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- PDB-3ihf: Crystal structure of mouse Bcl-xl mutant (R139A) at pH 5.0 -

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Basic information

Entry
Database: PDB / ID: 3ihf
TitleCrystal structure of mouse Bcl-xl mutant (R139A) 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 / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / synaptic vesicle recycling via endosome / positive regulation of synaptic vesicle exocytosis / positive regulation of synaptic vesicle clustering / RAS processing / apoptotic process in bone marrow cell / dendritic cell apoptotic process / dendritic cell proliferation / positive regulation of synaptic vesicle endocytosis ...The NLRP1 inflammasome / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / synaptic vesicle recycling via endosome / positive regulation of synaptic vesicle exocytosis / positive regulation of synaptic vesicle clustering / RAS processing / 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 mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / 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 / regulation of mitochondrial membrane permeability / fertilization / regulation of growth / Bcl-2 family protein complex / BH domain binding / clathrin binding / response to cycloheximide / regulation of long-term synaptic depression / negative regulation of release of cytochrome c from mitochondria / cellular response to alkaloid / positive regulation of ATP biosynthetic process / hepatocyte apoptotic process / negative regulation of reproductive process / negative regulation of developmental process / BH3 domain binding / germ cell development / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / ectopic germ cell programmed cell death / negative regulation of protein localization to plasma membrane / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / extrinsic apoptotic signaling pathway in absence of ligand / ovarian follicle development / MDM2/MDM4 family protein binding / release of cytochrome c from mitochondria / response to cytokine / epithelial cell proliferation / regulation of cytokinesis / regulation of mitochondrial membrane potential / response to ischemia / mitochondrion organization / cellular response to amino acid stimulus / mitochondrial membrane / response to virus / response to radiation / cellular response to gamma radiation / synaptic vesicle membrane / intrinsic apoptotic signaling pathway in response to DNA damage / male gonad development / GTPase binding / presynapse / spermatogenesis / defense response to virus / nuclear membrane / regulation of apoptotic process / in utero embryonic development / neuron apoptotic process / negative regulation of neuron apoptotic process / mitochondrial outer membrane / mitochondrial inner membrane / mitochondrial matrix / positive regulation of apoptotic process / centrosome / protein-containing complex binding / negative regulation of apoptotic process / apoptotic process / protein kinase binding / endoplasmic reticulum / mitochondrion / identical protein binding / 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-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl2-like / Bcl-2, Bcl-2 homology region 1-3 / BCL2-like apoptosis inhibitors family profile. / Apoptosis regulator proteins, Bcl-2 family / 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: 2.28 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
DepositionJul 30, 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
B: Bcl-2-like protein 1
C: Bcl-2-like protein 1
D: Bcl-2-like protein 1


Theoretical massNumber of molelcules
Total (without water)87,8804
Polymers87,8804
Non-polymers00
Water2,810156
1
A: Bcl-2-like protein 1


Theoretical massNumber of molelcules
Total (without water)21,9701
Polymers21,9701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bcl-2-like protein 1


Theoretical massNumber of molelcules
Total (without water)21,9701
Polymers21,9701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Bcl-2-like protein 1


Theoretical massNumber of molelcules
Total (without water)21,9701
Polymers21,9701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Bcl-2-like protein 1


Theoretical massNumber of molelcules
Total (without water)21,9701
Polymers21,9701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.353, 56.525, 96.443
Angle α, β, γ (deg.)89.98, 89.93, 89.82
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Bcl-2-like protein 1 / Bcl-xl / Bcl2-L-1 / Apoptosis regulator Bcl-X


Mass: 21970.094 Da / Num. of mol.: 4 / Fragment: UNP residues 1-196 / Mutation: R139A
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.: 156 / 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: 2.19 Å3/Da / Density % sol: 43.91 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.45M Ammonium sulphate, 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: 2.02→50 Å / Num. all: 39513 / Num. obs: 29247 / % possible obs: 90.42 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 32.8 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.09 / Net I/σ(I): 32.5
Reflection shellResolution: 2.02→2.09 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 5.6 / Num. unique all: 3141 / Rsym value: 0.11 / % possible all: 63.7

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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: 2.28→50 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.887 / SU B: 6.444 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.346 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26623 1538 5 %RANDOM
Rwork0.19311 ---
all0.19685 39513 --
obs0.19685 29247 90.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.856 Å2
Baniso -1Baniso -2Baniso -3
1--2.87 Å20.28 Å2-0.32 Å2
2--4.33 Å2-0.29 Å2
3----1.46 Å2
Refinement stepCycle: LAST / Resolution: 2.28→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4888 0 0 156 5044
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0225004
X-RAY DIFFRACTIONr_angle_refined_deg2.3081.9256780
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0525600
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.3624.091264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.50715800
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6751532
X-RAY DIFFRACTIONr_chiral_restr0.1890.2716
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023904
X-RAY DIFFRACTIONr_nbd_refined0.2690.22318
X-RAY DIFFRACTIONr_nbtor_refined0.3160.23408
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2218
X-RAY DIFFRACTIONr_metal_ion_refined0.1060.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3160.2172
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.215
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1620.21
X-RAY DIFFRACTIONr_mcbond_it1.251.53008
X-RAY DIFFRACTIONr_mcangle_it2.3624808
X-RAY DIFFRACTIONr_scbond_it3.3632119
X-RAY DIFFRACTIONr_scangle_it5.2644.51972
LS refinement shellResolution: 2.28→2.339 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 107 -
Rwork0.181 1832 -
obs-3960 76.64 %

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