+
Open data
-
Basic information
Entry | Database: PDB / ID: 2v4h | ||||||
---|---|---|---|---|---|---|---|
Title | NEMO CC2-LZ domain - 1D5 DARPin complex | ||||||
![]() |
| ||||||
![]() | ![]() ![]() | ||||||
Function / homology | ![]() IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Regulation of NF-kappa B signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / SUMOylation of immune response proteins / TNFR1-induced NF-kappa-B signaling pathway / IKK complex recruitment mediated by RIP1 / RIP-mediated NFkB activation via ZBP1 / Regulation of TNFR1 signaling / MAP3K8 (TPL2)-dependent MAPK1/3 activation ...IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Regulation of NF-kappa B signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / SUMOylation of immune response proteins / TNFR1-induced NF-kappa-B signaling pathway / IKK complex recruitment mediated by RIP1 / RIP-mediated NFkB activation via ZBP1 / Regulation of TNFR1 signaling / MAP3K8 (TPL2)-dependent MAPK1/3 activation / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() SYNTHETIC CONSTRUCT (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Grubisha, O. / Duquerroy, S. / Cordier, F. / Haouz, A. / Delepierre, M. / Veron, M. / Agou, F. | ||||||
![]() | ![]() Title: Darpin-Assisted Crystallography of the Cc2-Lz Domain of Nemo Reveals a Coupling between Dimerization and Ubiquitin-Binding. Authors: Grubisha, O. / Kaminska, M. / Duquerroy, S. / Fontan, E. / Cordier, F. / Haouz, A. / Raynal, B. / Chiaravalli, J. / Delepierre, M. / Israel, A. / Veron, M. / Agou, F. #1: Journal: Protein Sci. / Year: 2007 Title: Inhibition of NF-kappaB Activation with Designed Ankyrin-Repeat Proteins Targeting the Ubiquitin-Binding/Oligomerization Domain of Nemo. Authors: Wyler, E. / Kaminska, M. / Coic, Y. / Baleux, F. / Veron, M. / Agou, F. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 98.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 78 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 2jabS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 5
NCS ensembles :
NCS oper:
|
-
Components
#1: Protein | Mass: 12895.637 Da / Num. of mol.: 2 / Fragment: CC2-LZ DOMAIN, RESIDUES 251-337 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Protein | Mass: 14924.489 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: SEE SECONDARY REFERENCE / Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Plasmid: PQE-30 / Production host: ![]() ![]() ![]() #3: Water | ChemComp-HOH / | ![]() Sequence details | CHAINS C AND D CORRESPOND TO GENBANK REFERENCE AY326425 OR GENPEPT REFERENCE AAQ93812. THE ...CHAINS C AND D CORRESPOND | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.92 Å3/Da / Density % sol: 68.58 % Description: THEORETICAL MODEL OF NEMO CC2 AND LZ HELICES USED FOR MOLECULAR REPLACEMENT |
---|---|
Crystal grow![]() | pH: 7.5 / Details: 5% MPD, 5% ETHANOL, 100 MM HEPES, PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 2, 2007 |
Radiation | Monochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.9→50 Å / Num. obs: 86037 / % possible obs: 84.8 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.8 / % possible all: 42.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 2JAB Resolution: 2.9→47.67 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.889 / SU B: 31.453 / SU ML: 0.283 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.7 / ESU R Free: 0.377 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SOME RESIDUES COMING FROM THE TAG WERE VISIBLE IN THE DENSITY. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 mean: 52.694 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→47.67 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|