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- PDB-3fdl: Bim BH3 peptide in complex with Bcl-xL -

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Basic information

Entry
Database: PDB / ID: 3fdl
TitleBim BH3 peptide in complex with Bcl-xL
Components
  • Apoptosis regulator Bcl-X
  • Bcl-2-like protein 11
KeywordsAPOPTOSIS / helical bundle / peptide-protein complex / Alternative splicing / Membrane / Mitochondrion / Nucleus / Transmembrane / Phosphoprotein
Function / homology
Function and homology information


BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of mitochondrial membrane permeability involved in apoptotic process / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / Activation of BIM and translocation to mitochondria / developmental pigmentation / positive regulation of fibroblast apoptotic process / apoptotic process involved in embryonic digit morphogenesis ...BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of mitochondrial membrane permeability involved in apoptotic process / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / Activation of BIM and translocation to mitochondria / developmental pigmentation / positive regulation of fibroblast apoptotic process / apoptotic process involved in embryonic digit morphogenesis / apoptotic process in bone marrow cell / The NLRP1 inflammasome / dendritic cell apoptotic process / ear development / SARS-CoV-1-mediated effects on programmed cell death / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of dendritic cell apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / meiosis I / positive regulation of T cell apoptotic process / regulation of organ growth / mammary gland development / tube formation / 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 / NFE2L2 regulating tumorigenic genes / cellular response to glucocorticoid stimulus / cellular response to alkaloid / NRAGE signals death through JNK / response to cycloheximide / STAT5 activation downstream of FLT3 ITD mutants / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / hepatocyte apoptotic process / thymocyte apoptotic process / FOXO-mediated transcription of cell death genes / negative regulation of release of cytochrome c from mitochondria / negative regulation of reproductive process / negative regulation of developmental process / positive regulation of IRE1-mediated unfolded protein response / negative regulation of intrinsic apoptotic signaling pathway / apoptotic mitochondrial changes / odontogenesis of dentin-containing tooth / positive regulation of release of cytochrome c from mitochondria / germ cell development / T cell homeostasis / BH3 domain binding / B cell homeostasis / negative regulation of anoikis / ectopic germ cell programmed cell death / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / 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 / positive regulation of intrinsic apoptotic signaling pathway / spleen development / positive regulation of cell cycle / extrinsic apoptotic signaling pathway in absence of ligand / response to cytokine / FLT3 Signaling / endomembrane system / negative regulation of autophagy / response to endoplasmic reticulum stress / release of cytochrome c from mitochondria / thymus development / regulation of cytokinesis / cell-matrix adhesion / epithelial cell proliferation / post-embryonic development / regulation of mitochondrial membrane potential / cellular response to amino acid stimulus / positive regulation of protein-containing complex assembly / kidney development / cellular response to gamma radiation / endocytosis / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / RAS processing / synaptic vesicle membrane / Signaling by BRAF and RAF1 fusions / positive regulation of neuron apoptotic process / channel activity / Interleukin-4 and Interleukin-13 signaling / spermatogenesis / regulation of apoptotic process / neuron apoptotic process / microtubule binding / nuclear membrane / defense response to virus / in utero embryonic development / negative regulation of neuron apoptotic process / mitochondrial outer membrane / mitochondrial inner membrane
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 speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsFairlie, W.D. / Lee, E.F. / Smith, B.J. / Czabotar, P.E. / Colman, P.M.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2009
Title: High-Resolution Structural Characterization of a Helical alpha/beta-Peptide Foldamer Bound to the Anti-Apoptotic Protein Bcl-x(L)
Authors: Lee, E.F. / Sadowsky, J.D. / Smith, B.J. / Czabotar, P.E. / Peterson-Kaufman, K.J. / Colman, P.M. / Gellman, S.H. / Fairlie, W.D.
History
DepositionNov 26, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Aug 16, 2017Group: Source and taxonomy / Category: pdbx_entity_src_syn
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.4Nov 1, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Apoptosis regulator Bcl-X
B: Bcl-2-like protein 11


Theoretical massNumber of molelcules
Total (without water)21,1932
Polymers21,1932
Non-polymers00
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-17 kcal/mol
Surface area10560 Å2
MethodPISA
2
A: Apoptosis regulator Bcl-X
B: Bcl-2-like protein 11

A: Apoptosis regulator Bcl-X
B: Bcl-2-like protein 11


Theoretical massNumber of molelcules
Total (without water)42,3854
Polymers42,3854
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area8540 Å2
ΔGint-66 kcal/mol
Surface area16910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.111, 35.684, 62.760
Angle α, β, γ (deg.)90.00, 111.54, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Apoptosis regulator Bcl-X / Bcl-xL / Bcl-2-like 1 protein


Mass: 17917.959 Da / Num. of mol.: 1 / Fragment: residue 1-209, Deletion of amino acids 27 to 82
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Bcl-x / Plasmid: pGEX-6p3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q07817
#2: Protein/peptide Bcl-2-like protein 11 / Bcl2-interacting mediator of cell death


Mass: 3274.691 Da / Num. of mol.: 1 / Fragment: BH3 domain, UNP residues 141-166 / Source method: obtained synthetically / Details: Chemically synthesized / Source: (synth.) synthetic construct (others) / References: UniProt: O43521
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsBCL-XL WITH AMINO ACIDS 27 TO 82 DELETED AND A C-TERMINAL TRUNCATION OF THE LAST 24 RESIDUES THE ...BCL-XL WITH AMINO ACIDS 27 TO 82 DELETED AND A C-TERMINAL TRUNCATION OF THE LAST 24 RESIDUES THE NUMBERING OF THE PROTEIN IS NON-SEQUENTIAL. THE NUMBER ZERO IS SKIPPED.

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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: 1.82 Å3/Da / Density % sol: 32.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1M Sodium citrate, 0.1M Sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 3, 2007 / Details: AXCO capillary optic
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. all: 14858 / Num. obs: 14264 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.046
Reflection shellResolution: 1.78→1.84 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.163 / Mean I/σ(I) obs: 11.1 / Num. unique all: 1463 / % possible all: 94.9

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.4.0067refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2P1L without Beclin BH3 ligand

2p1l


Resolution: 1.78→29.19 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.61 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20769 728 5.1 %RANDOM
Rwork0.16045 ---
all0.16295 14140 --
obs0.16295 13529 95.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.516 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å20 Å2-0.41 Å2
2---0.49 Å20 Å2
3---0.74 Å2
Refinement stepCycle: LAST / Resolution: 1.78→29.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1385 0 0 209 1594
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221421
X-RAY DIFFRACTIONr_angle_refined_deg1.4521.9241923
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7525170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.93523.37777
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.60315236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.681513
X-RAY DIFFRACTIONr_chiral_restr0.2650.2197
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021115
X-RAY DIFFRACTIONr_mcbond_it1.1862842
X-RAY DIFFRACTIONr_mcangle_it2.05531347
X-RAY DIFFRACTIONr_scbond_it3.3394579
X-RAY DIFFRACTIONr_scangle_it4.926576
LS refinement shellResolution: 1.779→1.825 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 50 -
Rwork0.239 946 -
obs--91.54 %

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