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Open data
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Basic information
Entry | Database: PDB / ID: 6hv3 | ||||||
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Title | Yeast 20S proteasome with human beta2i (1-53) | ||||||
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![]() | HYDROLASE / Proteasome / Mutant | ||||||
Function / homology | ![]() spermatoproteasome complex / proteasome core complex / Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / proteasome core complex assembly / 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 ...spermatoproteasome complex / proteasome core complex / Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / proteasome core complex assembly / 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 / proteasome storage granule / humoral immune response / 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 / T cell proliferation / Neutrophil degranulation / proteasome complex / proteasomal protein catabolic process / 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 / SCF-beta-TrCP mediated degradation of Emi1 / AUF1 (hnRNP D0) binds and destabilizes mRNA / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / TNFR2 non-canonical NF-kB pathway / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Degradation of DVL / 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 / Degradation of AXIN / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Defective CFTR causes cystic fibrosis / Hedgehog ligand biogenesis / 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 / 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 / ABC-family proteins mediated transport / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / cell morphogenesis / 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 / UCH proteinases / The role of GTSE1 in G2/M progression after G2 checkpoint / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / ER-Phagosome pathway / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / Ub-specific processing proteases / mRNA binding / endoplasmic reticulum membrane / mitochondrion / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Huber, E.M. / Groll, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-Based Design of Inhibitors Selective for Human Proteasome beta 2c or beta 2i Subunits. Authors: Xin, B.T. / Huber, E.M. / de Bruin, G. / Heinemeyer, W. / Maurits, E. / Espinal, C. / Du, Y. / Janssens, M. / Weyburne, E.S. / Kisselev, A.F. / Florea, B.I. / Driessen, C. / van der Marel, G. ...Authors: Xin, B.T. / Huber, E.M. / de Bruin, G. / Heinemeyer, W. / Maurits, E. / Espinal, C. / Du, Y. / Janssens, M. / Weyburne, E.S. / Kisselev, A.F. / Florea, B.I. / Driessen, C. / van der Marel, G.A. / Groll, M. / Overkleeft, H.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 2.4 MB | Display | ![]() |
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PDB format | ![]() | 2 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 630.3 KB | Display | ![]() |
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Full document | ![]() | 676.7 KB | Display | |
Data in XML | ![]() | 200.5 KB | Display | |
Data in CIF | ![]() | 278.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6htbC ![]() 6htcC ![]() 6htdC ![]() 6htpC ![]() 6htrC ![]() 6hubC ![]() 6hucC ![]() 6huqC ![]() 6huuC ![]() 6huvC ![]() 6hv4C ![]() 6hv5C ![]() 6hv7C ![]() 6hvaC ![]() 6hvrC ![]() 6hvsC ![]() 6hvtC ![]() 6hvuC ![]() 6hvvC ![]() 6hvwC ![]() 6hvxC ![]() 6hvyC ![]() 6hw0C ![]() 6hw3C ![]() 6hw4C ![]() 6hw5C ![]() 6hw6C ![]() 6hw7C ![]() 6hw8C ![]() 6hw9C ![]() 6hwaC ![]() 6hwbC ![]() 6hwcC ![]() 6hwdC ![]() 6hweC ![]() 6hwfC ![]() 5cz4S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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) ![]() ![]() Strain: ATCC 204508 / S288c 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) ![]() ![]() Strain: ATCC 204508 / S288c 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) ![]() ![]() Strain: ATCC 204508 / S288c 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) ![]() ![]() Strain: ATCC 204508 / S288c 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) ![]() ![]() Strain: ATCC 204508 / S288c 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) ![]() ![]() Strain: ATCC 204508 / S288c 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) ![]() ![]() Strain: ATCC 204508 / S288c References: UniProt: P21242, proteasome endopeptidase complex |
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-Proteasome subunit beta type- ... , 7 types, 14 molecules HVIWJXKYLZMaNb
#8: Protein | Mass: 24443.674 Da / Num. of mol.: 2 Mutation: Chimera: 1-53 Homo sapiens,Chimera: 1-53 Homo sapiens Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: PSMB10, LMP10, MECL1, PUP1, YOR157C / Strain: ATCC 204508 / S288c / Production host: ![]() ![]() References: UniProt: P40306, UniProt: P25043, proteasome endopeptidase complex #9: Protein | Mass: 22627.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c 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) ![]() ![]() Strain: ATCC 204508 / S288c References: UniProt: P22141, proteasome endopeptidase complex #11: Protein | Mass: 23325.248 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c References: UniProt: P30656, proteasome endopeptidase complex #12: Protein | Mass: 24883.928 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c References: UniProt: P23724, proteasome endopeptidase complex #13: Protein | Mass: 27200.893 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c 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) ![]() ![]() Strain: ATCC 204508 / S288c References: UniProt: P38624, proteasome endopeptidase complex |
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-Non-polymers , 4 types, 618 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#15: Chemical | ChemComp-MG / #16: Chemical | #17: Chemical | #18: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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 / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 20, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 283072 / % possible obs: 96.9 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.7→2.8 Å / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 2.5 / % possible all: 98.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5CZ4 Resolution: 2.7→15 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 25.132 / SU ML: 0.215 / Cross valid method: THROUGHOUT / ESU R Free: 0.251 / 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: 62.324 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→15 Å
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Refine LS restraints |
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