+Open data
-Basic information
Entry | Database: PDB / ID: 4ljq | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the catalytic core of E3 ligase HOIP | ||||||
Components | E3 ubiquitin-protein ligase RNF31 | ||||||
Keywords | LIGASE / RNF31 / ZIBRA / RING domain / Zinc finger / IBR domain / RBR ligase / E3 ligase / Ubiquitin / HOIL-1 / Sharpin | ||||||
Function / homology | Function and homology information protein linear polyubiquitination / LUBAC complex / linear polyubiquitin binding / CD40 signaling pathway / RBR-type E3 ubiquitin transferase / positive regulation of xenophagy / CD40 receptor complex / negative regulation of necroptotic process / TNFR1-induced proapoptotic signaling / positive regulation of protein targeting to mitochondrion ...protein linear polyubiquitination / LUBAC complex / linear polyubiquitin binding / CD40 signaling pathway / RBR-type E3 ubiquitin transferase / positive regulation of xenophagy / CD40 receptor complex / negative regulation of necroptotic process / TNFR1-induced proapoptotic signaling / positive regulation of protein targeting to mitochondrion / K48-linked polyubiquitin modification-dependent protein binding / K63-linked polyubiquitin modification-dependent protein binding / TNFR1-induced NF-kappa-B signaling pathway / ubiquitin binding / Regulation of TNFR1 signaling / cytoplasmic side of plasma membrane / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / positive regulation of canonical NF-kappaB signal transduction / defense response to bacterium / ubiquitin protein ligase binding / zinc ion binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 Å | ||||||
Authors | Stieglitz, B. / Rana, R.R. / Koliopoulos, M.G. / Morris-Davies, A.C. / Christodoulou, E. / Howell, S. / Brown, N.R. / Rittinger, K. | ||||||
Citation | Journal: Nature / Year: 2013 Title: Structural basis for ligase-specific conjugation of linear ubiquitin chains by HOIP. Authors: Stieglitz, B. / Rana, R.R. / Koliopoulos, M.G. / Morris-Davies, A.C. / Schaeffer, V. / Christodoulou, E. / Howell, S. / Brown, N.R. / Dikic, I. / Rittinger, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4ljq.cif.gz | 160.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4ljq.ent.gz | 131.4 KB | Display | PDB format |
PDBx/mmJSON format | 4ljq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ljq_validation.pdf.gz | 459.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4ljq_full_validation.pdf.gz | 476.1 KB | Display | |
Data in XML | 4ljq_validation.xml.gz | 28.9 KB | Display | |
Data in CIF | 4ljq_validation.cif.gz | 39.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lj/4ljq ftp://data.pdbj.org/pub/pdb/validation_reports/lj/4ljq | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
4 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
5 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
6 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
|
-Components
#1: Protein | Mass: 25240.346 Da / Num. of mol.: 4 / Fragment: Catalytic domain (unp residues 853-1072) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RNF31, ZIBRA / Plasmid: pET49B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q96EP0, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.34 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 20% PEG 12000, 800 mM LiCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 77 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9798 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 18, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.45→29.6 Å / Num. all: 32557 / Num. obs: 30946 / % possible obs: 91.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.33 % / Biso Wilson estimate: 49.188 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 10.07 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Phasing
Phasing | Method: SAD |
---|---|
Phasing MAD | D res high: 2.45 Å / D res low: 29.61 Å / FOM : 0.389 / FOM acentric: 0.396 / FOM centric: 0 / Reflection: 30648 / Reflection acentric: 28521 / Reflection centric: 0 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.45→29.6 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.91 / Occupancy max: 1 / Occupancy min: 1 / SU B: 8.816 / SU ML: 0.199 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.555 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 178.4 Å2 / Biso mean: 49.3476 Å2 / Biso min: 6.14 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→29.6 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.445→2.508 Å / Total num. of bins used: 20
|