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- PDB-3iig: Crystal structure of mouse Bcl-xl mutant (F105A) at pH 5.0 -

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Basic information

Entry
Database: PDB / ID: 3iig
TitleCrystal structure of mouse Bcl-xl mutant (F105A) at pH 5.0
ComponentsBcl-2-like protein 1
KeywordsAPOPTOSIS / BH3 domain / Bcl-2 / Membrane / Mitochondrion / Transmembrane
Function / homology
Function and homology information


The NLRP1 inflammasome / synaptic vesicle recycling via endosome / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / positive regulation of synaptic vesicle exocytosis / positive regulation of synaptic vesicle clustering / RAS processing / BH domain binding / apoptotic process in bone marrow cell / dendritic cell apoptotic process / dendritic cell proliferation ...The NLRP1 inflammasome / synaptic vesicle recycling via endosome / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / positive regulation of synaptic vesicle exocytosis / positive regulation of synaptic vesicle clustering / RAS processing / BH domain binding / apoptotic process in bone marrow cell / dendritic cell apoptotic process / dendritic cell proliferation / positive regulation of synaptic vesicle endocytosis / positive regulation of mononuclear cell proliferation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of dendritic cell apoptotic process / negative regulation of execution phase of apoptosis / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / fertilization / regulation of mitochondrial membrane permeability / negative regulation of protein localization to plasma membrane / regulation of growth / Bcl-2 family protein complex / regulation of long-term synaptic depression / response to cycloheximide / clathrin binding / positive regulation of ATP biosynthetic process / cellular response to alkaloid / hepatocyte apoptotic process / negative regulation of reproductive process / negative regulation of developmental process / negative regulation of release of cytochrome c from mitochondria / BH3 domain binding / germ cell development / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / ectopic germ cell programmed cell death / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / ovarian follicle development / MDM2/MDM4 family protein binding / extrinsic apoptotic signaling pathway in absence of ligand / mitochondrion organization / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / regulation of cytokinesis / epithelial cell proliferation / response to cytokine / response to ischemia / mitochondrial membrane / cellular response to amino acid stimulus / response to virus / response to radiation / cellular response to gamma radiation / synaptic vesicle membrane / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / presynapse / GTPase binding / spermatogenesis / regulation of apoptotic process / nuclear membrane / neuron apoptotic process / defense response to virus / in utero embryonic development / mitochondrial outer membrane / negative regulation of neuron apoptotic process / mitochondrial inner membrane / mitochondrial matrix / positive regulation of apoptotic process / protein heterodimerization activity / centrosome / apoptotic process / protein-containing complex binding / negative regulation of apoptotic process / protein kinase binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / membrane / cytosol
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 (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
Bcl-2-like protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPriyadarshi, A. / Hwang, K.Y.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2010
Title: Structural insights into mouse anti-apoptotic Bcl-xl reveal affinity for Beclin 1 and gossypol.
Authors: Priyadarshi, A. / Roy, A. / Kim, K.S. / Kim, E.E. / Hwang, K.Y.
History
DepositionAug 1, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 20, 2013Group: Database references
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

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Assembly

Deposited unit
A: Bcl-2-like protein 1


Theoretical massNumber of molelcules
Total (without water)21,9801
Polymers21,9801
Non-polymers00
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.155, 63.155, 110.341
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 Bcl-2-like protein 1 / Bcl-xl / Bcl2-L-1 / Apoptosis regulator Bcl-X


Mass: 21980.113 Da / Num. of mol.: 1 / Fragment: UNP residues 1-196 / Mutation: F105A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bcl-xl, Bcl2l, Bcl2l1, Bclx / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q64373
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.5 Å3/Da / Density % sol: 50.86 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.6M Ammonium sulphate, 0.1M tri-Na citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 8, 2008 / Details: mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. all: 9693 / Num. obs: 9215 / % possible obs: 92.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Biso Wilson estimate: 48.8 Å2 / Rmerge(I) obs: 0.15 / Rsym value: 0.24 / Net I/σ(I): 20.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 3.1 / Num. unique all: 772 / Rsym value: 0.24 / % possible all: 76.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PQ0

1pq0


Resolution: 2.3→40 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.903 / SU B: 6.739 / SU ML: 0.166 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.283 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26924 464 4.8 %RANDOM
Rwork0.23587 ---
all0.23741 9693 --
obs0.23741 9215 92.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.869 Å2
Baniso -1Baniso -2Baniso -3
1-1.66 Å20 Å20 Å2
2--1.66 Å20 Å2
3----3.32 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1140 0 0 11 1151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0221168
X-RAY DIFFRACTIONr_angle_refined_deg2.1941.9191581
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9135139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.59423.87162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.10515187
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.986158
X-RAY DIFFRACTIONr_chiral_restr0.1610.2165
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02909
X-RAY DIFFRACTIONr_nbd_refined0.2820.2600
X-RAY DIFFRACTIONr_nbtor_refined0.3230.2813
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2260.249
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.23
X-RAY DIFFRACTIONr_mcbond_it1.5721.5716
X-RAY DIFFRACTIONr_mcangle_it2.58521112
X-RAY DIFFRACTIONr_scbond_it3.7023539
X-RAY DIFFRACTIONr_scangle_it5.6514.5469
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 27 -
Rwork0.251 527 -
obs--73.09 %

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