[English] 日本語
![](img/lk-miru.gif)
- PDB-4bur: Crystal structure of the reduced human Apoptosis inducing factor ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4bur | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the reduced human Apoptosis inducing factor complexed with NAD | ||||||
![]() | APOPTOSIS INDUCING FACTOR 1, MITOCHONDRIAL | ||||||
![]() | OXIDOREDUCTASE / APOPTOSIS / MITOCHONDRIA / NUCLEAR CHROMATINOLYSIS / DNA-BINDING / FLAVOPROTEIN | ||||||
Function / homology | ![]() Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors / regulation of apoptotic DNA fragmentation / mitochondrial respiratory chain complex assembly / NAD(P)H oxidase H2O2-forming activity / poly-ADP-D-ribose binding / protein import into mitochondrial intermembrane space / cellular response to aldosterone / positive regulation of necroptotic process / chromosome condensation / oxidoreductase activity, acting on NAD(P)H ...Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors / regulation of apoptotic DNA fragmentation / mitochondrial respiratory chain complex assembly / NAD(P)H oxidase H2O2-forming activity / poly-ADP-D-ribose binding / protein import into mitochondrial intermembrane space / cellular response to aldosterone / positive regulation of necroptotic process / chromosome condensation / oxidoreductase activity, acting on NAD(P)H / response to L-glutamate / NADH dehydrogenase activity / mitochondrial respiratory chain complex I assembly / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to nitric oxide / FAD binding / cellular response to estradiol stimulus / response to ischemia / mitochondrial intermembrane space / neuron differentiation / response to toxic substance / cellular response to hydrogen peroxide / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of neuron apoptotic process / cellular response to hypoxia / neuron apoptotic process / mitochondrial inner membrane / protein dimerization activity / positive regulation of apoptotic process / apoptotic process / perinuclear region of cytoplasm / mitochondrion / DNA binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Martinez-Julvez, M. / Herguedas, B. / Hermoso, J.A. / Ferreira, P. / Villanueva, R. / Medina, M. | ||||||
![]() | ![]() Title: Structural Insights Into the Coenzyme Mediated Monomer-Dimer Transition of the Pro-Apoptotic Apoptosis Inducing Factor. Authors: Ferreira, P. / Villanueva, R. / Martinez-Julvez, M. / Herguedas, B. / Marcuello, C. / Fernandez-Silva, P. / Cabon, L. / Hermoso, J.A. / Lostao, A. / Susin, S.A. / Medina, M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 364.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 297.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 4bv6C ![]() 1m6iS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3 | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
4 | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
NCS oper:
|
-
Components
#1: Protein | Mass: 55772.293 Da / Num. of mol.: 4 / Fragment: RESIDUES 103-613 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-FAD / #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.47 Å3/Da / Density % sol: 64.63 % / Description: NONE |
---|---|
Crystal grow | Details: 16-20% PEG 4K, 0.2 M LI2SO4 AND 0.1 M TRIS-HCL PH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Date: Nov 23, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97626 Å / Relative weight: 1 |
Reflection | Resolution: 2.87→343.36 Å / Num. obs: 66707 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.88→3.04 Å / Redundancy: 7 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.4 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1M6I Resolution: 2.88→40 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.919 / SU B: 13.049 / SU ML: 0.244 / Cross valid method: THROUGHOUT / ESU R: 0.966 / ESU R Free: 0.328 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY. RESIDUES 517-550 IN CHAIN A, 517-552 IN CHAIN B, 518-557 IN CHAIN C AND 510-558 IN CHAIN D ARE DISORDERED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 56.685 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.88→40 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|