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Yorodumi- PDB-5l62: Yeast 20S proteasome with human beta5c (1-138) and human beta6 (9... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5l62 | ||||||
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Title | Yeast 20S proteasome with human beta5c (1-138) and human beta6 (97-111; 118-133) in complex with epoxyketone inhibitor 16 | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex / Proteasome / Mutant / Inhibitor / Binding Analysis | ||||||
Function / homology | Function and homology information Regulation of ornithine decarboxylase (ODC) / proteasome core complex / Cross-presentation of soluble exogenous antigens (endosomes) / proteasome core complex assembly / Somitogenesis / nuclear outer membrane-endoplasmic reticulum membrane network / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A ...Regulation of ornithine decarboxylase (ODC) / proteasome core complex / Cross-presentation of soluble exogenous antigens (endosomes) / proteasome core complex assembly / Somitogenesis / nuclear outer membrane-endoplasmic reticulum membrane network / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway / Neddylation / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / proteasome storage granule / Antigen processing: Ubiquitination & Proteasome degradation / endopeptidase activator activity / proteasome assembly / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / Ub-specific processing proteases / threonine-type endopeptidase activity / Neutrophil degranulation / proteasome complex / Regulation of activated PAK-2p34 by proteasome mediated degradation / proteolysis involved in protein catabolic process / 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 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants are degraded by ERAD / Degradation of AXIN / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / Hedgehog ligand biogenesis / G2/M Checkpoints / Defective CFTR causes cystic fibrosis / Negative regulation of NOTCH4 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Autodegradation of the E3 ubiquitin ligase COP1 / Vif-mediated degradation of APOBEC3G / Regulation of RUNX3 expression and activity / 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 / MAPK6/MAPK4 signaling / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / 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 / 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 / The role of GTSE1 in G2/M progression after G2 checkpoint / UCH proteinases / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / peroxisome / Downstream TCR signaling / peptidase activity / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / ER-Phagosome pathway / secretory granule lumen / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / ficolin-1-rich granule lumen / response to oxidative stress / Ub-specific processing proteases / mRNA binding / centrosome / Neutrophil degranulation / endoplasmic reticulum membrane / mitochondrion / proteolysis / extracellular exosome / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Groll, M. / Huber, E.M. | ||||||
Funding support | Germany, 1items
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Citation | Journal: EMBO J. / Year: 2016 Title: A humanized yeast proteasome identifies unique binding modes of inhibitors for the immunosubunit beta 5i. Authors: Huber, E.M. / Heinemeyer, W. / de Bruin, G. / Overkleeft, H.S. / Groll, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5l62.cif.gz | 2.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5l62.ent.gz | 2 MB | Display | PDB format |
PDBx/mmJSON format | 5l62.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5l62_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 5l62_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 5l62_validation.xml.gz | 200.1 KB | Display | |
Data in CIF | 5l62_validation.cif.gz | 274.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l6/5l62 ftp://data.pdbj.org/pub/pdb/validation_reports/l6/5l62 | HTTPS FTP |
-Related structure data
Related structure data | 5l52C 5l54C 5l55C 5l5aC 5l5bC 5l5dC 5l5eC 5l5fC 5l5hC 5l5iC 5l5jC 5l5oC 5l5pC 5l5qC 5l5rC 5l5sC 5l5tC 5l5uC 5l5vC 5l5wC 5l5xC 5l5yC 5l5zC 5l60C 5l61C 5l63C 5l64C 5l65C 5l66C 5l67C 5l68C 5l69C 5l6aC 5l6bC 5l6cC 5lttC 5cz4S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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-Components
-Proteasome subunit alpha type- ... , 6 types, 12 molecules AOBPCQDRESGU
#1: Protein | Mass: 27191.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P23639, proteasome endopeptidase complex #2: Protein | Mass: 28748.230 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P23638, proteasome endopeptidase complex #3: Protein | Mass: 28478.111 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P40303, proteasome endopeptidase complex #4: Protein | Mass: 28649.086 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P32379, proteasome endopeptidase complex #5: Protein | Mass: 25634.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P40302, proteasome endopeptidase complex #7: Protein | Mass: 28033.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P21243, proteasome endopeptidase complex |
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-Protein , 1 types, 2 molecules FT
#6: Protein | Mass: 31575.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P21242, proteasome endopeptidase complex |
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-Proteasome subunit beta type- ... , 7 types, 14 molecules HVIWJXKYLZMaNb
#8: Protein | Mass: 25114.459 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P25043, proteasome endopeptidase complex #9: Protein | Mass: 22627.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P25451, proteasome endopeptidase complex #10: Protein | Mass: 22545.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P22141, proteasome endopeptidase complex #11: Protein | Mass: 23177.207 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: PSMB5, LMPX, MB1, X, PRE2, DOA3, PRG1, YPR103W, P8283.10 Production host: Saccharomyces cerevisiae S288c (yeast) References: UniProt: P28074, UniProt: P30656, proteasome endopeptidase complex #12: Protein | Mass: 24979.010 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast), (gene. exp.) Homo sapiens (human), (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: PRE7, PRS3, PTS1, YBL041W, YBL0407, PSMB1, PSC5 / Production host: Saccharomyces cerevisiae S288c (yeast) References: UniProt: P23724, UniProt: P20618, proteasome endopeptidase complex #13: Protein | Mass: 27200.893 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P30657, proteasome endopeptidase complex #14: Protein | Mass: 21517.186 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P38624, proteasome endopeptidase complex |
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-Non-polymers , 5 types, 311 molecules
#15: Chemical | ChemComp-MG / #16: Chemical | ChemComp-CL / #17: Chemical | ChemComp-MES / #18: Chemical | #19: Water | ChemComp-HOH / | |
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-Details
Has protein modification | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.67 Å3/Da / Density % sol: 66.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 20 mM MgAC2, 13% MPD, 0.1 M MES / PH range: 6.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2015 |
Radiation | Monochromator: LN2 COOLED FIXED-EXIT. SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. obs: 257546 / % possible obs: 97.7 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2.8→2.9 Å / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 2.8 / % possible all: 96.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CZ4 Resolution: 2.8→15 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.943 / SU B: 24.414 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R Free: 0.264 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.238 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→15 Å
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Refine LS restraints |
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