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- PDB-7vy4: Snapshots of Human PSMD10(Gankyrin) unfolding by urea: 2 hours in... -
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Basic information
Entry | Database: PDB / ID: 7vy4 | ||||||
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Title | Snapshots of Human PSMD10(Gankyrin) unfolding by urea: 2 hours incubation | ||||||
![]() | 26S proteasome non-ATPase regulatory subunit 10 | ||||||
![]() | ONCOPROTEIN / Proteasomal Chaperone / Urea denaturation | ||||||
Function / homology | ![]() cytoplasmic sequestering of NF-kappaB / proteasome regulatory particle assembly / Regulation of ornithine decarboxylase (ODC) / intermediate filament cytoskeleton / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / protein localization to chromosome, telomeric region / negative regulation of MAPK cascade / negative regulation of NF-kappaB transcription factor activity / negative regulation of release of cytochrome c from mitochondria ...cytoplasmic sequestering of NF-kappaB / proteasome regulatory particle assembly / Regulation of ornithine decarboxylase (ODC) / intermediate filament cytoskeleton / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / protein localization to chromosome, telomeric region / negative regulation of MAPK cascade / negative regulation of NF-kappaB transcription factor activity / negative regulation of release of cytochrome c from mitochondria / positive regulation of telomere capping / negative regulation of DNA damage response, signal transduction by p53 class mediator / transcription factor binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / NAD+-protein poly-ADP-ribosyltransferase activity / cytoskeletal protein binding / proteasome complex / Regulation of activated PAK-2p34 by proteasome mediated degradation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / positive regulation of protein ubiquitination / 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 / protein localization to plasma membrane / 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 / 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 / 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 / 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 / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of canonical Wnt signaling pathway / Downstream TCR signaling / protein-macromolecule adaptor activity / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / ER-Phagosome pathway / positive regulation of cell growth / RNA polymerase II-specific DNA-binding transcription factor binding / transmembrane transporter binding / cytoskeleton / Ub-specific processing proteases / neuron projection / apoptotic process / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mukund Sudharsan, M.G. / Dalvi, S. / Venkatraman, P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Snapshots of urea-induced early structural changes and unfolding of an ankyrin repeat protein at atomic resolution. Authors: Medur Gurushankar, M.S. / Dalvi, S. / Venkatraman, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 60 KB | Display | ![]() |
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PDB format | ![]() | 41.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 11.3 KB | Display | |
Data in CIF | ![]() | 14.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7vxvC ![]() 7vxwC ![]() 7vy7C ![]() 1uohS C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 24459.855 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Gankyrin pBluescript II SK (1) construct (kind gift from Dr. Jun Fujita, Kyoto University) Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-URE / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density meas: 47 Mg/m3 / Density % sol: 53.13 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 60% Tacsimate pH7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 10, 2021 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.22→52.221 Å / Num. obs: 13221 / % possible obs: 98.2 % / Redundancy: 8.6 % / Rpim(I) all: 0.099 / Rrim(I) all: 0.295 / Rsym value: 0.277 / Net I/av σ(I): 2.7 / Net I/σ(I): 7.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1UOH Resolution: 2.22→52.22 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.874 / SU B: 12.73 / SU ML: 0.286 / SU R Cruickshank DPI: 0.3214 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.321 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 101.04 Å2 / Biso mean: 38.776 Å2 / Biso min: 17.51 Å2
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Refinement step | Cycle: final / Resolution: 2.22→52.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.224→2.281 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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