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- PDB-1af3: RAT BCL-XL AN APOPTOSIS INHIBITORY PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1af3
TitleRAT BCL-XL AN APOPTOSIS INHIBITORY PROTEIN
ComponentsAPOPTOSIS REGULATOR BCL-X
KeywordsREGULATORY PROTEIN / BCL-XL / APOPTOSIS / MITOCHONDRION / ALTERNATIVE SPLICING
Function / homology
Function and homology information


cellular response to astaxanthin / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / The NLRP1 inflammasome / response to erythropoietin / positive regulation of synaptic vesicle exocytosis / synaptic vesicle recycling via endosome / cellular response to erythropoietin / positive regulation of synaptic vesicle clustering / RAS processing / BH domain binding ...cellular response to astaxanthin / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / The NLRP1 inflammasome / response to erythropoietin / positive regulation of synaptic vesicle exocytosis / synaptic vesicle recycling via endosome / cellular response to erythropoietin / positive regulation of synaptic vesicle clustering / RAS processing / BH domain binding / cellular response to prolactin / apoptotic process in bone marrow cell / dendritic cell apoptotic process / positive regulation of synaptic vesicle endocytosis / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / negative regulation of dendritic cell apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / response to anesthetic / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / negative regulation of execution phase of apoptosis / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / fertilization / regulation of growth / regulation of mitochondrial membrane permeability / Bcl-2 family protein complex / clathrin binding / regulation of long-term synaptic depression / response to cycloheximide / cellular response to alkaloid / positive regulation of ATP biosynthetic process / hepatocyte apoptotic process / negative regulation of release of cytochrome c from mitochondria / negative regulation of reproductive process / negative regulation of developmental process / negative regulation of intrinsic apoptotic signaling pathway / regulation of synaptic vesicle endocytosis / germ cell development / BH3 domain binding / cellular response to interleukin-1 / ectopic germ cell programmed cell death / negative regulation of protein localization to plasma membrane / response to electrical stimulus / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / ovarian follicle development / extrinsic apoptotic signaling pathway in absence of ligand / cellular response to cAMP / MDM2/MDM4 family protein binding / response to cytokine / cellular response to nitric oxide / cellular response to dexamethasone stimulus / response to endoplasmic reticulum stress / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / regulation of cytokinesis / epithelial cell proliferation / response to ischemia / mitochondrion organization / cellular response to amino acid stimulus / response to lead ion / mitochondrial membrane / response to radiation / cellular response to gamma radiation / : / cerebral cortex development / response to virus / response to hydrogen peroxide / response to peptide hormone / synaptic vesicle membrane / endocytosis / intrinsic apoptotic signaling pathway in response to DNA damage / male gonad development / synaptic vesicle / cellular response to xenobiotic stimulus / cellular response to tumor necrosis factor / presynapse / channel activity / GTPase binding / neuron apoptotic process / regulation of apoptotic process / spermatogenesis / nuclear membrane / cellular response to hypoxia / negative regulation of neuron apoptotic process / response to oxidative stress / response to lipopolysaccharide / in utero embryonic development / mitochondrial outer membrane / response to hypoxia / mitochondrial inner membrane / mitochondrial matrix / positive regulation of apoptotic process / response to xenobiotic stimulus / apoptotic process / centrosome / protein-containing complex binding / negative regulation of apoptotic process / protein kinase binding / endoplasmic reticulum
Similarity search - Function
Apoptosis regulator, Bcl-X / Apoptosis regulator, Bcl-2/ BclX / Apoptosis regulator, Bcl-2, BH4 motif, conserved site / Apoptosis regulator, Bcl-2 family BH4 motif signature. / Apoptosis regulator, Bcl-2 protein, BH4 / Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2 family BH4 motif profile. / BH4 Bcl-2 homology region 4 / Blc2-like / Apoptosis Regulator Bcl-x ...Apoptosis regulator, Bcl-X / Apoptosis regulator, Bcl-2/ BclX / Apoptosis regulator, Bcl-2, BH4 motif, conserved site / Apoptosis regulator, Bcl-2 family BH4 motif signature. / Apoptosis regulator, Bcl-2 protein, BH4 / Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2 family BH4 motif profile. / BH4 Bcl-2 homology region 4 / 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-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl2-like / Bcl-2, Bcl-2 homology region 1-3 / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Bcl-2-like protein 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.5 Å
AuthorsAritomi, M. / Kunishima, N. / Inohara, N. / Ishibashi, Y. / Ohta, S. / Morikawa, K.
CitationJournal: J.Biol.Chem. / Year: 1997
Title: Crystal structure of rat Bcl-xL. Implications for the function of the Bcl-2 protein family.
Authors: Aritomi, M. / Kunishima, N. / Inohara, N. / Ishibashi, Y. / Ohta, S. / Morikawa, K.
History
DepositionMar 21, 1997Processing site: BNL
Revision 1.0Jul 7, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: APOPTOSIS REGULATOR BCL-X


Theoretical massNumber of molelcules
Total (without water)22,0821
Polymers22,0821
Non-polymers00
Water91951
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.050, 64.050, 112.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein APOPTOSIS REGULATOR BCL-X


Mass: 22082.246 Da / Num. of mol.: 1 / Fragment: SOLUBLE REGION
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: P53563
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53 %
Crystal growpH: 5.6 / Details: pH 5.6
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17 mg/mlBcl-Xl(B)1drop
250 mMMES1drop
35 %(v/v)glycerol1drop
41 mMdithiothreitol1drop
5100 mM1dropNaCl
60.7 Mammonium sulfate1drop
7100 mMMES1reservoir
810 %(v/v)glycerol1reservoir
92 mMdithiothreitol1reservoir
101.4 M1reservoirNa2SO4

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE M18X / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Sep 1, 1996 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 8614 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 8 % / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 6
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.962 / Mean I/σ(I) obs: 2 / Rsym value: 0.962 / % possible all: 99.3
Reflection
*PLUS
Num. measured all: 68982

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Processing

Software
NameClassification
MLPHAREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.5→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.273 560 6.5 %RANDOM
Rwork0.222 ---
obs0.225 8564 99 %-
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1176 0 0 51 1227
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection all: 8564
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 59.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_angle_deg2.66

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