+Open data
-Basic information
Entry | Database: PDB / ID: 5lf4 | ||||||||||||
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Title | Human 20S proteasome complex with Delanzomib at 2.0 Angstrom | ||||||||||||
Components |
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Keywords | HYDROLASE / Proteasome / Multicatalytic Proteinase / NTN-Hydrolase | ||||||||||||
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 / : / sarcomere / proteasome complex / Regulation of activated PAK-2p34 by proteasome mediated degradation / ciliary basal body / 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 / 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 / GLI3 is processed to GLI3R by the proteasome / Orc1 removal from chromatin / 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 / response to virus / Degradation of beta-catenin by the destruction complex / ABC-family proteins mediated transport / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / response to organic cyclic compound / CLEC7A (Dectin-1) signaling / Regulation of expression of SLITs and ROBOs / FCERI mediated NF-kB activation / nuclear matrix / Regulation of PTEN stability and activity / Interleukin-1 signaling / 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 / regulation of inflammatory response / Downstream TCR signaling / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / positive regulation of NF-kappaB transcription factor activity / peptidase activity / ER-Phagosome pathway / endopeptidase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / secretory granule lumen / response to oxidative stress / ficolin-1-rich granule lumen / postsynapse / nuclear body / ribosome / Ub-specific processing proteases / cadherin binding / intracellular membrane-bounded organelle / centrosome / ubiquitin protein ligase binding / synapse / Neutrophil degranulation / mitochondrion / proteolysis / RNA binding Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.99 Å | ||||||||||||
Authors | Schrader, J. / Henneberg, F. / Mata, R. / Tittmann, K. / Schneider, T.R. / Stark, H. / Bourenkov, G. / Chari, A. | ||||||||||||
Funding support | Germany, 3items
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Citation | Journal: Science / Year: 2016 Title: The inhibition mechanism of human 20S proteasomes enables next-generation inhibitor design. Authors: Schrader, J. / Henneberg, F. / Mata, R.A. / Tittmann, K. / Schneider, T.R. / Stark, H. / Bourenkov, G. / Chari, A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lf4.cif.gz | 2.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5lf4.ent.gz | 2 MB | Display | PDB format |
PDBx/mmJSON format | 5lf4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lf4_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 5lf4_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 5lf4_validation.xml.gz | 257.9 KB | Display | |
Data in CIF | 5lf4_validation.cif.gz | 369.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lf/5lf4 ftp://data.pdbj.org/pub/pdb/validation_reports/lf/5lf4 | HTTPS FTP |
-Related structure data
Related structure data | 5le5SC 5lexC 5leyC 5lezC 5lf0C 5lf1C 5lf3C 5lf6C 5lf7C 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 :
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-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) / Cell line: HELA 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) / Cell line: HELA References: UniProt: P25789, proteasome endopeptidase complex #3: Protein | Mass: 27986.941 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA 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) / Cell line: HELA References: UniProt: P28066, proteasome endopeptidase complex #5: Protein | Mass: 29720.752 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA 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) / Cell line: HELA References: UniProt: P25788, proteasome endopeptidase complex #7: Protein | Mass: 27739.760 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA References: UniProt: P60900, proteasome endopeptidase complex |
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-Proteasome subunit beta type- ... , 7 types, 14 molecules HVIWJXKYLZMaNb
#8: Protein | Mass: 25321.980 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA References: UniProt: Q99436, 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) / Cell line: HELA References: UniProt: P49720, proteasome endopeptidase complex #10: Protein | Mass: 22989.402 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA References: UniProt: P49721, proteasome endopeptidase complex #11: Protein | Mass: 22484.369 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA References: UniProt: P28074, proteasome endopeptidase complex #12: Protein | Mass: 23578.986 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA References: UniProt: P20618, proteasome endopeptidase complex #13: Protein | Mass: 24414.740 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA References: UniProt: P28070, proteasome endopeptidase complex #14: Protein | Mass: 21921.836 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA References: UniProt: P28072, proteasome endopeptidase complex |
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-Non-polymers , 6 types, 3775 molecules
#15: Chemical | ChemComp-CL / #16: Chemical | ChemComp-K / #17: Chemical | ChemComp-MG / #18: Chemical | ChemComp-1PE / #19: Chemical | ChemComp-6V7 / [( #20: Water | ChemComp-HOH / | |
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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: 2.54 Å3/Da / Density % sol: 51.65 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M Bis-Tris, 0.2 M Magnesium Chloride, 10 % PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 20, 2015 / Details: CRL Transfocator |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→170.38 Å / Num. obs: 462522 / % possible obs: 99.1 % / Redundancy: 9.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.128 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.99→2.06 Å / Mean I/σ(I) obs: 1 / CC1/2: 0.34 / % possible all: 90 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 5LE5 Resolution: 1.99→170.38 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 12.567 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.148 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.303 Å2
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Refinement step | Cycle: LAST / Resolution: 1.99→170.38 Å
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Refine LS restraints |
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