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Open data
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Basic information
Entry | Database: PDB / ID: 1gv4 | ||||||
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Title | Murine apoptosis-inducing factor (AIF) | ||||||
![]() | PROGRAMED CELL DEATH PROTEIN 8 | ||||||
![]() | OXIDOREDUCTASE / FLAVOPROTEIN / FAD / NUCLEAR PROTEIN / APOPTOSI | ||||||
Function / homology | ![]() electron-transferring-flavoprotein dehydrogenase activity / regulation of apoptotic DNA fragmentation / Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors / mitochondrial respiratory chain complex assembly / protein import into mitochondrial intermembrane space / poly-ADP-D-ribose binding / NAD(P)H oxidase H2O2-forming activity / positive regulation of necroptotic process / NADH dehydrogenase activity / apoptotic mitochondrial changes ...electron-transferring-flavoprotein dehydrogenase activity / regulation of apoptotic DNA fragmentation / Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors / mitochondrial respiratory chain complex assembly / protein import into mitochondrial intermembrane space / poly-ADP-D-ribose binding / NAD(P)H oxidase H2O2-forming activity / positive regulation of necroptotic process / NADH dehydrogenase activity / apoptotic mitochondrial changes / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / FAD binding / mitochondrial intermembrane space / response to oxidative stress / neuron apoptotic process / mitochondrial outer membrane / mitochondrial inner membrane / protein dimerization activity / positive regulation of apoptotic process / perinuclear region of cytoplasm / mitochondrion / DNA binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mate, M.J. / Alzari, P.M. | ||||||
![]() | ![]() Title: The Crystal Structure of the Mouse Apoptosis-Inducing Factor Aif Authors: Mate, M.J. / Ortiz-Lombardia, M. / Alzari, P.M. / Boitel, B. / Haouz, A. / Tello, D. / Susin, S.A. / Penninger, J. / Kroemer, G. / Alzari, P.M. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 209.9 KB | Display | ![]() |
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PDB format | ![]() | 164.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 941.9 KB | Display | ![]() |
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Full document | ![]() | 974.3 KB | Display | |
Data in XML | ![]() | 43.5 KB | Display | |
Data in CIF | ![]() | 61.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1d7yS 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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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.99998, 0.00603, -0.00151), Vector: |
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Components
#1: Protein | Mass: 57571.426 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 43.5 % / Description: PHASE COMBINATION WITH MAD PHASES | ||||||||||||||||||||||||||||
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Crystal grow | pH: 7.75 Details: 18% PEG MONOMETHYL ETHER 5000, 100 MM MGCL2, 50 MM HEPES PH, pH 7.75 | ||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Detector: CCD / Date: Jun 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 62596 / % possible obs: 96.5 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 4.4 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 2.5 / % possible all: 92.3 |
Reflection | *PLUS Lowest resolution: 20 Å / % possible obs: 96.5 % / Rmerge(I) obs: 0.11 |
Reflection shell | *PLUS % possible obs: 92.6 % / Rmerge(I) obs: 0.273 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1D7Y Resolution: 2→15 Å / SU B: 5.03 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R Free: 0.183 Details: DISORDERED RESIDUES WERE MODELED USING ROTAMERS DATA BASE AND HAVE OCC=0.00 IN THE PDB
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Refinement step | Cycle: LAST / Resolution: 2→15 Å
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Refinement | *PLUS Num. reflection obs: 71317 / % reflection Rfree: 5 % / Rfactor obs: 0.216 / Rfactor Rfree: 0.257 / Rfactor Rwork: 0.216 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.339 / Rfactor Rwork: 0.24 / Rfactor obs: 0.24 |