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- PDB-4hcn: Crystal structure of Burkholderia pseudomallei effector protein C... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4hcn | ||||||
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Title | Crystal structure of Burkholderia pseudomallei effector protein CHBP in complex with ubiquitin | ||||||
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![]() | PROTEIN BINDING / UBIQUITIN/NEDD8 DEAMIDASE / UBIQUITIN / NEDD8 | ||||||
Function / homology | ![]() symbiont-mediated perturbation of host cell cycle progression / Josephin domain DUBs / RAS processing / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / protein-glutamine glutaminase activity / UCH proteinases / protein-glutamine glutaminase / Pexophagy / Interleukin-1 signaling ...symbiont-mediated perturbation of host cell cycle progression / Josephin domain DUBs / RAS processing / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / protein-glutamine glutaminase activity / UCH proteinases / protein-glutamine glutaminase / Pexophagy / Interleukin-1 signaling / Aggrephagy / Peroxisomal protein import / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Metalloprotease DUBs / Endosomal Sorting Complex Required For Transport (ESCRT) / E3 ubiquitin ligases ubiquitinate target proteins / Translesion Synthesis by POLH / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Termination of translesion DNA synthesis / Negative regulators of DDX58/IFIH1 signaling / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / CDK-mediated phosphorylation and removal of Cdc6 / Neddylation / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Formation of TC-NER Pre-Incision Complex / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Gap-filling DNA repair synthesis and ligation in TC-NER / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Antigen processing: Ubiquitination & Proteasome degradation / L13a-mediated translational silencing of Ceruloplasmin expression / Dual incision in TC-NER / Ub-specific processing proteases / modification-dependent protein catabolic process / protein tag activity / toxin activity / protein ubiquitination / ubiquitin protein ligase binding / host cell nucleus / extracellular region / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Yao, Q. / Cui, J. / Zhu, Y. / Shao, F. | ||||||
![]() | ![]() Title: Structural mechanism of ubiquitin and NEDD8 deamidation catalyzed by bacterial effectors that induce macrophage-specific apoptosis. Authors: Yao, Q. / Cui, J. / Wang, J. / Li, T. / Wan, X. / Luo, T. / Gong, Y.N. / Xu, Y. / Huang, N. / Shao, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 78.9 KB | Display | ![]() |
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PDB format | ![]() | 57.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 469 KB | Display | ![]() |
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Full document | ![]() | 471.1 KB | Display | |
Data in XML | ![]() | 14.2 KB | Display | |
Data in CIF | ![]() | 19.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4hcpC ![]() 1ubqS ![]() 3eirS C: citing same article ( S: Starting model for refinement |
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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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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 28557.408 Da / Num. of mol.: 1 / Fragment: unp RESIDUES 78-328 / Mutation: A156C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 11097.469 Da / Num. of mol.: 1 / Fragment: unp RESIDUES 1-76 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: SCD2, UBI4, YLL039C / Plasmid: PET28A / Production host: ![]() ![]() |
-Non-polymers , 4 types, 75 molecules ![](data/chem/img/PEG.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-PEG / | ||||
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#4: Chemical | #5: Chemical | ChemComp-PO4 / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.67 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 7.2 Details: 12.5% PEG3350, 125MM MAGNESIUM FORMATE, pH 7.2, EVAPORATION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE |
Radiation | Monochromator: SINGLE WAVELENGTH / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. obs: 10218 / % possible obs: 95.3 % / Observed criterion σ(I): 4 / Redundancy: 5.7 % |
Reflection shell | Resolution: 2.6→2.64 Å / % possible all: 93.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY: 1UBQ AND PDB ENTRY: 3EIR Resolution: 2.6→19.35 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.856 / Cross valid method: THROUGHOUT / ESU R Free: 0.381 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.66 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→19.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.67 Å / Total num. of bins used: 20
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