FTP |
-Related structure data
| Similar structure data |
|---|
-
Links
-
Assembly
| Deposited unit | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
|
-
Components
-Proteasome subunit alpha type- ... , 7 types, 14 molecules AOBPCQDRESFTGU
| #1: Protein | Mass: 25927.535 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)References: UniProt: P25787, proteasome endopeptidase complex #2: Protein | Mass: 29525.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)References: UniProt: P25789, proteasome endopeptidase complex #3: Protein | Mass: 27929.891 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)References: UniProt: O14818, proteasome endopeptidase complex #4: Protein | Mass: 26435.977 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)References: UniProt: P28066, proteasome endopeptidase complex #5: Protein | Mass: 29595.627 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)References: UniProt: P25786, proteasome endopeptidase complex #6: Protein | Mass: 28469.252 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)References: UniProt: P25788, proteasome endopeptidase complex #7: Protein | Mass: 27432.459 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)References: UniProt: P60900, proteasome endopeptidase complex |
|---|
-Proteasome subunit beta type- ... , 7 types, 14 molecules HVIWJXKYLZMaNb
| #8: Protein | Mass: 28970.287 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)References: UniProt: P40306, proteasome endopeptidase complex #9: Protein | Mass: 22972.896 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)References: UniProt: P49720, proteasome endopeptidase complex #10: Protein | Mass: 22864.277 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)References: UniProt: P49721, proteasome endopeptidase complex #11: Protein | Mass: 30389.285 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)References: UniProt: P28062, proteasome endopeptidase complex #12: Protein | Mass: 26522.396 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)References: UniProt: P20618, proteasome endopeptidase complex #13: Protein | Mass: 29231.178 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)References: UniProt: P28070, proteasome endopeptidase complex #14: Protein | Mass: 23286.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)References: UniProt: P28065, proteasome endopeptidase complex |
|---|
-Non-polymers , 4 types, 82 molecules 






| #15: Chemical | | #16: Chemical | ChemComp-NA / #17: Chemical | ChemComp-HUJ / [( #18: Water | ChemComp-HOH / | |
|---|
-Details
| Has protein modification | Y |
|---|
-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
|---|
-
Sample preparation
| Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.61 % |
|---|---|
| Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 39% (v/v) 2-methyl-2,4-pentanediol (MPD), 0.2M sodium thiocyanate |
-Data collection
| Diffraction | Mean temperature: 100 K |
|---|---|
| Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99983 Å |
| Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2017 |
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.99983 Å / Relative weight: 1 |
| Reflection | Resolution: 2.77→154.58 Å / Num. obs: 179824 / % possible obs: 97 % / Redundancy: 2.8 % / Biso Wilson estimate: 56.094 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.102 / Χ2: 1.122 / Net I/σ(I): 10.64 |
| Reflection shell | Highest resolution: 2.77 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 37.45 / Num. unique obs: 653 / CC1/2: 0.996 / Rrim(I) all: 0.034 / % possible all: 96.5 |
-
Processing
| Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.77→154.58 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.88 / SU B: 28.502 / SU ML: 0.506 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.423 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso max: 209.66 Å2 / Biso mean: 71.807 Å2 / Biso min: 26.66 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refinement step | Cycle: final / Resolution: 2.77→154.58 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| LS refinement shell | Resolution: 2.77→2.842 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|
Movie
Controller
About Yorodumi




Homo sapiens (human)
X-RAY DIFFRACTION
Citation



















PDBj








