- PDB-2jby: A viral protein unexpectedly mimics the structure and function of... -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 2jby
Title
A viral protein unexpectedly mimics the structure and function of pro- survival Bcl-2
Components
BCL-2 HOMOLOGOUS ANTAGONIST/KILLER 2
M11L PROTEIN
Keywords
APOPTOSIS
Function / homology
Function and homology information
Activation and oligomerization of BAK protein / response to mycotoxin / B cell negative selection / BAK complex / apoptotic process involved in blood vessel morphogenesis / response to fungus / negative regulation of endoplasmic reticulum calcium ion concentration / limb morphogenesis / Release of apoptotic factors from the mitochondria / endocrine pancreas development ...Activation and oligomerization of BAK protein / response to mycotoxin / B cell negative selection / BAK complex / apoptotic process involved in blood vessel morphogenesis / response to fungus / negative regulation of endoplasmic reticulum calcium ion concentration / limb morphogenesis / Release of apoptotic factors from the mitochondria / endocrine pancreas development / post-embryonic camera-type eye morphogenesis / establishment or maintenance of transmembrane electrochemical gradient / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / B cell apoptotic process / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / activation of cysteine-type endopeptidase activity / positive regulation of endoplasmic reticulum unfolded protein response / endoplasmic reticulum calcium ion homeostasis / regulation of mitochondrial membrane permeability / calcium ion transport into cytosol / BH domain binding / response to UV-C / fibroblast apoptotic process / mitochondrial fusion / Bcl-2 family protein complex / myeloid cell homeostasis / positive regulation of calcium ion transport into cytosol / porin activity / thymocyte apoptotic process / pore complex / negative regulation of release of cytochrome c from mitochondria / negative regulation of peptidyl-serine phosphorylation / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / vagina development / B cell homeostasis / positive regulation of proteolysis / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / blood vessel remodeling / cellular response to unfolded protein / Pyroptosis / animal organ regeneration / extrinsic apoptotic signaling pathway in absence of ligand / heat shock protein binding / intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / epithelial cell proliferation / establishment of localization in cell / response to gamma radiation / apoptotic signaling pathway / positive regulation of protein-containing complex assembly / response to hydrogen peroxide / response to organic cyclic compound / cellular response to mechanical stimulus / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to UV / protein-folding chaperone binding / regulation of apoptotic process / response to ethanol / transmembrane transporter binding / mitochondrial outer membrane / regulation of cell cycle / response to xenobiotic stimulus / positive regulation of apoptotic process / protein heterodimerization activity / negative regulation of cell population proliferation / negative regulation of gene expression / protein-containing complex binding / apoptotic process / endoplasmic reticulum / protein homodimerization activity / mitochondrion / identical protein binding / membrane / metal ion binding / cytosol Similarity search - Function
Poxvirus F1/C10 / Apoptosis regulator M11L like / Blc2-like / Apoptosis Regulator Bcl-x / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. ...Poxvirus F1/C10 / Apoptosis regulator M11L like / Blc2-like / Apoptosis Regulator Bcl-x / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family / Bcl-2, Bcl-2 homology region 1-3 / Bcl2-like / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily / Orthogonal Bundle / Mainly Alpha Similarity search - Domain/homology
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.99 Å / Relative weight: 1
Reflection
Resolution: 2.4→20 Å / Num. obs: 11933 / % possible obs: 93.8 % / Observed criterion σ(I): 3 / Redundancy: 7.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 22
Reflection shell
Resolution: 2.4→2.49 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2 / % possible all: 59.3
-
Processing
Software
Name
Version
Classification
REFMAC
5.2.0005
refinement
HKL-2000
datareduction
HKL-2000
datascaling
SHARP
phasing
Refinement
Method to determine structure: SIRAS Starting model: NONE Resolution: 2.41→20 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.895 / SU B: 24.057 / SU ML: 0.246 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.359 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM SG IN CYS28 CHAIN A APPEARS MOSTLY DISORDERED AND HAS BEEN ASSIGNED AN OCCUPANCY OF 0.2.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.292
1089
9.7 %
RANDOM
Rwork
0.287
-
-
-
obs
0.288
10139
94.1 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK