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- PDB-1pq1: Crystal structure of Bcl-xl/Bim -

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Basic information

Entry
Database: PDB / ID: 1pq1
TitleCrystal structure of Bcl-xl/Bim
Components
  • Apoptosis regulator Bcl-X
  • BCL2-like protein 11
KeywordsAPOPTOSIS / Bcl-xl/Bim
Function / homology
Function and homology information


Activation of BIM and translocation to mitochondria / The NLRP1 inflammasome / leukocyte homeostasis / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / positive regulation of lymphocyte apoptotic process / NRAGE signals death through JNK / lymphocyte homeostasis / regulation of developmental pigmentation / RAS processing / lymphocyte apoptotic process ...Activation of BIM and translocation to mitochondria / The NLRP1 inflammasome / leukocyte homeostasis / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / positive regulation of lymphocyte apoptotic process / NRAGE signals death through JNK / lymphocyte homeostasis / regulation of developmental pigmentation / RAS processing / lymphocyte apoptotic process / positive regulation of mitochondrial membrane permeability involved in apoptotic process / developmental pigmentation / positive regulation of fibroblast apoptotic process / apoptotic process involved in embryonic digit morphogenesis / apoptotic process in bone marrow cell / dendritic cell apoptotic process / ear development / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / T cell apoptotic process / negative regulation of dendritic cell apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of T cell apoptotic process / regulation of organ growth / tube formation / mammary gland development / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / negative regulation of execution phase of apoptosis / regulation of mitochondrial membrane permeability / fertilization / regulation of growth / Bcl-2 family protein complex / myeloid cell homeostasis / response to cycloheximide / thymocyte apoptotic process / hepatocyte apoptotic process / cellular response to alkaloid / negative regulation of release of cytochrome c from mitochondria / odontogenesis of dentin-containing tooth / positive regulation of release of cytochrome c from mitochondria / negative regulation of reproductive process / negative regulation of developmental process / germ cell development / dynein complex binding / BH3 domain binding / T cell homeostasis / B cell homeostasis / ectopic germ cell programmed cell death / negative regulation of protein localization to plasma membrane / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / ovarian follicle development / spleen development / positive regulation of cell cycle / response to cytokine / extrinsic apoptotic signaling pathway in absence of ligand / response to endoplasmic reticulum stress / release of cytochrome c from mitochondria / thymus development / cell-matrix adhesion / epithelial cell proliferation / regulation of cytokinesis / regulation of mitochondrial membrane potential / post-embryonic development / mitochondrion organization / cellular response to amino acid stimulus / symbiont-mediated activation of host apoptosis / kidney development / positive regulation of protein-containing complex assembly / cellular response to gamma radiation / response to radiation / mitochondrial membrane / response to virus / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / synaptic vesicle membrane / positive regulation of neuron apoptotic process / neuron apoptotic process / spermatogenesis / nuclear membrane / regulation of apoptotic process / microtubule binding / defense response to virus / in utero embryonic development / negative regulation of neuron apoptotic process / mitochondrial outer membrane / mitochondrial inner membrane / positive regulation of apoptotic process / mitochondrial matrix / intracellular membrane-bounded organelle / apoptotic process / centrosome / protein kinase binding / negative regulation of apoptotic process / endoplasmic reticulum / mitochondrion / identical protein binding / membrane / cytoplasm / cytosol
Similarity search - Function
Apoptosis, Bim N-terminal / Bcl-2-like protein 11 / : / Bim protein N-terminus / Bcl-x interacting, BH3 domain / Bcl-x interacting, BH3 domain / 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, Bim N-terminal / Bcl-2-like protein 11 / : / Bim protein N-terminus / Bcl-x interacting, BH3 domain / Bcl-x interacting, BH3 domain / 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 11 / Bcl-2-like protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsLiu, X. / Dai, S. / Zhu, Y. / Marrack, P. / Kappler, J.W.
CitationJournal: Immunity / Year: 2003
Title: The structure of a Bcl-xl/Bim fragment complex: Implications for Bim function
Authors: Liu, X. / Dai, S. / Zhu, Y. / Marrack, P. / Kappler, J.W.
History
DepositionJun 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Apoptosis regulator Bcl-X
B: BCL2-like protein 11


Theoretical massNumber of molelcules
Total (without water)26,1772
Polymers26,1772
Non-polymers00
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-10 kcal/mol
Surface area9100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.100, 47.340, 49.280
Angle α, β, γ (deg.)90.00, 110.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Apoptosis regulator Bcl-X / BCL2-like 1 protein


Mass: 22056.209 Da / Num. of mol.: 1 / Fragment: BIM
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: BCL2L1 OR BCL2L OR BCLX / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi-five / References: UniProt: Q64373
#2: Protein/peptide BCL2-like protein 11 / BCL2 interacting mediator of cell death


Mass: 4120.569 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: BCL2L11 OR BIM / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi-five / References: UniProt: O54918
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: NH4H2PO4, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
116 %ammonium sulfate1reservoir
20.1 MMES1reservoirpH6.5
35 %1,4-dioxane1reservoir
415 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 18, 2002
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. all: 19877 / Num. obs: 19877 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 8.6
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 2.7 / Num. unique all: 1765 / % possible all: 90.9
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 90.9 % / Num. unique obs: 1765

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: mouse Bcl-xl, pdb entry 1PQ0

1pq0


Resolution: 1.65→19.9 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.237 923 4.7 %RANDOM
Rwork0.219 ---
all0.23 19462 --
obs0.219 19462 95 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.2048 Å2 / ksol: 0.393725 e/Å3
Displacement parametersBiso mean: 23.9 Å2
Baniso -1Baniso -2Baniso -3
1-3.17 Å20 Å2-1.28 Å2
2--0.49 Å20 Å2
3----3.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.65→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1458 0 0 169 1627
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d18.7
X-RAY DIFFRACTIONc_improper_angle_d0.68
LS refinement shellResolution: 1.65→1.75 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.309 140 4.7 %
Rwork0.271 2856 -
obs-1621 87.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3&_1_PARAMETER_INFILE_3
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rwork: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0052
X-RAY DIFFRACTIONc_angle_deg1.11
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.68
LS refinement shell
*PLUS
Rfactor Rfree: 0.313 / Rfactor Rwork: 0.27

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